Showing papers by "University of Bergen published in 2013"
Wellcome Trust Sanger Institute1, Cambridge University Hospitals NHS Foundation Trust2, Wellcome Trust3, University of British Columbia4, University of Cambridge5, The Breast Cancer Research Foundation6, Oslo University Hospital7, University of Oslo8, University of Münster9, Université libre de Bruxelles10, German Cancer Research Center11, University of Iceland12, Erasmus University Rotterdam13, Paris Descartes University14, French Institute of Health and Medical Research15, University of Paris16, Broad Institute17, University of Bergen18, University of Queensland19, University of Oviedo20, University of Glasgow21, Harvard University22, United States Department of Veterans Affairs23, Netherlands Cancer Institute24, University of Kiel25, Radboud University Nijmegen26, King's College London27, Curie Institute28, Bankstown Lidcombe Hospital29, University of New South Wales30, University of Barcelona31
TL;DR: It is shown that hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types, and this results reveal the diversity of mutational processes underlying the development of cancer.
Abstract: All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
7,904 citations
TL;DR: In this paper, the authors performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array-and-sequencing-based technologies, and classified them into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy number high.
Abstract: We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.
3,719 citations
University of Maryland, Baltimore1, Centers for Disease Control and Prevention2, International Centre for Diarrhoeal Disease Research, Bangladesh3, Aga Khan University4, Medical Research Council5, University of Barcelona6, GlaxoSmithKline7, United States Department of Veterans Affairs8, Center for Drug Evaluation and Research9, University of Bergen10, Norwegian Institute of Public Health11, Royal Children's Hospital12
TL;DR: Interventions targeting five pathogens can substantially reduce the burden of moderate-to-severe diarrhoea and suggest new methods and accelerated implementation of existing interventions (rotavirus vaccine and zinc) are needed to prevent disease and improve outcomes.
2,766 citations
National Health Service1, University of Oslo2, Karolinska Institutet3, University of Bergen4, Queen's University Belfast5, Curie Institute6, Umeå University7, Mount Vernon Hospital8, Leeds Teaching Hospitals NHS Trust9, Cancer Research UK10, Norwegian University of Science and Technology11, Comenius University in Bratislava12, University of São Paulo13, Algeta14, Bayer Corporation15, Tulane University16
TL;DR: In this study, which was terminated for efficacy at the prespecified interim analysis, radium-223 improved overall survival and was associated with low myelosuppression rates and fewer adverse events.
Abstract: efit (median, 14.9 months vs. 11.3 months; hazard ratio, 0.70; 95% CI, 0.58 to 0.83; P<0.001). Assessments of all main secondary efficacy end points also showed a benefit of radium-233 as compared with placebo. Radium-223 was associated with low myelosuppression rates and fewer adverse events. Conclusions In this study, which was terminated for efficacy at the prespecified interim analysis, radium-223 improved overall survival. (Funded by Algeta and Bayer HealthCare Phar -
2,614 citations
University of Western Ontario1, York University2, University of Bergen3, The Mind Research Network4, National Institutes of Health5, University of New Mexico6, University of Chieti-Pescara7, Washington University in St. Louis8, Stanford University9, Georgia Institute of Technology10, Oulu University Hospital11, Indiana University12, Otto-von-Guericke University Magdeburg13, Leibniz Institute for Neurobiology14
TL;DR: Emerging evidence suggests that dynamic FC metrics may index changes in macroscopic neural activity patterns underlying critical aspects of cognition and behavior, though limitations with regard to analysis and interpretation remain.
2,332 citations
TL;DR: In unconscious survivors of out-of-hospital cardiac arrest of presumed cardiac cause, hypothermia at a targetedTemperature of 33°C did not confer a benefit as compared with a targeted temperature of 36°C.
Abstract: In total, 939 patients were included in the primary analysis. At the end of the trial, 50% of the patients in the 33°C group (235 of 473 patients) had died, as compared with 48% of the patients in the 36°C group (225 of 466 patients) (hazard ratio with a temperature of 33°C, 1.06; 95% confidence interval [CI], 0.89 to 1.28; P = 0.51). At the 180-day follow-up, 54% of the patients in the 33°C group had died or had poor neurologic function according to the CPC, as compared with 52% of patients in the 36°C group (risk ratio, 1.02; 95% CI, 0.88 to 1.16; P = 0.78). In the analysis using the modified Rankin scale, the comparable rate was 52% in both groups (risk ratio, 1.01; 95% CI, 0.89 to 1.14; P = 0.87). The results of analyses adjusted for known prognostic factors were similar. Conclusions In unconscious survivors of out-of-hospital cardiac arrest of presumed cardiac cause, hypothermia at a targeted temperature of 33°C did not confer a benefit as compared with a targeted temperature of 36°C. (Funded by the Swedish Heart–Lung Foundation and others; TTM ClinicalTrials.gov number, NCT01020916.)
2,159 citations
National Oceanography Centre, Southampton1, Stanford University2, Bar-Ilan University3, Centre national de la recherche scientifique4, University of Tasmania5, University of Otago6, McGill University7, University of Essex8, Pierre-and-Marie-Curie University9, ETH Zurich10, University of East Anglia11, University of Exeter12, Cornell University13, University of Vigo14, University of Pennsylvania15, University of California, Irvine16, Nagoya University17, Leibniz Institute of Marine Sciences18, Woods Hole Oceanographic Institution19, University of Bergen20, University of Tokyo21, University of Concepción22
TL;DR: In this paper, the authors reveal two broad regimes of phytoplankton nutrient limitation in the modern upper ocean: Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow.
Abstract: Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have revealed two broad regimes of phytoplankton nutrient limitation in the modern upper ocean. Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow. In contrast, iron often limits productivity where subsurface nutrient supply is enhanced, including within the main oceanic upwelling regions of the Southern Ocean and the eastern equatorial Pacific. Phosphorus, vitamins and micronutrients other than iron may also (co-)limit marine phytoplankton. The spatial patterns and importance of co-limitation, however, remain unclear. Variability in the stoichiometries of nutrient supply and biological demand are key determinants of oceanic nutrient limitation. Deciphering the mechanisms that underpin this variability, and the consequences for marine microbes, will be a challenge. But such knowledge will be crucial for accurately predicting the consequences of ongoing anthropogenic perturbations to oceanic nutrient biogeochemistry.
1,516 citations
TL;DR: It is shown that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents, and is called for for accelerated collection of spatially and temporally explicit species data.
Abstract: Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km2 to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere.
1,297 citations
Ashley Beecham1, Nikolaos A. Patsopoulos2, Nikolaos A. Patsopoulos3, Dionysia K. Xifara4 +203 more•Institutions (73)
TL;DR: This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
Abstract: Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 10 × 10(-4)) In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 50 × 10(-8)), 3 of which we found after conditioning on previously identified variants Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals
1,197 citations
Goethe University Frankfurt1, University of Pavia2, Policlinico Umberto I3, Paris Descartes University4, University of Verona5, École Normale Supérieure6, University of Bergen7, Haukeland University Hospital8, Innsbruck Medical University9, University of Medicine and Pharmacy of Craiova10, University of Bologna11
TL;DR: The technical part of these Guidelines and Recommendations provides an introduction to the physical principles and technology on which all forms of current commercially available ultrasound elastography are based.
Abstract: The technical part of these Guidelines and Recommendations, produced under the auspices of EFSUMB, provides an introduction to the physical principles and technology on which all forms of current commercially available ultrasound elastography are based. A difference in shear modulus is the common underlying physical mechanism that provides tissue contrast in all elastograms. The relationship between the alternative technologies is considered in terms of the method used to take advantage of this. The practical advantages and disadvantages associated with each of the techniques are described, and guidance is provided on optimisation of scanning technique, image display, image interpretation and some of the known image artefacts.
1,020 citations
Federal Urdu University1, Columbia University2, Woods Hole Oceanographic Institution3, Addis Ababa University4, Indian Institute of Tropical Meteorology5, University of Trieste6, Swiss Federal Institute for Forest, Snow and Landscape Research7, University of Montpellier8, University of Bergen9, University of Chile10, Austral University of Chile11, University of Tasmania12, Australian Antarctic Division13, National Oceanic and Atmospheric Administration14, University of Mainz15, Xishuangbanna Tropical Botanical Garden16, Nepal Academy of Science and Technology17, Chinese Academy of Sciences18, University of Melbourne19, Complutense University of Madrid20, Université catholique de Louvain21, University of the Witwatersrand22, Hydrologic Research Center23, University of Bern24, University of Helsinki25, Northern Arizona University26, Fukushima University27, Stockholm University28, Université Paris-Saclay29, National Institute of Water and Atmospheric Research30, University of Giessen31, Swansea University32, Desert Research Institute33, National Scientific and Technical Research Council34, British Antarctic Survey35, Nagoya University36, University of Brighton37, Florida State University38, Alfred Wegener Institute for Polar and Marine Research39, University of New South Wales40, University of Exeter41, Centro de Estudios Científicos42, University of Florence43, University of Texas at Austin44, Russian Academy of Sciences45, University of Washington46, National Centre for Antarctic and Ocean Research47, University of Arizona48, Ghent University49, University of Ottawa50, University of Copenhagen51, University of Colorado Boulder52, Shinshu University53
TL;DR: The authors reconstructed past temperatures for seven continental-scale regions during the past one to two millennia and found that the most coherent feature in nearly all of the regional temperature reconstructions is a long-term cooling trend, which ended late in the nineteenth century.
Abstract: Past global climate changes had strong regional expression To elucidate their spatio-temporal pattern, we reconstructed past temperatures for seven continental-scale regions during the past one to two millennia The most coherent feature in nearly all of the regional temperature reconstructions is a long-term cooling trend, which ended late in the nineteenth century At multi-decadal to centennial scales, temperature variability shows distinctly different regional patterns, with more similarity within each hemisphere than between them There were no globally synchronous multi-decadal warm or cold intervals that define a worldwide Medieval Warm Period or Little Ice Age, but all reconstructions show generally cold conditions between ad 1580 and 1880, punctuated in some regions by warm decades during the eighteenth century The transition to these colder conditions occurred earlier in the Arctic, Europe and Asia than in North America or the Southern Hemisphere regions Recent warming reversed the long-term cooling; during the period ad 1971–2000, the area-weighted average reconstructed temperature was higher than any other time in nearly 1,400 years
TL;DR: The authors used latent class analysis on these variables to derive seven classes of social class in the UK, and demonstrate the existence of an elite class whose wealth separates them from an established middle class, as well as a class of technical experts.
Abstract: The social scientific analysis of social class is attracting renewed interest given the accentuation of economic and social inequalities throughout the world. The most widely validated measure of social class, the Nuffield class schema, developed in the 1970s, was codified in the UK’s National Statistics Socio-Economic Classification (NS-SEC) and places people in one of seven main classes according to their occupation and employment status. This principally distinguishes between people working in routine or semi-routine occupations employed on a ‘labour contract’ on the one hand, and those working in professional or managerial occupations employed on a ‘service contract’ on the other. However, this occupationally based class schema does not effectively capture the role of social and cultural processes in generating class divisions. We analyse the largest survey of social class ever conducted in the UK, the BBC’s 2011 Great British Class Survey, with 161,400 web respondents, as well as a nationally representative sample survey, which includes unusually detailed questions asked on social, cultural and economic capital. Using latent class analysis on these variables, we derive seven classes. We demonstrate the existence of an ‘elite’, whose wealth separates them from an established middle class, as well as a class of technical experts and a class of ‘new affluent’ workers. We also show that at the lower levels of the class structure, alongside an ageing traditional working class, there is a ‘precariat’ characterised by very low levels of capital, and a group of emergent service workers. We think that this new seven class model recognises both social polarisation in British society and class fragmentation in its middle layers, and will attract enormous interest from a wide social scientific community in offering an up-to-date multi-dimensional model of social class.
University of Bologna1, The Royal Marsden NHS Foundation Trust2, Goethe University Frankfurt3, Paris Descartes University4, University of Bergen5, Innsbruck Medical University6, University of Pavia7, Policlinico Umberto I8, University of Verona9, École Normale Supérieure10, Haukeland University Hospital11, University of Medicine and Pharmacy of Craiova12
TL;DR: The clinical part of these Guidelines and Recommendations produced under the auspices of the European Federation of Societies for Ultrasound in Medicine and Biology EFSUMB assesses the clinically used applications of all forms of elastography, stressing the evidence from meta-analyses and giving practical advice for their uses and interpretation.
Abstract: The clinical part of these Guidelines and Recommendations produced under the auspices of the European Federation of Societies for Ultrasound in Medicine and Biology EFSUMB assesses the clinically used applications of all forms of elastography, stressing the evidence from meta-analyses and giving practical advice for their uses and interpretation. Diffuse liver disease forms the largest section, reflecting the wide experience with transient and shear wave elastography . Then follow the breast, thyroid, gastro-intestinal tract, endoscopic elastography, the prostate and the musculo-skeletal system using strain and shear wave elastography as appropriate. The document is intended to form a reference and to guide clinical users in a practical way.
TL;DR: It is shown that two large-scale projects with time series data show that several recent claims about cyber bullying made in the media and by some researchers are greatly exaggerated and lack scientific support.
Abstract: After sketching how my own interest and research into bullying problems began, I address a number of potentially controversial issues related to the definition and measurement of such problems. The importance of maintaining the distinctions between bullying victimization and general victimization and between bullying perpetration and general aggression is strongly emphasized. There are particular problems with the common method of peer nominations for purposes of prevalence estimation, comparisons of such estimates and mean levels across groups and time, and measurement of change. Two large-scale projects with time series data show that several recent claims about cyber bullying made in the media and by some researchers are greatly exaggerated and lack scientific support. Recent meta-analyses of the long-term outcomes for former bullies and victims provide convincing evidence that being involved in such problems is not just a harmless and passing school problem but something that has serious adjustment and public health consequences that also entail great costs to society. Another section presents my view of why the theme of bullying took quite some time to reach the peer relations research community in the United States and the role of a dominant research tradition focusing on "likeability" in this account. In a final section, I summarize some reasons why it may be considered important and interesting to focus both research and intervention on bully/victim problems.
TL;DR: The Cherenkov Telescope Array (CTA) as discussed by the authors is a very high-energy (VHE) gamma ray observatory with an international collaboration with more than 1000 members from 27 countries in Europe, Asia, Africa and North and South America.
TL;DR: In this paper, the results of the four LEP experiments were combined to determine fundamental properties of the W boson and the electroweak theory, including the branching fraction of W and the trilinear gauge-boson self-couplings.
TL;DR: A comprehensive, integrated checklist of determinants of practice (the TICD checklist) is described that aims to be comprehensive and to build on the strengths of each of the 12 included checklists.
Abstract: Background: Determinants of practice are factors that might prevent or enable improvements. Several checklists, frameworks, taxonomies, and classifications of determinants of healthcare professional practice have been published. In this paper, we describe the development of a comprehensive, integrated checklist of determinants of practice (the TICD checklist). Methods: We performed a systematic review of frameworks of determinants of practice followed by a consensus process. We searched electronic databases and screened the reference lists of key background documents. Two authors independently assessed titles and abstracts, and potentially relevant full text articles. We compiled a list of attributes that a checklist should have: comprehensiveness, relevance, applicability, simplicity, logic, clarity, usability, suitability, and usefulness. We assessed included articles using these criteria and collected information about the theory, model, or logic underlying how the factors (determinants) were selected, described, and grouped, the strengths and weaknesses of the checklist, and the determinants and the domains in each checklist. We drafted a preliminary checklist based on an aggregated list of determinants from the included checklists, and finalized the checklist by a consensus process among implementation researchers. Results: We screened 5,778 titles and abstracts and retrieved 87 potentially relevant papers in full text. Several of these papers had references to papers that we also retrieved in full text. We also checked potentially relevant papers we had on file that were not retrieved by the searches. We included 12 checklists. None of these were completely comprehensive when compared to the aggregated list of determinants and domains. We developed a checklist with 57 potential determinants of practice grouped in seven domains: guideline factors, individual health professional factors, patient factors, professional interactions, incentives and resources, capacity for organisational change, and social, political, and legal factors. We also developed five worksheets to facilitate the use of the checklist. Conclusions: Based on a systematic review and a consensus process we developed a checklist that aims to be comprehensive and to build on the strengths of each of the 12 included checklists. The checklist is accompanied with five worksheets to facilitate its use in implementation research and quality improvement projects.
TL;DR: In patients with systolic heart failure and a QRS duration of less than 130 msec, CRT does not reduce the rate of death or hospitalization for heart failure, and may increase mortality.
Abstract: BACKGROUND Cardiac-resynchronization therapy (CRT) reduces morbidity and mortality in chronic systolic heart failure with a wide QRS complex. Mechanical dyssynchrony also occurs in patients with a narrow QRS complex, which suggests the potential usefulness of CRT in such patients. METHODS We conducted a randomized trial involving 115 centers to evaluate the effect of CRT in patients with New York Heart Association class III or IV heart failure, a left ventricular ejection fraction of 35% or less, a QRS duration of less than 130 msec, and echocardiographic evidence of left ventricular dyssynchrony. All patients underwent device implantation and were randomly assigned to have CRT capability turned on or off. The primary efficacy outcome was the composite of death from any cause or first hospitalization for worsening heart failure. RESULTS On March 13, 2013, the study was stopped for futility on the recommendation of the data and safety monitoring board. At study closure, the 809 patients who had undergone randomization had been followed for a mean of 19.4 months. The primary outcome occurred in 116 of 404 patients in the CRT group, as compared with 102 of 405 in the control group (28.7% vs. 25.2%; hazard ratio, 1.20; 95% confidence interval [CI], 0.92 to 1.57; P = 0.15). There were 45 deaths in the CRT group and 26 in the control group (11.1% vs. 6.4%; hazard ratio, 1.81; 95% CI, 1.11 to 2.93; P = 0.02). CONCLUSIONS In patients with systolic heart failure and a QRS duration of less than 130 msec, CRT does not reduce the rate of death or hospitalization for heart failure and may increase mortality. (Funded by Biotronik and GE Healthcare; EchoCRT ClinicalTrials.gov number, NCT00683696.)
TL;DR: The genome of the ctenophore the warty comb jelly or sea walnut, Mnemiopsis leidyi, is sequenced and it is concluded that c tenophores alone, not sponges or the clade consisting of both ctenphores and cnidarians, are the most basal extant animals.
Abstract: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.
TL;DR: In this paper, the spin and parity quantum numbers of the Higgs boson were studied based on the collision data collected by the ATLAS experiment at the LHC, and the results showed that the standard model spin-parity J(...
TL;DR: The concept for this analysis is to a large degree based on earlier BABAR work and we acknowledge the guidance provided by M. Mazur as discussed by the authors, who consulted with theorists A. Datta, S. Westhoff,S. Fajfer, J. Kamenik, and I. Nisandzic on the calculations of the charged Higgs contributions to the decay rates.
Abstract: The concept for this analysis is to a large degree based on earlier BABAR work and we acknowledge the guidance provided by M. Mazur. The authors consulted with theorists A. Datta, S. Westhoff, S. Fajfer, J. Kamenik, and I. Nisandzic on the calculations of the charged Higgs contributions to the decay rates. We are grateful for the extraordinary contributions of our PEP-II colleagues in achieving the excellent luminosity and machine conditions that have made this work possible. The success of this project also relied critically on the expertise and dedication of the computing organizations that support BABAR. The collaborating institutions wish to thank SLAC for its support and the kind hospitality extended to them. This work is supported by the U.S. Department of Energy and National Science Foundation, the Natural Sciences and Engineering Research Council (Canada), the Commissariat a l'Energie Atomique and Institut National de Physique Nucleaire et de Physique des Particules (France), the Bundesministerium fur Bildung und Forschung and Deutsche Forschungsgemeinschaft (Germany), the Istituto Nazionale di Fisica Nucleare (Italy), the Foundation for Fundamental Research on Matter (Netherlands), the Research Council of Norway, the Ministry of Education and Science of the Russian Federation, Ministerio de Economia y Competitividad (Spain), and the Science and Technology Facilities Council (United Kingdom). Individuals have received support from the Marie-Curie IEF program (European Union) and the A. P. Sloan Foundation (USA).
Bergen University College1, University of Bergen2, Aligarh Muslim University3, Gangneung–Wonju National University4, Korea Institute of Science and Technology Information5, COMSATS Institute of Information Technology6, University of Oslo7, Lawrence Livermore National Laboratory8, Czech Technical University in Prague9, Academy of Sciences of the Czech Republic10, Yale University11, Panjab University, Chandigarh12, CERN13, Hungarian Academy of Sciences14, University of Bologna15, Goethe University Frankfurt16, Variable Energy Cyclotron Centre17, GSI Helmholtz Centre for Heavy Ion Research18, Kurchatov Institute19
TL;DR: In this paper, the ALICE detector was used to measure the correlations between charged trigger and associated particles in p-Pb collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T, P-assoc < P -T,Ptrig < 4 GeV/c.
Stig E. Bojesen1, Stig E. Bojesen2, Karen A. Pooley3, Sharon E. Johnatty4 +452 more•Institutions (129)
TL;DR: Using the Illumina custom genotyping array iCOGs, SNPs at the TERT locus in breast, ovarian and BRCA1 mutation carrier cancer cases and controls and leukocyte telomere measurements are analyzed to find associations cluster into three independent peaks.
Abstract: TERT-locus SNPs and leukocyte telomere measures are reportedly associated with risks of multiple cancers. Using the Illumina custom genotyping array iCOG, we analyzed similar to 480 SNPs at the TERT locus in breast (n = 103,991), ovarian (n = 39,774) and BRCA1 mutation carrier (n = 11,705) cancer cases and controls. Leukocyte telomere measurements were also available for 53,724 participants. Most associations cluster into three independent peaks. The minor allele at the peak 1 SNP rs2736108 associates with longer telomeres (P = 5.8 x 10(-7)), lower risks for estrogen receptor (ER)-negative (P = 1.0 x 10(-8)) and BRCA1 mutation carrier (P = 1.1 x 10(-5)) breast cancers and altered promoter assay signal. The minor allele at the peak 2 SNP rs7705526 associates with longer telomeres (P = 2.3 x 10(-14)), higher risk of low-malignant-potential ovarian cancer (P = 1.3 x 10(-15)) and greater promoter activity. The minor alleles at the peak 3 SNPs rs10069690 and rs2242652 increase ER-negative (P = 1.2 x 10(-12)) and BRCA1 mutation carrier (P = 1.6 x 10-14) breast and invasive ovarian (P = 1.3 x 10(-11)) cancer risks but not via altered telomere length. The cancer risk alleles of rs2242652 and rs10069690, respectively, increase silencing and generate a truncated TERT splice variant.
TL;DR: In this article, the production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs were measured using the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of 7 TeV and 8 TeV, corresponding to an integrated luminosity of about 25/fb.
TL;DR: In this article, the luminosity calibration for the ATLAS detector at the LHC during pp collisions at root s = 7 TeV in 2010 and 2011 is presented, and a luminosity uncertainty of delta L/L = +/- 3.5 % is obtained.
Abstract: The luminosity calibration for the ATLAS detector at the LHC during pp collisions at root s = 7 TeV in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at root s = 7 TeV. A luminosity uncertainty of delta L/L = +/- 3.5 % is obtained for the 47 pb(-1) of data delivered to ATLAS in 2010, and an uncertainty of delta L/L = +/- 1.8 % is obtained for the 5.5 fb(-1) delivered in 2011.
04 Mar 2013
TL;DR: In this paper, the authors measured the transverse-momentum (p(T)) distributions and yields of pi, K, and p in Pb-Pb collisions at root s(NN) = 2.76 TeV.
Abstract: In this paper measurements are presented of pi(+/-), K-+/-, p, and (p) over bar production at midrapidity (vertical bar y vertical bar < 0.5), in Pb-Pb collisions at root s(NN) = 2.76 TeV as a function of centrality. The measurement covers the transverse-momentum (p(T)) range from 100, 200, and 300 MeV/c up to 3, 3, and 4.6 GeV/c for pi, K, and p, respectively. The measured p(T) distributions and yields are compared to expectations based on hydrodynamic, thermal and recombination models. The spectral shapes of central collisions show a stronger radial flow than measured at lower energies, which can be described in hydrodynamic models. In peripheral collisions, the p(T) distributions are not well reproduced by hydrodynamic models. Ratios of integrated particle yields are found to be nearly independent of centrality. The yield of protons normalized to pions is a factor similar to 1.5 lower than the expectation from thermal models.
TL;DR: Use of prenatal folic acid supplements around the time of conception was associated with a lower risk of autistic disorder in the MoBa cohort, and similar analyses for prenatal fish oil supplements showed no such association with autistic disorder, even though fish oil use wasassociated with the same maternal characteristics as folic Acid use.
Abstract: Importance Prenatal folic acid supplements reduce the risk of neural tube defects in children, but it has not been determined whether they protect against other neurodevelopmental disorders. Objective To examine the association between maternal use of prenatal folic acid supplements and subsequent risk of autism spectrum disorders (ASDs) (autistic disorder, Asperger syndrome, pervasive developmental disorder–not otherwise specified [PDD-NOS]) in children. Design, Setting, and Patients The study sample of 85 176 children was derived from the population-based, prospective Norwegian Mother and Child Cohort Study (MoBa). The children were born in 2002-2008; by the end of follow-up on March 31, 2012, the age range was 3.3 through 10.2 years (mean, 6.4 years). The exposure of primary interest was use of folic acid from 4 weeks before to 8 weeks after the start of pregnancy, defined as the first day of the last menstrual period before conception. Relative risks of ASDs were estimated by odds ratios (ORs) with 95% CIs in a logistic regression analysis. Analyses were adjusted for maternal education level, year of birth, and parity. Main Outcome Measure Specialist-confirmed diagnosis of ASDs. Results At the end of follow-up, 270 children in the study sample had been diagnosed with ASDs: 114 with autistic disorder, 56 with Asperger syndrome, and 100 with PDD-NOS. In children whose mothers took folic acid, 0.10% (64/61 042) had autistic disorder, compared with 0.21% (50/24 134) in those unexposed to folic acid. The adjusted OR for autistic disorder in children of folic acid users was 0.61 (95% CI, 0.41-0.90). No association was found with Asperger syndrome or PDD-NOS, but power was limited. Similar analyses for prenatal fish oil supplements showed no such association with autistic disorder, even though fish oil use was associated with the same maternal characteristics as folic acid use. Conclusions and Relevance Use of prenatal folic acid supplements around the time of conception was associated with a lower risk of autistic disorder in the MoBa cohort. Although these findings cannot establish causality, they do support prenatal folic acid supplementation.
TL;DR: Two-particle correlations in relative azimuthal angle and pseudorapidity are measured using the ATLAS detector at the LHC and the resultant Δø correlation is approximately symmetric about π/2, and is consistent with a dominant cos2Δø modulation for all ΣE(T)(Pb) ranges and particle p(T).
Abstract: Two-particle correlations in relative azimuthal angle (Delta phi) and pseudorapidity (Delta eta) are measured in root S-NN = 5.02 TeV p + Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 mu b(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (Sigma E-T(Pb)) summed over 3.1 < eta < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < vertical bar Delta eta vertical bar < 5) "near-side" (Delta phi similar to 0) correlation that grows rapidly with increasing Sigma E-T(Pb). A long-range "away-side" (Delta phi similar to pi) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small Sigma E-T(Pb), is found to match the near-side correlation in magnitude, shape (in Delta eta and Delta phi) and Sigma E-T(Pb) dependence. The resultant Delta phi correlation is approximately symmetric about pi/2, and is consistent with a dominant cos2 Delta phi modulation for all Sigma E-T(Pb) ranges and particle p(T).
California State University San Marcos1, Alfred Wegener Institute for Polar and Marine Research2, University of Alberta3, United States Department of Energy4, J. Craig Venter Institute5, Institut national de la recherche agronomique6, Ruhr University Bochum7, University of Maryland, College Park8, Monterey Bay Aquarium Research Institute9, University College London10, Centre national de la recherche scientifique11, Harvard University12, Ghent University13, Rothamsted Research14, Pierre-and-Marie-Curie University15, University of Essex16, Pontifical Catholic University of Chile17, Plymouth Marine Laboratory18, Columbia University19, Woods Hole Oceanographic Institution20, University of Cologne21, Natural History Museum22, Rutgers University23, Georgia Institute of Technology24, Moscow Institute of Physics and Technology25, University of Ostrava26, National Institutes of Health27, University of Nebraska Medical Center28, University of Southampton29, Oregon State University30, Dalhousie University31, University of Texas Health Science Center at Houston32, University of East Anglia33, University of Potsdam34, University of Bergen35, University of Washington36, University of Freiburg37, University of Marburg38, University of Los Andes39, Bigelow Laboratory For Ocean Sciences40, University of Exeter41, Oak Ridge National Laboratory42, California State University, Chico43, University of Tsukuba44
TL;DR: Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires, and reveals a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome.
Abstract: Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
Oklahoma Medical Research Foundation1, University of Oklahoma2, University of Paris-Sud3, University Hospitals Birmingham NHS Foundation Trust4, Queen Elizabeth II Hospital5, Linköping University6, Uppsala University7, University of Bergen8, Stavanger University Hospital9, Veterans Health Administration10, Cincinnati Children's Hospital Medical Center11, Karolinska Institutet12, Örebro University13, King's College London14, University of Colorado Denver15, University of Minnesota16, Carolinas Medical Center17, Harvard University18, Washington University in St. Louis19, National Institutes of Health20, Hannover Medical School21, University of Adelaide22, Newcastle University23, Del Rosario University24
TL;DR: The results highlight the importance of genes that are involved in both innate and adaptive immunity in Sjögren's syndrome, including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2 and PHIP, among others.
Abstract: Sjogren's syndrome is a common autoimmune disease (affecting ∼0.7% of European Americans) that typically presents as keratoconjunctivitis sicca and xerostomia. Here we report results of a large-scale association study of Sjogren's syndrome. In addition to strong association within the human leukocyte antigen (HLA) region at 6p21 (Pmeta = 7.65 × 10(-114)), we establish associations with IRF5-TNPO3 (Pmeta = 2.73 × 10(-19)), STAT4 (Pmeta = 6.80 × 10(-15)), IL12A (Pmeta = 1.17 × 10(-10)), FAM167A-BLK (Pmeta = 4.97 × 10(-10)), DDX6-CXCR5 (Pmeta = 1.10 × 10(-8)) and TNIP1 (Pmeta = 3.30 × 10(-8)). We also observed suggestive associations (Pmeta < 5 × 10(-5)) with variants in 29 other regions, including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2 and PHIP, among others. These results highlight the importance of genes that are involved in both innate and adaptive immunity in Sjogren's syndrome.