Showing papers by "Pompeu Fabra University published in 2014"
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TL;DR: This paper discusses all of these topics, identifying key challenges for future research and preliminary 5G standardization activities, while providing a comprehensive overview of the current literature, and in particular of the papers appearing in this special issue.
Abstract: What will 5G be? What it will not be is an incremental advance on 4G. The previous four generations of cellular technology have each been a major paradigm shift that has broken backward compatibility. Indeed, 5G will need to be a paradigm shift that includes very high carrier frequencies with massive bandwidths, extreme base station and device densities, and unprecedented numbers of antennas. However, unlike the previous four generations, it will also be highly integrative: tying any new 5G air interface and spectrum together with LTE and WiFi to provide universal high-rate coverage and a seamless user experience. To support this, the core network will also have to reach unprecedented levels of flexibility and intelligence, spectrum regulation will need to be rethought and improved, and energy and cost efficiencies will become even more critical considerations. This paper discusses all of these topics, identifying key challenges for future research and preliminary 5G standardization activities, while providing a comprehensive overview of the current literature, and in particular of the papers appearing in this special issue.
7,139 citations
TL;DR: In this article, the authors describe five technologies that could lead to both architectural and component disruptive design changes: device-centric architectures, millimeter wave, massive MIMO, smarter devices, and native support for machine-to-machine communications.
Abstract: New research directions will lead to fundamental changes in the design of future fifth generation (5G) cellular networks. This article describes five technologies that could lead to both architectural and component disruptive design changes: device-centric architectures, millimeter wave, massive MIMO, smarter devices, and native support for machine-to-machine communications. The key ideas for each technology are described, along with their potential impact on 5G and the research challenges that remain.
3,711 citations
University of North Carolina at Chapel Hill1, Buck Institute for Research on Aging2, University of California, San Francisco3, Broad Institute4, Pompeu Fabra University5, University of California, Santa Cruz6, Brown University7, Washington University in St. Louis8, University of Texas MD Anderson Cancer Center9, University of Southern California10, Sage Bionetworks11, BC Cancer Agency12, Catalan Institution for Research and Advanced Studies13, National Institutes of Health14
TL;DR: An integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types revealed a unified classification into 11 major subtypes, revealing several distinct cancer types found to converge into common subtypes.
1,259 citations
Broad Institute1, Harvard University2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, University of Edinburgh13, Sultan Qaboos University14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, University College London40, Amgen41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Tarapacá47, University of Chile48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: It is shown that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians; and early European farmers, who were mainly of Near Eastern origin but also harboured west Europeanhunter-gatherer related ancestry.
Abstract: We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
1,077 citations
TL;DR: In this paper, the authors identify the effects of monetary policy on credit risk-taking with an exhaustive credit register of loan applications and contracts, and find that a lower overnight interest rate induces lowly capitalized banks to grant more loan applications to ex ante risky firms and to commit larger loan volumes with fewer collateral requirements to these firms, yet with a higher ex post likelihood of default.
Abstract: We identify the effects of monetary policy on credit risk-taking with an exhaustive credit register of loan applications and contracts. We separate the changes in the composition of the supply of credit from the concurrent changes in the volume of supply and quality, and the volume of demand. We employ a two-stage model that analyzes the granting of loan applications in the first stage and loan outcomes for the applications granted in the second stage, and that controls for both observed and unobserved, time-varying, firm and bank heterogeneity through time*firm and time*bank fixed effects. We find that a lower overnight interest rate induces lowly capitalized banks to grant more loan applications to ex ante risky firms and to commit larger loan volumes with fewer collateral requirements to these firms, yet with a higher ex post likelihood of default. A lower long-term interest rate and other relevant macroeconomic variables have no such effects.
965 citations
TL;DR: It is reported that geriatric satellite cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and that this irreversibly affects their intrinsic regenerative and self-renewal capacities.
Abstract: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with ageing. Here we report that geriatric satellite cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and that this irreversibly affects their intrinsic regenerative and self-renewal capacities. In geriatric mice, resting satellite cells lose reversible quiescence by switching to an irreversible pre-senescence state, caused by derepression of p16INK4a (also called Cdkn2a). On injury, these cells fail to activate and expand, undergoing accelerated entry into a full senescence state (geroconversion), even in a youthful environment. p16INK4a silencing in geriatric satellite cells restores quiescence and muscle regenerative functions. Our results demonstrate that maintenance of quiescence in adult life depends on the active repression of senescence pathways. As p16INK4a is dysregulated in human geriatric satellite cells, these findings provide the basis for stem-cell rejuvenation in sarcopenic muscles. This study shows that ageing satellite cells undergo an irreversible transition from a quiescent to a pre-senescent state that results in the loss of muscle regeneration in sarcopenia; furthermore, increased expression of p16INK4a is identified as a common feature of senescent satellite cells. One of the properties crucial to the function of adult mammalian stem cells is the capacity to remain in a quiescent state for prolonged periods — and to respond when the need to regenerate arises. Loss of skeletal muscle mass and function are common features of advanced ageing in humans, associated with a loss of regenerative capacity of the skeletal muscle stem cells, known as satellite cells. Pura Munoz-Canoves and colleagues show that ageing satellite cells undergo an irreversible transition from quiescence to a pre-senescence state associated with increased expression of p16INK4a, a tumour-suppressor protein that has been identified as a marker for senescence. Repression of p16INK4a during adult life is shown to maintain satellite cells in a reversible quiescence state that allows muscle regeneration; p16INK4a is dysregulated in human geriatric satellite cells and the potential for muscle regeneration is lost.
771 citations
TL;DR: The historical, economic, and political factors that link precarious employment to health and health equity are identified; concepts, models, instruments, and findings on precarious employment and health inequalities are reviewed; the strengths and weaknesses of this literature are summarized; and substantive and methodological challenges are highlighted.
Abstract: Employment precariousness is a social determinant that affects the health of workers, families, and communities. Its recent popularity has been spearheaded by three main developments: the surge in “flexible employment” and its associated erosion of workers' employment and working conditions since the mid-1970s; the growing interest in social determinants of health, including employment conditions; and the availability of new data and information systems. This article identifies the historical, economic, and political factors that link precarious employment to health and health equity; reviews concepts, models, instruments, and findings on precarious employment and health inequalities; summarizes the strengths and weaknesses of this literature; and highlights substantive and methodological challenges that need to be addressed. We identify two crucial future aims: to provide a compelling research program that expands our understanding of employment precariousness and to develop and evaluate policy programs ...
748 citations
Whitney Laboratory for Marine Bioscience1, Auburn University2, Florida State University3, Pompeu Fabra University4, University of Massachusetts Medical School5, University of Illinois at Urbana–Champaign6, University of Groningen7, Sunnybrook Research Institute8, Russian Academy of Sciences9, University of Florida10, Genetic Information Research Institute11, University of Washington12, Royal Holloway, University of London13, Catalan Institution for Research and Advanced Studies14
TL;DR: The draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, are presented, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes.
Abstract: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.
610 citations
TL;DR: The best characterized pathway, the ER-associated protein degradation (ERAD), monitors the folding of membrane and secretory proteins whose biogenesis takes place in the endoplasmic reticulum (ER).
Abstract: Even with the assistance of many cellular factors, a significant fraction of newly synthesized proteins ends up misfolded. Cells evolved protein quality control systems to ensure that these potentially toxic species are detected and eliminated. The best characterized of these pathways, the ER-associated protein degradation (ERAD), monitors the folding of membrane and secretory proteins whose biogenesis takes place in the endoplasmic reticulum (ER). There is also increasing evidence that ERAD controls other ER-related functions through regulated degradation of certain folded ER proteins, further highlighting the role of ERAD in cellular homeostasis.
518 citations
University of California, Los Angeles1, Cornell University2, University of Porto3, Sichuan University4, Budapest University of Technology and Economics5, Pompeu Fabra University6, National Institutes of Health7, Bilkent University8, Spanish National Research Council9, Tel Aviv University10, University of Zagreb11, Life Technologies12, Stanford University13, Catalan Institution for Research and Advanced Studies14
TL;DR: It is found that none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade, suggesting that a re-evaluation of past hypotheses regarding dog origins is necessary.
Abstract: To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.
504 citations
TL;DR: It is estimated that between one in two and one in five silent mutations in oncogenes have been selected, equating to ~6%- 8% of all selected single-nucleotide changes in these genes.
TL;DR: A reference genome sequence for sugar beet is presented as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions and provides evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses.
Abstract: Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.
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TL;DR: In this paper, the authors identify key challenges for future research and preliminary 5G standardization activities, while providing a comprehensive overview of the current literature, and in particular of the papers appearing in this special issue.
Abstract: What will 5G be? What it will not be is an incremental advance on 4G. The previous four generations of cellular technology have each been a major paradigm shift that has broken backwards compatibility. And indeed, 5G will need to be a paradigm shift that includes very high carrier frequencies with massive bandwidths, extreme base station and device densities and unprecedented numbers of antennas. But unlike the previous four generations, it will also be highly integrative: tying any new 5G air interface and spectrum together with LTE and WiFi to provide universal high-rate coverage and a seamless user experience. To support this, the core network will also have to reach unprecedented levels of flexibility and intelligence, spectrum regulation will need to be rethought and improved, and energy and cost efficiencies will become even more critical considerations. This paper discusses all of these topics, identifying key challenges for future research and preliminary 5G standardization activities, while providing a comprehensive overview of the current literature, and in particular of the papers appearing in this special issue.
Broad Institute1, Harvard University2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, University of Edinburgh13, Sultan Qaboos University14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, University College London40, Amgen41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Tarapacá47, University of Chile48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: The authors showed that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunters-gatherer related ancestry.
Abstract: We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
TL;DR: This paper reviewed empirical work published since 2000 by researchers in the field of organizational psychology and management on workplace creativity and concluded that the nature of the actor-context interaction needs further theoretical advancement and refinement.
Abstract: Workplace creativity exhibited by individual employees and teams is a key driver of organizational innovation and success. After briefly touching upon issues related to the historical roots of research on workplace creativity, we focus on reviewing empirical work published since 2000 by researchers in the field of organizational psychology and management. We observe that although earlier research tended to take either an actor-centered or a context-centered approach, continuing to do so may have diminishing returns. To understand creativity in all its complexity and potential, an interactionist perspective that emphasizes actor–context interactive effects on creativity holds much promise. Moreover, after reviewing existing work taking an interactionist approach, we conclude that the nature of the actor–context interaction needs further theoretical advancement and refinement. Toward this end, we propose a typology that reveals a complex and intriguing set of actor–context interactions, including ones that ...
TL;DR: Evidence is revealed that a Turing network implemented by Bmp, Sox9, and Wnt drives digit specification and a realistic two-dimensional simulation of digit patterning is developed, which shows that this network, when modulated by morphogen gradients, recapitulates the expression patterns of Sox9 in the wild type and in perturbation experiments.
Abstract: During limb development, digits emerge from the undifferentiated mesenchymal tissue that constitutes the limb bud. It has been proposed that this process is controlled by a self-organizing Turing mechanism, whereby diffusible molecules interact to produce a periodic pattern of digital and interdigital fates. However, the identities of the molecules remain unknown. By combining experiments and modeling, we reveal evidence that a Turing network implemented by Bmp, Sox9, and Wnt drives digit specification. We develop a realistic two-dimensional simulation of digit patterning and show that this network, when modulated by morphogen gradients, recapitulates the expression patterns of Sox9 in the wild type and in perturbation experiments. Our systems biology approach reveals how a combination of growth, morphogen gradients, and a self-organizing Turing network can achieve robust and reproducible pattern formation.
TL;DR: It is found that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes, indicating that they play an important role in de novo protein evolution.
Abstract: Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides. We find that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes. The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution.
Washington University in St. Louis1, Broad Institute2, University of Texas Health Science Center at Houston3, University of North Carolina at Chapel Hill4, University of Oxford5, University of Lübeck6, University of Washington7, University of Wisconsin–Milwaukee8, Stanford University9, University of Pennsylvania10, University of Amsterdam11, Technische Universität München12, University of California, Los Angeles13, Cleveland Clinic14, University of Vermont15, University of Missouri–Kansas City16, Ohio State University17, Baylor College of Medicine18, University of Virginia19, Boston University20, University of Michigan21, Harvard University22, Mayo Clinic23, University of Copenhagen24, Vanderbilt University25, University of Dundee26, King Abdulaziz University27, University of Cambridge28, Pompeu Fabra University29, University of Ottawa30, University of Mississippi31
TL;DR: In this paper, the exons of the Niemann-Pick C1-like 1 (NPC1L1) protein were sequenced in 7364 patients with coronary heart disease and in 14,728 controls without such disease who were of European, African or South Asian ancestry.
Abstract: Ezetimibe lowers plasma levels of low-density lipoprotein (LDL) cholesterol by inhibiting the activity of the Niemann-Pick C1-like 1 (NPC1L1) protein. However, whether such inhibition reduces the risk of coronary heart disease is not known. Human mutations that inactivate a gene encoding a drug target can mimic the action of an inhibitory drug and thus can be used to infer potential effects of that drug.We sequenced the exons of NPC1L1 in 7364 patients with coronary heart disease and in 14,728 controls without such disease who were of European, African, or South Asian ancestry. We identified carriers of inactivating mutations (nonsense, splice-site, or frameshift mutations). In addition, we genotyped a specific inactivating mutation (p.Arg406X) in 22,590 patients with coronary heart disease and in 68,412 controls. We tested the association between the presence of an inactivating mutation and both plasma lipid levels and the risk of coronary heart disease.With sequencing, we identified 15 distinct NPC1L1 inactivating mutations; approximately 1 in every 650 persons was a heterozygous carrier for 1 of these mutations. Heterozygous carriers of NPC1L1 inactivating mutations had a mean LDL cholesterol level that was 12 mg per deciliter (0.31 mmol per liter) lower than that in noncarriers (P=0.04). Carrier status was associated with a relative reduction of 53% in the risk of coronary heart disease (odds ratio for carriers, 0.47; 95% confidence interval, 0.25 to 0.87; P=0.008). In total, only 11 of 29,954 patients with coronary heart disease had an inactivating mutation (carrier frequency, 0.04%) in contrast to 71 of 83,140 controls (carrier frequency, 0.09%).Naturally occurring mutations that disrupt NPC1L1 function were found to be associated with reduced plasma LDL cholesterol levels and a reduced risk of coronary heart disease. (Funded by the National Institutes of Health and others.).
University of Washington1, University of Missouri2, Baylor College of Medicine3, University of Düsseldorf4, Pompeu Fabra University5, Ghent University6, Johns Hopkins University7, Agricultural Research Service8, University of British Columbia9, University of Houston10, University of Illinois at Urbana–Champaign11, Purdue University12, University of Pittsburgh13, Australian National University14, Martin Luther University of Halle-Wittenberg15, Lawrence Berkeley National Laboratory16, National Institutes of Health17, University of North Carolina at Greensboro18, King Abdullah University of Science and Technology19, Clemson University20, Swiss Institute of Bioinformatics21
TL;DR: Improved honey bee genome assembly with a new gene annotation set and a number of genes similar to that of other insect genomes are reported, contrary to what was suggested in OGSv1.0.
Abstract: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Queen Elizabeth Hospital Birmingham1, Medical University of Vienna2, Leiden University3, University of La Laguna4, University of Copenhagen5, University of Pisa6, National Research Council7, University of Michigan8, Osaka University9, Charité10, Medical University of Graz11, Pompeu Fabra University12, University of Glasgow13, University of Groningen14, University of Oslo15
TL;DR: A consensus meeting was held in Vienna on September 8-9, 2013, to discuss diagnostic and therapeutic challenges surrounding development of diabetes mellitus after transplantation as mentioned in this paper, where 24 transplant nephrologists, surgeons, diabetologists and clinical scientists met with the aim to review previous guidelines in light of emerging clinical data and research.
Abstract: Although agree–disagree (AD) rating scales suffer from acquiescence response bias, entail enhanced cognitive burden, and yield data of lower quality, these scales remain popular with researchers du...
TL;DR: This work reviews methods and emerging results that exhibit remarkable accuracy in mapping and predicting both spontaneous and task-based healthy network dynamics and how whole-brain computational models can help generate and predict the dynamical interactions and consequences of brain networks over many timescales.
University of Milan1, University of Florence2, Centre national de la recherche scientifique3, University of Belgrade4, University of Niš5, University of Liège6, University of Porto7, Russian Academy of Sciences8, American Museum of Natural History9, Pompeu Fabra University10, Braunschweig University of Technology11, Research Institute for Nature and Forest12, University of Twente13, Spanish National Research Council14
TL;DR: This analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles and highlights the need to add temporal and altitudinal data for all records to allow tracking potential species distribution changes.
Abstract: A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with 50 × 50 km resolution maps based on ca. 85 000 grid records was published by the Societas Europaea Herpetologica (SEH) in 1997. Since then, more detailed species distribution maps covering large parts of Europe became available, while taxonomic progress has led to a plethora of taxonomic changes including new species descriptions. To account for these progresses, we compiled information from different data sources: published in books and websites, ongoing national atlases, personal data kindly provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility (GBIF). Databases were homogenised, deleting all information except species names and coordinates, projected to the same coordinate system (WGS84) and transformed into a 50 × 50 km grid. The newly compiled database comprises more than 384 000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism and defined species distribution types (i.e. groups of species with similar distribution patterns) by hierarchical cluster analysis using Jaccard’s index as association measure. Our analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles. The NA2RE system will serve as well to monitor potential temporal changes in their distributions. Grid maps of all species are made available along with this paper as a tool for decision-making and conservation-related studies and actions. We also identify taxonomic and geographic gaps of knowledge that need to be filled, and we highlight the need to add temporal and altitudinal data for all records, to allow tracking potential species distribution changes as well as detailed modelling of the impacts of land use and climate change on European amphibians and reptiles.
Oregon Health & Science University1, Baylor College of Medicine2, University of Arizona3, Stony Brook University4, Pompeu Fabra University5, Howard Hughes Medical Institute6, University of Washington7, University College London8, German Primate Center9, University of Bari10, Louisiana State University11, University of Toulouse12, Johns Hopkins University13, University of Utah14, Texas A&M University15, Babeș-Bolyai University16, Children's Hospital Oakland Research Institute17, University of Colorado Denver18, Max Delbrück Center for Molecular Medicine19, University of Barcelona20, Indiana University21, Washington University in St. Louis22, Institute for Systems Biology23, Pennsylvania State University24, University of Pittsburgh25, Harvard University26, Stanford University27, University of Cambridge28, University of California, San Francisco29, Paul Ehrlich Institute30, Gibbon Conservation Center31, University of Chicago32, Broad Institute33
TL;DR: The assembly and analysis of a northern white-cheeked gibbon genome is presented and the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site is described, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage.
Abstract: Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ~5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.
TL;DR: An overview of the key findings of resting-state activity covering a range of neuroimaging modalities is provided and how to best define and analyze anatomical and functional brain networks is described and how unbalancing these networks may lead to problems with mental health is described.
TL;DR: High-throughput sequencing assays on the transcriptome and epigenome reveal that, in general, differences dominate similarities between the two species, and indicate that there is considerable RNA expression diversity between humans and mice.
Abstract: Although the similarities between humans and mice are typically highlighted, morphologically and genetically, there are many differences. To better understand these two species on a molecular level, we performed a comparison of the expression profiles of 15 tissues by deep RNA sequencing and examined the similarities and differences in the transcriptome for both protein-coding and -noncoding transcripts. Although commonalities are evident in the expression of tissue-specific genes between the two species, the expression for many sets of genes was found to be more similar in different tissues within the same species than between species. These findings were further corroborated by associated epigenetic histone mark analyses. We also find that many noncoding transcripts are expressed at a low level and are not detectable at appreciable levels across individuals. Moreover, the majority lack obvious sequence homologs between species, even when we restrict our attention to those which are most highly reproducible across biological replicates. Overall, our results indicate that there is considerable RNA expression diversity between humans and mice, well beyond what was described previously, likely reflecting the fundamental physiological differences between these two organisms.
University of California, Santa Cruz1, University of Florida2, Mississippi State University3, Pompeu Fabra University4, University of Texas at Arlington5, University of Colorado Denver6, University UCINF7, Austral University of Chile8, Genetic Information Research Institute9, Institute for Systems Biology10, University of Georgia11, University of Münster12, Uppsala University13, University of Sydney14, University of the Republic15, Occidental College16, University of Arizona17, Harvard University18, North Carolina State University19, Howard Hughes Medical Institute20, University of Copenhagen21, University of Tokyo22, University of Iowa23, University of Delaware24, Louisiana State University25, University of California, Los Angeles26, Catalan Institution for Research and Advanced Studies27, Texas Tech University28
TL;DR: An exceptionally slow rate of genome evolution within crocodilians at all levels is observed, consistent with a single underlying cause of a reduced rate of evolutionary change rather than intrinsic differences in base repair machinery.
Abstract: ?? To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
TL;DR: This work examines how learning and using two languages affect language acquisition and processing as well as various aspects of cognition in monolingual and bilingual adults.
Abstract: The ability to speak two languages often marvels monolinguals, although bilinguals report no difficulties in achieving this feat. Here, we examine how learning and using two languages affect language acquisition and processing as well as various aspects of cognition. We do so by addressing three main questions. First, how do infants who are exposed to two languages acquire them without apparent difficulty? Second, how does language processing differ between monolingual and bilingual adults? Last, what are the collateral effects of bilingualism on the executive control system across the lifespan? Research in all three areas has not only provided some fascinating insights into bilingualism but also revealed new issues related to brain plasticity and language learning.
TL;DR: Physical activity level in COPD is consistently associated with mortality and exacerbations, but there is poor evidence about determinants of physical activity, including the impact of treatment.
Abstract: Background The relationship between physical activity, disease severity, health status and prognosis in patients with COPD has not been systematically assessed. Our aim was to identify and summarise studies assessing associations between physical activity and its determinants and/or outcomes in patients with COPD and to develop a conceptual model for physical activity in COPD. Methods We conducted a systematic search of four databases (Medline, Embase, CINAHL and Psychinfo) prior to November 2012. Teams of two reviewers independently selected articles, extracted data and used the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) to assess quality of evidence. Results 86 studies were included: 59 were focused on determinants, 23 on outcomes and 4 on both. Hyperinflation, exercise capacity, dyspnoea, previous exacerbations, gas exchange, systemic inflammation, quality of life and self-efficacy were consistently related to physical activity, but often based on cross-sectional studies and low-quality evidence. Results from studies of pharmacological and non-pharmacological treatments were inconsistent and the quality of evidence was low to very low. As outcomes, COPD exacerbations and mortality were consistently associated with low levels of physical activity based on moderate quality evidence. Physical activity was associated with other outcomes such as dyspnoea, health-related quality of life, exercise capacity and FEV1 but based on cross-sectional studies and low to very low quality evidence. Conclusions Physical activity level in COPD is consistently associated with mortality and exacerbations, but there is poor evidence about determinants of physical activity, including the impact of treatment.
Harvard University1, German Cancer Research Center2, Fred Hutchinson Cancer Research Center3, Mayo Clinic4, National Institutes of Health5, New York University6, University of California, San Francisco7, University of Toronto8, Monash University9, American Cancer Society10, Group Health Cooperative11, Johns Hopkins University12, University of Hawaii at Manoa13, University of Texas MD Anderson Cancer Center14, Carlos III Health Institute15, Memorial Sloan Kettering Cancer Center16, Yale University17, University at Buffalo18, University of Washington19, Vanderbilt University20, Institut Gustave Roussy21, Westat22, Heidelberg University23, Utrecht University24, Sapienza University of Rome25, University of Liverpool26, University of Pisa27, Veterans Health Administration28, University of Minnesota29, University of Southern California30, Mercy Medical Center (Baltimore, Maryland)31, University of North Carolina at Chapel Hill32, International Agency for Research on Cancer33, University of Oxford34, University of Cambridge35, Cleveland Clinic36, Lithuanian University of Health Sciences37, National Institute for Health and Welfare38, University of Melbourne39, University of Tokyo40, Duke University41, Imperial College London42, University of Bologna43, Casa Sollievo della Sofferenza44, Pompeu Fabra University45, Autonomous University of Barcelona46, Umeå University47, Medical University of Łódź48, Academy of Sciences of the Czech Republic49
TL;DR: This study identified multiple new susceptibility alleles for pancreatic cancer that are worthy of follow-up studies and an independent signal in exon 2 of TERT at the established region 5p15.
Abstract: We performed a multistage genome-wide association study including 7,683 individuals with pancreatic cancer and 14,397 controls of European descent. Four new loci reached genome-wide significance: rs6971499 at 7q32.3 (LINC-PINT, per-allele odds ratio (OR) = 0.79, 95% confidence interval (CI) 0.74-0.84, P = 3.0 × 10(-12)), rs7190458 at 16q23.1 (BCAR1/CTRB1/CTRB2, OR = 1.46, 95% CI 1.30-1.65, P = 1.1 × 10(-10)), rs9581943 at 13q12.2 (PDX1, OR = 1.15, 95% CI 1.10-1.20, P = 2.4 × 10(-9)) and rs16986825 at 22q12.1 (ZNRF3, OR = 1.18, 95% CI 1.12-1.25, P = 1.2 × 10(-8)). We identified an independent signal in exon 2 of TERT at the established region 5p15.33 (rs2736098, OR = 0.80, 95% CI 0.76-0.85, P = 9.8 × 10(-14)). We also identified a locus at 8q24.21 (rs1561927, P = 1.3 × 10(-7)) that approached genome-wide significance located 455 kb telomeric of PVT1. Our study identified multiple new susceptibility alleles for pancreatic cancer that are worthy of follow-up studies.