Showing papers by "Pompeu Fabra University published in 2015"

Capital in the 21st Century

Abstract: On 19 December 2014, the Centre for Economic Policy Research and the Bank of England hosted a discussion forum based around Thomas Piketty’s book, Capital in the twenty-first century, with a number of economists from academia, public sector bodies and private sector institutions. Four speakers presented research on various issues relating to inequality, including: access to education; wealth and taxation policy; and the role of governance and institutions. This article presents each speaker’s key arguments, and includes a summary of the open-floor debate that followed.

The human transcriptome across tissues and individuals

Abstract: Transcriptional regulation and posttranscriptional processing underlie many cellular and organismal phenotypes. We used RNA sequence data generated by Genotype-Tissue Expression (GTEx) project to investigate the patterns of transcriptome variation across individuals and tissues. Tissues exhibit characteristic transcriptional signatures that show stability in postmortem samples. These signatures are dominated by a relatively small number of genes—which is most clearly seen in blood—though few are exclusive to a particular tissue and vary more across tissues than individuals. Genes exhibiting high interindividual expression variation include disease candidates associated with sex, ethnicity, and age. Primary transcription is the major driver of cellular specificity, with splicing playing mostly a complementary role; except for the brain, which exhibits a more divergent splicing program. Variation in splicing, despite its stochasticity, may play in contrast a comparatively greater role in defining individual phenotypes.

Genome-wide patterns of selection in 230 ancient Eurasians

Abstract: Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

Abstract: DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380,000 associations between >16,000 genes and 13,000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

Abstract: Cancers exhibit extensive mutational heterogeneity, and the resulting long-tail phenomenon complicates the discovery of genes and pathways that are significantly mutated in cancer. We perform a pan-cancer analysis of mutated networks in 3,281 samples from 12 cancer types from The Cancer Genome Atlas (TCGA) using HotNet2, a new algorithm to find mutated subnetworks that overcomes the limitations of existing single-gene, pathway and network approaches. We identify 16 significantly mutated subnetworks that comprise well-known cancer signaling pathways as well as subnetworks with less characterized roles in cancer, including cohesin, condensin and others. Many of these subnetworks exhibit co-occurring mutations across samples. These subnetworks contain dozens of genes with rare somatic mutations across multiple cancers; many of these genes have additional evidence supporting a role in cancer. By illuminating these rare combinations of mutations, pan-cancer network analyses provide a roadmap to investigate new diagnostic and therapeutic opportunities across cancer types.

International consensus on standardization of data collection for complications associated with esophagectomy: Esophagectomy Complications Consensus Group (ECCG)

Abstract: Introduction: Perioperative complications influence long- and short-term outcomes after esophagectomy. The absence of a standardized system for defining and recording complications and quality measures after esophageal resection has meant that there is wide variation in evaluating their impact on these outcomes. Methods: The Esophageal Complications Consensus Group comprised 21 high-volume esophageal surgeons from 14 countries, supported by all the major thoracic and upper gastrointestinal professional societies. Delphi surveys and group meetings were used to achieve a consensus on standardized methods for defining complications and quality measures that could be collected in institutional databases and national audits. Results: A standardized list of complications was created to provide a template for recording individual complications associated with esophagectomy. Where possible, these were linked to preexisting international definitions. A Delphi survey facilitated production of specific definitions for anastomotic leak, conduit necrosis, chyle leak, and recurrent nerve palsy. An additional Delphi survey documented consensus regarding critical quality parameters recommended for routine inclusion in databases. These quality parameters were documentation on mortality, comorbidities, completeness of data collection, blood transfusion, grading of complication severity, changes in level of care, discharge location, and readmission rates. Conclusions: The proposed system for defining and recording perioperative complications associated with esophagectomy provides an infrastructure to standardize international data collection and facilitate future comparative studies and quality improvement projects.

Transition-Based Dependency Parsing with Stack Long Short-Term Memory

Abstract: This work was sponsored in part by the U. S. Army Research Laboratory and the U. S. Army Research Office/nunder contract/grant number W911NF-10-1-0533, and in part by NSF CAREER grant IIS-1054319./nMiguel Ballesteros is supported by the European Commission under the contract numbers FP7-ICT-610411 (project MULTISENSOR) and H2020-RIA-645012 (project KRISTINA).

Non-coding recurrent mutations in chronic lymphocytic leukaemia

Abstract: Genomic approaches in more than 500 patients are used to extend the number of chronic lymphocytic leukaemia (CLL) driver alterations, and also identify novel recurrent mutations in non-coding regions, including an enhancer of PAX5 and the 3′ untranslated region of NOTCH1, which lead to aberrant splicing events, increased NOTCH1 protein stability and activity, and an adverse clinical outcome.

The BioMart community portal: an innovative alternative to large, centralized data repositories

Abstract: The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Transition-Based Dependency Parsing with Stack Long Short-Term Memory

Abstract: We propose a technique for learning representations of parser states in transition-based dependency parsers. Our primary innovation is a new control structure for sequence-to-sequence neural networks---the stack LSTM. Like the conventional stack data structures used in transition-based parsing, elements can be pushed to or popped from the top of the stack in constant time, but, in addition, an LSTM maintains a continuous space embedding of the stack contents. This lets us formulate an efficient parsing model that captures three facets of a parser's state: (i) unbounded look-ahead into the buffer of incoming words, (ii) the complete history of actions taken by the parser, and (iii) the complete contents of the stack of partially built tree fragments, including their internal structures. Standard backpropagation techniques are used for training and yield state-of-the-art parsing performance.

Green spaces and cognitive development in primary schoolchildren

Abstract: Exposure to green space has been associated with better physical and mental health. Although this exposure could also influence cognitive development in children, available epidemiological evidence on such an impact is scarce. This study aimed to assess the association between exposure to green space and measures of cognitive development in primary schoolchildren. This study was based on 2,593 schoolchildren in the second to fourth grades (7–10 y) of 36 primary schools in Barcelona, Spain (2012–2013). Cognitive development was assessed as 12-mo change in developmental trajectory of working memory, superior working memory, and inattentiveness by using four repeated (every 3 mo) computerized cognitive tests for each outcome. We assessed exposure to green space by characterizing outdoor surrounding greenness at home and school and during commuting by using high-resolution (5 m × 5 m) satellite data on greenness (normalized difference vegetation index). Multilevel modeling was used to estimate the associations between green spaces and cognitive development. We observed an enhanced 12-mo progress in working memory and superior working memory and a greater 12-mo reduction in inattentiveness associated with greenness within and surrounding school boundaries and with total surrounding greenness index (including greenness surrounding home, commuting route, and school). Adding a traffic-related air pollutant (elemental carbon) to models explained 20–65% of our estimated associations between school greenness and 12-mo cognitive development. Our study showed a beneficial association between exposure to green space and cognitive development among schoolchildren that was partly mediated by reduction in exposure to air pollution.

Ion channels enable electrical communication in bacterial communities

Abstract: The study of bacterial ion channels has provided fundamental insights into the structural basis of neuronal signalling; however, the native role of ion channels in bacteria has remained elusive. Here we show that ion channels conduct long-range electrical signals within bacterial biofilm communities through spatially propagating waves of potassium. These waves result from a positive feedback loop, in which a metabolic trigger induces release of intracellular potassium, which in turn depolarizes neighbouring cells. Propagating through the biofilm, this wave of depolarization coordinates metabolic states among cells in the interior and periphery of the biofilm. Deletion of the potassium channel abolishes this response. As predicted by a mathematical model, we further show that spatial propagation can be hindered by specific genetic perturbations to potassium channel gating. Together, these results demonstrate a function for ion channels in bacterial biofilms, and provide a prokaryotic paradigm for active, long-range electrical signalling in cellular communities.

Rethinking segregation and integration: contributions of whole-brain modelling.

Abstract: The brain regulates information flow by balancing the segregation and integration of incoming stimuli to facilitate flexible cognition and behaviour. The topological features of brain networks--in particular, network communities and hubs--support this segregation and integration but do not provide information about how external inputs are processed dynamically (that is, over time). Experiments in which the consequences of selective inputs on brain activity are controlled and traced with great precision could provide such information. However, such strategies have thus far had limited success. By contrast, recent whole-brain computational modelling approaches have enabled us to start assessing the effect of input perturbations on brain dynamics in silico.

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis

Abstract: Genetic association studies have identified 21 loci associated with atopic dermatitis risk predominantly in populations of European ancestry. To identify further susceptibility loci for this common, complex skin disease, we performed a meta-analysis of >15 million genetic variants in 21,399 cases and 95,464 controls from populations of European, African, Japanese and Latino ancestry, followed by replication in 32,059 cases and 228,628 controls from 18 studies. We identified ten new risk loci, bringing the total number of known atopic dermatitis risk loci to 31 (with new secondary signals at four of these loci). Notably, the new loci include candidate genes with roles in the regulation of innate host defenses and T cell function, underscoring the important contribution of (auto)immune mechanisms to atopic dermatitis pathogenesis.

Re-theorizing Family Demographics

Abstract: Two dominant theories within family research foresee a long-term decline in marriage, fertility, and partner stability. They also assume that this “less-family” scenario will be spearheaded by higher-educated strata. Trends in the latter half of the twentieth century seemed to provide ample support for both predictions. However, recent signs of change in family behavior raise doubts about their continued validity. In a number of countries we see a halt to, and even reversal of, fertility decline and of couple instability. In parallel, we observe a reversal of the social gradient on both dimensions. Applying a multiple equilibrium framework, we propose a theoretical framework that helps explain both the phase of marital and fertility decline and the subsequent recovery. We focus especially on the endogenous dynamics of the process, which, we argue, depend on the conditions that favor rapid diffusion. Our core argument is that the turnaround is driven by the diffusion of gender-egalitarian norms.

Preventing occupational stress in healthcare workers

Abstract: Background Healthcare workers can suffer from occupational stress as a result of lack of skills, organisational factors, and low social support at work. which may lead to distress, burnout and psychosomatic problems, and deterioration in quality of life and service provision. Objectives To evaluate the effectiveness of work- and person-directed interventions compared to no intervention or alternative interventions in preventing stress at work in healthcare workers. Search methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, PsycINFO, CINAHL, NIOSHTIC-2 and Web of Science up to November 2013. Selection criteria Randomised controlled trials (RCTs) of interventions aimed at preventing psychological stress in healthcare workers. For organisational interventions, interrupted time-series and controlled before-and-after (CBA) studies were also eligible. Data collection and analysis Two review authors independently extracted data and assessed trial quality. We used Standardised Mean Differences (SMDs) where authors of trials used different scales to measure stress or burnout. We combined studies that were similar in meta-analyses. We used the GRADE system to rate the quality of the evidence. Main results In this update, we added 39 studies, making a total of 58 studies (54 RCTs and four CBA studies), with 7188 participants. We categorised interventions as cognitive-behavioural training (CBT) (n = 14), mental and physical relaxation (n = 21), combined CBT and relaxation (n = 6) and organisational interventions (n = 20). Follow-up was less than one month in 24 studies, one to six in 22 studies and more than six months in 12 studies. We categorised outcomes as stress, anxiety or general health.There was low-quality evidence that CBT with or without relaxation was no more effective in reducing stress symptoms than no intervention at one month follow-up in six studies (SMD -0.27 (95% Confidence Interval (CI) -0.66 to 0.13; 332 participants). But at one to six months follow-up in seven studies (SMD -0.38, 95% CI -0.59 to -0.16; 549 participants, 13% relative risk reduction), and at more than six months follow-up in two studies (SMD -1.04, 95% CI -1.37 to -0.70; 157 participants) CBT with or without relaxation reduced stress more than no intervention.CBT interventions did not lead to a considerably greater effect than an alternative intervention, in three studies.Physical relaxation (e.g. massage) was more effective in reducing stress than no intervention at one month follow-up in four studies (SMD -0.48, 95% CI -0.89 to -0.08; 97 participants) and at one to six months follow-up in six studies (SMD -0.47; 95% CI -0.70 to -0.24; 316 participants). Two studies did not find a considerable difference in stress between massage and taking extra breaks.Mental relaxation (e.g. meditation) led to similar stress symptom levels as no intervention at one to six months follow-up in six studies (SMD -0.50, 95% CI -1.15 to 0.15; 205 participants) but to less stress in one study at more than six months follow-up. One study showed that mental relaxation reduced stress more effectively than attending a course on theory analysis and another that it was more effective than just relaxing in a chair.Organisational interventions consisted of changes in working conditions, organising support, changing care, increasing communication skills and changing work schedules. Changing work schedules (from continuous to having weekend breaks and from a four-week to a two-week schedule) reduced stress with SMD -0.55 (95% CI -0.84 to -0.25; 2 trials, 180 participants). Other organisational interventions were not more effective than no intervention or an alternative intervention.We graded the quality of the evidence for all but one comparison as low. For CBT this was due to the possibility of publication bias, and for the other comparisons to a lack of precision and risk of bias. Only for relaxation versus no intervention was the evidence of moderate quality. Authors' conclusions There is low-quality evidence that CBT and mental and physical relaxation reduce stress more than no intervention but not more than alternative interventions. There is also low-quality evidence that changing work schedules may lead to a reduction of stress. Other organisational interventions have no effect on stress levels. More randomised controlled trials are needed with at least 120 participants that compare the intervention to a placebo-like intervention. Organisational interventions need better focus on reduction of specific stressors.

Association between Traffic-Related Air Pollution in Schools and Cognitive Development in Primary School Children: A Prospective Cohort Study

Abstract: Background Air pollution is a suspected developmental neurotoxicant. Many schools are located in close proximity to busy roads, and traffic air pollution peaks when children are at school. We aimed to assess whether exposure of children in primary school to traffic-related air pollutants is associated with impaired cognitive development.

Metabolic co-dependence gives rise to collective oscillations within biofilms.

Abstract: Cells that reside within a community can cooperate and also compete with each other for resources. It remains unclear how these opposing interactions are resolved at the population level. Here we investigate such an internal conflict within a microbial (Bacillus subtilis) biofilm community: cells in the biofilm periphery not only protect interior cells from external attack but also starve them through nutrient consumption. We discover that this conflict between protection and starvation is resolved through emergence of long-range metabolic co-dependence between peripheral and interior cells. As a result, biofilm growth halts periodically, increasing nutrient availability for the sheltered interior cells. We show that this collective oscillation in biofilm growth benefits the community in the event of a chemical attack. These findings indicate that oscillations support population-level conflict resolution by coordinating competing metabolic demands in space and time, suggesting new strategies to control biofilm growth.

Human N-methyl D-aspartate receptor antibodies alter memory and behaviour in mice

Abstract: Anti-N-methyl D-aspartate receptor (NMDAR) encephalitis is a severe neuropsychiatric disorder that associates with prominent memory and behavioural deficits. Patients’ antibodies react with the N-terminal domain of the GluN1 (previously known as NR1) subunit of NMDAR causing in cultured neurons a selective and reversible internalization of cell-surface receptors. These effects and the frequent response to immunotherapy have suggested an antibody-mediated pathogenesis, but to date there is no animal model showing that patients’ antibodies cause memory and behavioural deficits. To develop such a model, C57BL6/J mice underwent placement of ventricular catheters connected to osmotic pumps that delivered a continuous infusion of patients’ or control cerebrospinal fluid (flow rate 0.25 µl/h, 14 days). During and after the infusion period standardized tests were applied, including tasks to assess memory (novel object recognition in open field and V-maze paradigms), anhedonic behaviours (sucrose preference test), depressive-like behaviours (tail suspension, forced swimming tests), anxiety (black and white, elevated plus maze tests), aggressiveness (resident-intruder test), and locomotor activity (horizontal and vertical). Animals sacrificed at Days 5, 13, 18, 26 and 46 were examined for brain-bound antibodies and the antibody effects on total and synaptic NMDAR clusters and protein concentration using confocal microscopy and immunoblot analysis. These experiments showed that animals infused with patients’ cerebrospinal fluid, but not control cerebrospinal fluid, developed progressive memory deficits, and anhedonic and depressive-like behaviours, without affecting other behavioural or locomotor tasks. Memory deficits gradually worsened until Day 18 (4 days after the infusion stopped) and all symptoms resolved over the next week. Accompanying brain tissue studies showed progressive increase of brain-bound human antibodies, predominantly in the hippocampus (maximal on Days 13–18), that after acid extraction and characterization with GluN1-expressing human embryonic kidney cells were confirmed to be against the NMDAR. Confocal microscopy and immunoblot analysis of the hippocampus showed progressive decrease of the density of total and synaptic NMDAR clusters and total NMDAR protein concentration (maximal on Day 18), without affecting the post-synaptic density protein 95 (PSD95) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. These effects occurred in parallel with memory and other behavioural deficits and gradually improved after Day 18, with reversibility of symptoms accompanied by a decrease of brain-bound antibodies and restoration of NMDAR levels. Overall, these findings establish a link between memory and behavioural deficits and antibody-mediated reduction of NMDAR, provide the biological basis by which removal of antibodies and antibody-producing cells improve neurological function, and offer a model for testing experimental therapies in this and similar disorders.

The genomes of two key bumblebee species with primitive eusocial organization

Abstract: The shift from solitary to social behavior is one of the major evolutionary transitions Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Radio and the Rise of The Nazis in Prewar Germany

Abstract: How far can the media protect or undermine democratic institutions in unconsolidated democracies, and how persuasive can they be in ensuring public support for dictator's policies? We study this question in the context of Germany between 1929 and 1939. Using geographical and temporal variation in radio availability, we show that radio had a significant negative effect on the Nazi electoral support between 1929 and 1932, when political news were slanted against Nazi party. This effect was reversed in just 5 weeks following Hitler's appointment as chancellor and the transfer of control of the radio to the Nazis. Pro-Nazi radio propaganda caused higher vote for the Nazis in March 1933 election. After full consolidation of power, radio propaganda helped the Nazis to enroll new party members and encouraged denunciations of Jews and other open expressions of anti-Semitism. The effect of Nazi propaganda was not uniform. Depending on listeners' priors about the message, propaganda could be very effective or could backfire. Nazi radio was most effective in places where anti-Semitism was historically high and had a negative effect on the support for anti-Semitic policies in places with historically low anti-Semitism.

The endocannabinoid system in guarding against fear, anxiety and stress

Abstract: Endocannabinoid signalling affects the behavioural domains of acquired fear, anxiety and stress-coping by modulating synaptic functions in specific brain circuits. Lutz and colleagues discuss the cellular mechanisms involved in these effects and the potential for endocannabinoid-based therapies to treat anxiety and stress-related disorders.