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Showing papers by "Lund University published in 2012"


Journal ArticleDOI
Georges Aad1, T. Abajyan2, Brad Abbott3, Jalal Abdallah4  +2964 moreInstitutions (200)
TL;DR: In this article, a search for the Standard Model Higgs boson in proton-proton collisions with the ATLAS detector at the LHC is presented, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7×10−9.

9,282 citations


Journal ArticleDOI
Kaoru Hagiwara, Ken Ichi Hikasa1, Koji Nakamura, Masaharu Tanabashi1, M. Aguilar-Benitez, Claude Amsler2, R. M. Barnett3, P. R. Burchat4, C. D. Carone5, C. Caso6, G. Conforto7, Olav Dahl3, Michael Doser8, Semen Eidelman9, Jonathan L. Feng10, L. K. Gibbons11, M. C. Goodman12, Christoph Grab13, D. E. Groom3, Atul Gurtu14, Atul Gurtu8, K. G. Hayes15, J.J. Hernández-Rey16, K. Honscheid17, Christopher Kolda18, Michelangelo L. Mangano8, D. M. Manley19, Aneesh V. Manohar20, John March-Russell8, Alberto Masoni, Ramon Miquel3, Klaus Mönig, Hitoshi Murayama21, Hitoshi Murayama3, S. Sánchez Navas13, Keith A. Olive22, Luc Pape8, C. Patrignani6, A. Piepke23, Matts Roos24, John Terning25, Nils A. Tornqvist24, T. G. Trippe3, Petr Vogel26, C. G. Wohl3, Ron L. Workman27, W-M. Yao3, B. Armstrong3, P. S. Gee3, K. S. Lugovsky, S. B. Lugovsky, V. S. Lugovsky, Marina Artuso28, D. Asner29, K. S. Babu30, E. L. Barberio8, Marco Battaglia8, H. Bichsel31, O. Biebel32, P. Bloch8, Robert N. Cahn3, Ariella Cattai8, R.S. Chivukula33, R. Cousins34, G. A. Cowan35, Thibault Damour36, K. Desler, R. J. Donahue3, D. A. Edwards, Victor Daniel Elvira37, Jens Erler38, V. V. Ezhela, A Fassò8, W. Fetscher13, Brian D. Fields39, B. Foster40, Daniel Froidevaux8, Masataka Fukugita41, Thomas K. Gaisser42, L. A. Garren37, H J Gerber13, Frederick J. Gilman43, Howard E. Haber44, C. A. Hagmann29, J.L. Hewett4, Ian Hinchliffe3, Craig J. Hogan31, G. Höhler45, P. Igo-Kemenes46, John David Jackson3, Kurtis F Johnson47, D. Karlen48, B. Kayser37, S. R. Klein3, Konrad Kleinknecht49, I.G. Knowles50, P. Kreitz4, Yu V. Kuyanov, R. Landua8, Paul Langacker38, L. S. Littenberg51, Alan D. Martin52, Tatsuya Nakada8, Tatsuya Nakada53, Meenakshi Narain33, Paolo Nason, John A. Peacock54, H. R. Quinn55, Stuart Raby17, Georg G. Raffelt32, E. A. Razuvaev, B. Renk49, L. Rolandi8, Michael T Ronan3, L.J. Rosenberg54, C.T. Sachrajda55, A. I. Sanda56, Subir Sarkar57, Michael Schmitt58, O. Schneider53, Douglas Scott59, W. G. Seligman60, M. H. Shaevitz60, Torbjörn Sjöstrand61, George F. Smoot3, Stefan M Spanier4, H. Spieler3, N. J. C. Spooner62, Mark Srednicki63, Achim Stahl, Todor Stanev42, M. Suzuki3, N. P. Tkachenko, German Valencia64, K. van Bibber29, Manuella Vincter65, D. R. Ward66, Bryan R. Webber66, M R Whalley52, Lincoln Wolfenstein43, J. Womersley37, C. L. Woody51, Oleg Zenin 
Tohoku University1, University of Zurich2, Lawrence Berkeley National Laboratory3, Stanford University4, College of William & Mary5, University of Genoa6, University of Urbino7, CERN8, Budker Institute of Nuclear Physics9, University of California, Irvine10, Cornell University11, Argonne National Laboratory12, ETH Zurich13, Tata Institute of Fundamental Research14, Hillsdale College15, Spanish National Research Council16, Ohio State University17, University of Notre Dame18, Kent State University19, University of California, San Diego20, University of California, Berkeley21, University of Minnesota22, University of Alabama23, University of Helsinki24, Los Alamos National Laboratory25, California Institute of Technology26, George Washington University27, Syracuse University28, Lawrence Livermore National Laboratory29, Oklahoma State University–Stillwater30, University of Washington31, Max Planck Society32, Boston University33, University of California, Los Angeles34, Royal Holloway, University of London35, Université Paris-Saclay36, Fermilab37, University of Pennsylvania38, University of Illinois at Urbana–Champaign39, University of Bristol40, University of Tokyo41, University of Delaware42, Carnegie Mellon University43, University of California, Santa Cruz44, Karlsruhe Institute of Technology45, Heidelberg University46, Florida State University47, Carleton University48, University of Mainz49, University of Edinburgh50, Brookhaven National Laboratory51, Durham University52, University of Lausanne53, Massachusetts Institute of Technology54, University of Southampton55, Nagoya University56, University of Oxford57, Northwestern University58, University of British Columbia59, Columbia University60, Lund University61, University of Sheffield62, University of California, Santa Barbara63, Iowa State University64, University of Alberta65, University of Cambridge66
TL;DR: The Particle Data Group's biennial review as mentioned in this paper summarizes much of particle physics, using data from previous editions, plus 2658 new measurements from 644 papers, and lists, evaluates, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons.
Abstract: This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, V-cb & V-ub, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter. A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov.

4,465 citations


Journal ArticleDOI
TL;DR: These guidelines are presented for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

4,316 citations


Journal ArticleDOI
TL;DR: The Systemic Lupus International Collaborating Clinics (SLICC) group revised and validated the American College of Rheumatology (ACR) systemic lupus erythematosus (SLE) classification criteria in order to improve clinical relevance, meet stringent methodology requirements, and incorporate new knowledge regarding the immunology of SLE.
Abstract: Objective The Systemic Lupus International Collaborating Clinics (SLICC) group revised and validated the American College of Rheumatology (ACR) systemic lupus erythematosus (SLE) classification criteria in order to improve clinical relevance, meet stringent methodology requirements, and incorporate new knowledge regarding the immunology of SLE. Methods The classification criteria were derived from a set of 702 expert-rated patient scenarios. Recursive partitioning was used to derive an initial rule that was simplified and refined based on SLICC physician consensus. The SLICC group validated the classification criteria in a new validation sample of 690 new expert-rated patient scenarios. Results Seventeen criteria were identified. In the derivation set, the SLICC classification criteria resulted in fewer misclassifications compared with the current ACR classification criteria (49 versus 70; P = 0.0082) and had greater sensitivity (94% versus 86%; P < 0.0001) and equal specificity (92% versus 93%; P = 0.39). In the validation set, the SLICC classification criteria resulted in fewer misclassifications compared with the current ACR classification criteria (62 versus 74; P = 0.24) and had greater sensitivity (97% versus 83%; P < 0.0001) but lower specificity (84% versus 96%; P < 0.0001). Conclusion The new SLICC classification criteria performed well in a large set of patient scenarios rated by experts. According to the SLICC rule for the classification of SLE, the patient must satisfy at least 4 criteria, including at least one clinical criterion and one immunologic criterion OR the patient must have biopsy-proven lupus nephritis in the presence of antinuclear antibodies or antidouble-stranded DNA antibodies. (Less)

3,609 citations


Journal ArticleDOI
TL;DR: This article conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent, and identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association.
Abstract: To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.

1,899 citations


Journal ArticleDOI
Benjamin F. Voight1, Benjamin F. Voight2, Benjamin F. Voight3, Gina M. Peloso4, Gina M. Peloso5, Marju Orho-Melander6, Ruth Frikke-Schmidt7, Maja Barbalić8, Majken K. Jensen3, George Hindy6, Hilma Holm9, Eric L. Ding3, Toby Johnson10, Heribert Schunkert11, Nilesh J. Samani12, Nilesh J. Samani13, Robert Clarke14, Jemma C. Hopewell14, John F. Thompson12, Mingyao Li2, Gudmar Thorleifsson9, Christopher Newton-Cheh, Kiran Musunuru3, Kiran Musunuru1, James P. Pirruccello1, James P. Pirruccello3, Danish Saleheen15, Li Chen16, Alexandre F.R. Stewart16, Arne Schillert11, Unnur Thorsteinsdottir17, Unnur Thorsteinsdottir9, Gudmundur Thorgeirsson17, Sonia S. Anand18, James C. Engert19, Thomas M. Morgan20, John A. Spertus21, Monika Stoll22, Klaus Berger22, Nicola Martinelli23, Domenico Girelli23, Pascal P. McKeown24, Christopher Patterson24, Stephen E. Epstein25, Joseph M. Devaney25, Mary Susan Burnett25, Vincent Mooser26, Samuli Ripatti27, Ida Surakka27, Markku S. Nieminen27, Juha Sinisalo27, Marja-Liisa Lokki27, Markus Perola4, Aki S. Havulinna4, Ulf de Faire28, Bruna Gigante28, Erik Ingelsson28, Tanja Zeller29, Philipp S. Wild29, Paul I.W. de Bakker, Olaf H. Klungel30, Anke-Hilse Maitland-van der Zee30, Bas J M Peters30, Anthonius de Boer30, Diederick E. Grobbee30, Pieter Willem Kamphuisen31, Vera H.M. Deneer, Clara C. Elbers30, N. Charlotte Onland-Moret30, Marten H. Hofker31, Cisca Wijmenga31, W. M. Monique Verschuren, Jolanda M. A. Boer, Yvonne T. van der Schouw30, Asif Rasheed, Philippe M. Frossard, Serkalem Demissie5, Serkalem Demissie4, Cristen J. Willer32, Ron Do3, Jose M. Ordovas33, Jose M. Ordovas34, Gonçalo R. Abecasis32, Michael Boehnke32, Karen L. Mohlke35, Mark J. Daly1, Mark J. Daly3, Candace Guiducci1, Noël P. Burtt1, Aarti Surti1, Elena Gonzalez1, Shaun Purcell3, Shaun Purcell1, Stacey Gabriel1, Jaume Marrugat, John F. Peden14, Jeanette Erdmann11, Patrick Diemert11, Christina Willenborg11, Inke R. König11, Marcus Fischer36, Christian Hengstenberg36, Andreas Ziegler11, Ian Buysschaert37, Diether Lambrechts37, Frans Van de Werf37, Keith A.A. Fox38, Nour Eddine El Mokhtari39, Diana Rubin, Jürgen Schrezenmeir, Stefan Schreiber39, Arne Schäfer39, John Danesh15, Stefan Blankenberg29, Robert Roberts16, Ruth McPherson16, Hugh Watkins14, Alistair S. Hall40, Kim Overvad41, Eric B. Rimm3, Eric Boerwinkle8, Anne Tybjærg-Hansen7, L. Adrienne Cupples5, L. Adrienne Cupples4, Muredach P. Reilly2, Olle Melander6, Pier Mannuccio Mannucci42, Diego Ardissino, David S. Siscovick43, Roberto Elosua, Kari Stefansson9, Kari Stefansson17, Christopher J. O'Donnell3, Christopher J. O'Donnell4, Veikko Salomaa4, Daniel J. Rader2, Leena Peltonen44, Leena Peltonen27, Stephen M. Schwartz43, David Altshuler, Sekar Kathiresan 
11 Aug 2012
TL;DR: In this paper, a Mendelian randomisation analysis was performed to compare the effect of HDL cholesterol, LDL cholesterol, and genetic score on risk of myocardial infarction.
Abstract: Methods We performed two mendelian randomisation analyses. First, we used as an instrument a single nucleotide polymorphism (SNP) in the endothelial lipase gene (LIPG Asn396Ser) and tested this SNP in 20 studies (20 913 myocardial infarction cases, 95 407 controls). Second, we used as an instrument a genetic score consisting of 14 common SNPs that exclusively associate with HDL cholesterol and tested this score in up to 12 482 cases of myocardial infarction and 41 331 controls. As a positive control, we also tested a genetic score of 13 common SNPs exclusively associated with LDL cholesterol. – ¹³) but similar levels of other lipid and non-lipid risk factors for myocardial infarction compared with noncarriers. This diff erence in HDL cholesterol is expected to decrease risk of myocardial infarction by 13% (odds ratio [OR] 0·87, 95% CI 0·84–0·91). However, we noted that the 396Ser allele was not associated with risk of myocardial infarction (OR 0·99, 95% CI 0·88–1·11, p=0·85). From observational epidemiology, an increase of 1 SD in HDL cholesterol was associated with reduced risk of myocardial infarction (OR 0·62, 95% CI 0·58–0·66). However, a 1 SD increase in HDL cholesterol due to genetic score was not associated with risk of myocardial infarction (OR 0·93, 95% CI 0·68–1·26, p=0·63). For LDL cholesterol, the estimate from observational epidemiology (a 1 SD increase in LDL cholesterol associated with OR 1·54, 95% CI 1·45–1·63) was concordant with that from genetic score (OR 2·13, 95% CI 1·69–2·69, p=2×10

1,878 citations


Journal ArticleDOI
25 May 2012-Cell
TL;DR: This work generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes, finding a remarkable phenomenon of localized hypermutation, termed “kataegis,” was observed.

1,699 citations


Journal ArticleDOI
TL;DR: It is shown that this zero-bias conductance peak structure in the Nb-InSb nanowire-Nb hybrid quantum device can persist over a large range of applied magnetic fields and could be interpreted as a transport signature of Majorana fermions in the InSb Nanowire.
Abstract: Semiconductor InSb nanowires are expected to provide an excellent material platform for the study of Majorana fermions in solid state systems. Here, we report on the realization of a Nb-InSb nanowire-Nb hybrid quantum device and the observation of a zero-bias conductance peak structure in the device. An InSb nanowire quantum dot is formed in the device between the two Nb contacts. Due to the proximity effect, the InSb nanowire segments covered by the superconductor Nb contacts turn to superconductors with a superconducting energy gap Δ(InSb) ∼ 0.25 meV. A tunable critical supercurrent is observed in the device in high back gate voltage regions in which the Fermi level in the InSb nanowire is located above the tunneling barriers of the quantum dot and the device is open to conduction. When a perpendicular magnetic field is applied to the devices, the critical supercurrent is seen to decrease as the magnetic field increases. However, at sufficiently low back gate voltages, the device shows the quasi-particle Coulomb blockade characteristics and the supercurrent is strongly suppressed even at zero magnetic field. This transport characteristic changes when a perpendicular magnetic field stronger than a critical value, at which the Zeeman energy in the InSb nanowire is E(z) ∼ Δ(InSb), is applied to the device. In this case, the transport measurements show a conductance peak at the zero bias voltage and the entire InSb nanowire in the device behaves as in a topological superconductor phase. We also show that this zero-bias conductance peak structure can persist over a large range of applied magnetic fields and could be interpreted as a transport signature of Majorana fermions in the InSb nanowire.

1,374 citations


Journal ArticleDOI
25 May 2012-Cell
TL;DR: Algorithms were developed to decipher this narrative and applied them to 21 breast cancers, finding that expansion of the dominant subclone to an appreciable mass may represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.

1,290 citations


Journal ArticleDOI
TL;DR: Light is shed on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility and within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways.
Abstract: Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10(-8)). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10(-4), Bonferroni corrected), of which six reached P < 5 × 10(-8), including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.

1,076 citations


Journal ArticleDOI
01 Feb 2012-Chest
TL;DR: In this article, the authors focus on the common important management questions for which, at a minimum, low-quality published evidence is available to guide best practices and provide guidance for many common anticoagulation-related management problems.

Journal ArticleDOI
TL;DR: A common Mendelian genetic lesion in C9orf72 is implicated in many cases of sporadic and familial ALS and FTD, suggesting a one-off expansion occurring about 1500 years ago.
Abstract: Background We aimed to accurately estimate the frequency of a hexanucleotide repeat expansion in C9orf72 that has been associated with a large proportion of cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Methods We screened 4448 patients diagnosed with ALS (El Escorial criteria) and 1425 patients with FTD (Lund-Manchester criteria) from 17 regions worldwide for the GGGGCC hexanucleotide expansion using a repeat-primed PCR assay. We assessed familial disease status on the basis of self-reported family history of similar neurodegenerative diseases at the time of sample collection. We compared haplotype data for 262 patients carrying the expansion with the known Finnish founder risk haplotype across the chromosomal locus. We calculated age-related penetrance using the Kaplan-Meier method with data for 603 individuals with the expansion. Findings In patients with sporadic ALS, we identified the repeat expansion in 236 (7·0%) of 3377 white individuals from the USA, Europe, and Australia, two (4·1%) of 49 black individuals from the USA, and six (8·3%) of 72 Hispanic individuals from the USA. The mutation was present in 217 (39·3%) of 552 white individuals with familial ALS from Europe and the USA. 59 (6·0%) of 981 white Europeans with sporadic FTD had the mutation, as did 99 (24·8%) of 400 white Europeans with familial FTD. Data for other ethnic groups were sparse, but we identified one Asian patient with familial ALS (from 20 assessed) and two with familial FTD (from three assessed) who carried the mutation. The mutation was not carried by the three Native Americans or 360 patients from Asia or the Pacific Islands with sporadic ALS who were tested, or by 41 Asian patients with sporadic FTD. All patients with the repeat expansion had (partly or fully) the founder haplotype, suggesting a one-off expansion occurring about 1500 years ago. The pathogenic expansion was non-penetrant in individuals younger than 35 years, 50% penetrant by 58 years, and almost fully penetrant by 80 years. Interpretation A common Mendelian genetic lesion in C9orf72 is implicated in many cases of sporadic and familial ALS and FTD. Testing for this pathogenic expansion should be considered in the management and genetic counselling of patients with these fatal neurodegenerative diseases. Funding Full funding sources listed at end of paper (see Acknowledgments).

Journal ArticleDOI
Stephen Kaptoge1, Emanuele Di Angelantonio1, Lisa Pennells1, Angela M. Wood1, Ian R. White2, Pei Gao1, Matthew G. Walker1, Alexander M. W. Cargill Thompson1, Nadeem Sarwar1, Muriel J. Caslake3, Adam S. Butterworth1, Philippe Amouyel4, Gerd Assmann, Stephan J. L. Bakker5, Elizabeth L M Barr6, Elizabeth Barrett-Connor7, Emelia J. Benjamin8, Cecilia Björkelund9, Hermann Brenner10, Eric J. Brunner11, Robert Clarke12, Jackie A. Cooper11, Peter Cremer13, Mary Cushman14, Gilles R. Dagenais, Ralph B. D'Agostino8, Rachel Dankner, George Davey-Smith15, Dorly J. H. Deeg16, Jacqueline M. Dekker16, Gunnar Engström17, Aaron R. Folsom18, F. Gerry R. Fowkes19, John Gallacher20, J. Michael Gaziano21, Simona Giampaoli22, Richard F. Gillum23, Albert Hofman24, Barbara V. Howard25, Erik Ingelsson26, Hiroyasu Iso27, Torben Jørgensen28, Stefan Kiechl29, Akihiko Kitamura, Yutaka Kiyohara30, Wolfgang Koenig31, Daan Kromhout32, Lewis H. Kuller33, Debbie A Lawlor15, Tom W. Meade34, Aulikki Nissinen35, Børge G. Nordestgaard28, Altan Onat36, Demosthenes B. Panagiotakos37, Bruce M. Psaty38, Beatriz L. Rodriguez39, Annika Rosengren9, Veikko Salomaa35, Jussi Kauhanen40, Jukka T. Salonen41, Jonathan A. Shaffer42, Steven Shea42, Ian Ford3, Coen D.A. Stehouwer43, Timo E. Strandberg44, Robert W. Tipping45, Alberto Tosetto, Sylvia Wassertheil-Smoller46, Patrik Wennberg47, Rudi G. J. Westendorp48, Peter H. Whincup49, Lars Wilhelmsen9, Mark Woodward50, Gordon D.O. Lowe3, Nicholas J. Wareham2, Kay-Tee Khaw1, Naveed Sattar3, Chris J. Packard3, Vilmundur Gudnason51, Paul M. Ridker21, Mark B. Pepys11, Simon G. Thompson1, John Danesh1 
TL;DR: It is estimated that under current treatment guidelines, assessment of the CRP or fibrinogen level in people at intermediate risk for a cardiovascular event could help prevent one additional event over a period of 10 years for every 400 to 500 people screened.
Abstract: Background There is debate about the value of assessing levels of C-reactive protein (CRP) and other biomarkers of inflammation for the prediction of first cardiovascular events. Methods We analyzed data from 52 prospective studies that included 246,669 participants without a history of cardiovascular disease to investigate the value of adding CRP or fibrinogen levels to conventional risk factors for the prediction of cardiovascular risk. We calculated measures of discrimination and reclassification during follow-up and modeled the clinical implications of initiation of statin therapy after the assessment of CRP or fibrinogen. Results The addition of information on high-density lipoprotein cholesterol to a prognostic model for cardiovascular disease that included age, sex, smoking status, blood pressure, history of diabetes, and total cholesterol level increased the C-index, a measure of risk discrimination, by 0.0050. The further addition to this model of information on CRP or fibrinogen increased the C-index by 0.0039 and 0.0027, respectively (P = 20%) (P = 20% and for those with certain other risk factors, such as diabetes, irrespective of their 10-year predicted risk), additional targeted assessment of CRP or fibrinogen levels in the 13,199 remaining participants at intermediate risk could help prevent approximately 30 additional cardiovascular events over the course of 10 years. Conclusions In a study of people without known cardiovascular disease, we estimated that under current treatment guidelines, assessment of the CRP or fibrinogen level in people at intermediate risk for a cardiovascular event could help prevent one additional event over a period of 10 years for every 400 to 500 people screened. (Funded by the British Heart Foundation and others.)

Journal ArticleDOI
TL;DR: Evidence for brain maintenance at different levels is discussed: cellular, neurochemical, gray- and white-matter integrity, and systems-level activation patterns, and it is argued that it constitutes the primary determinant of successful memory aging.

Journal ArticleDOI
TL;DR: In this paper, the authors argue that there are two interrelated problems requiring attention: the institutional embeddedness of socio-technical development processes within specific territorial spaces, and an explicit multi-scalar conception of socio technical trajectories.

Journal ArticleDOI
TL;DR: In this paper, the FERMI free-electron laser operating in the high-gain harmonic generation regime was demonstrated, allowing high stability, transverse and longitudinal coherence and polarization control.
Abstract: Researchers demonstrate the FERMI free-electron laser operating in the high-gain harmonic generation regime, allowing high stability, transverse and longitudinal coherence and polarization control.

Journal ArticleDOI
TL;DR: This study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyang iitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature ofproteinase 3 ANCA -associated vasulitis.
Abstract: BACKGROUND Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener's granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis. METHODS A genomewide association study was performed in a discovery cohort of 1233 U. K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria. RESULTS We found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti-proteinase 3 ANCA was associated with HLA-DP and the genes encoding alpha(1)-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P = 6.2x10(-89), P = 5.6x10(-12), and P = 2.6x10(-7), respectively). Anti-myeloperoxidase ANCA was associated with HLA-DQ (P = 2.1x10(-8)). CONCLUSIONS This study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA-associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA-associated vasculitis and myeloperoxidase ANCA-associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.)

Journal ArticleDOI
28 Mar 2012-JAMA
TL;DR: Adjuvant imatinib administered for 12 months after surgery has improved recurrence-free survival (RFS) of patients with operable gastrointestinal stromal tumor (GIST) compared with placebo and overall survival of GIST patients with a high risk of Gist recurrence.
Abstract: Context Adjuvant imatinib administered for 12 months after surgery has improved recurrence-free survival (RFS) of patients with operable gastrointestinal stromal tumor (GIST) compared with placebo. Objective To investigate the role of imatinib administration duration as adjuvant treatment of patients who have a high estimated risk for GIST recurrence after surgery. Design, Setting, and Patients Patients with KIT-positive GIST removed at surgery were entered between February 2004 and September 2008 to this randomized, open-label phase 3 study conducted in 24 hospitals in Finland, Germany, Norway, and Sweden. The risk of GIST recurrence was estimated using the modified National Institutes of Health Consensus Criteria. Intervention Imatinib, 400 mg per day, orally for either 12 months or 36 months, started within 12 weeks of surgery. Main Outcome Measures The primary end point was RFS; the secondary end points included overall survival and treatment safety. Results Two hundred patients were allocated to each group. The median follow-up time after randomization was 54 months in December 2010. Diagnosis of GIST was confirmed in 382 of 397 patients (96%) in the intention-to-treat population at a central pathology review. KIT or PDGFRA mutation was detected in 333 of 366 tumors (91%) available for testing. Patients assigned for 36 months of imatinib had longer RFS compared with those assigned for 12 months (hazard ratio [HR], 0.46; 95% CI, 0.32-0.65; P Conclusion Compared with 12 months of adjuvant imatinib, 36 months of imatinib improved RFS and overall survival of GIST patients with a high risk of GIST recurrence. Trial Registration clinicaltrials.gov Identifier: NCT00116935

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TL;DR: Six previously unknown loci associated with fasting insulin at P < 5 × 10−8 in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals are presented.
Abstract: Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and β-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 × 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.

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TL;DR: These EAU guidelines are a short comprehensive overview of the updated guidelines of male infertility as recently published by the EAU and are also available in the National Guideline Clearinghouse ( www.guideline.gov/).

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29 Mar 2012-Nature
TL;DR: The genomic landscape of neuroblastoma reveals two novel molecular defects, chromothripsis and neuritogenesis gene alterations, which frequently occur in high-risk tumours.
Abstract: Neuroblastoma is a childhood tumour of the peripheral sympathetic nervous system. The pathogenesis has for a long time been quite enigmatic, as only very few gene defects were identified in this often lethal tumour. Frequently detected gene alterations are limited to MYCN amplification (20%) and ALK activations (7%). Here we present a whole-genome sequence analysis of 87 neuroblastoma of all stages. Few recurrent amino-acid-changing mutations were found. In contrast, analysis of structural defects identified a local shredding of chromosomes, known as chromothripsis, in 18% of high-stage neuroblastoma. These tumours are associated with a poor outcome. Structural alterations recurrently affected ODZ3, PTPRD and CSMD1, which are involved in neuronal growth cone stabilization. In addition, ATRX, TIAM1 and a series of regulators of the Rac/Rho pathway were mutated, further implicating defects in neuritogenesis in neuroblastoma. Most tumours with defects in these genes were aggressive high-stage neuroblastomas, but did not carry MYCN amplifications. The genomic landscape of neuroblastoma therefore reveals two novel molecular defects, chromothripsis and neuritogenesis gene alterations, which frequently occur in high-risk tumours.

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TL;DR: In this article, the authors measured the accretion rate onto seed masses ranging from a large planetesimal to a fully grown 10-Earth-mass core and test different particle sizes, concluding that pebble accretion can resolve the long-standing core accretion timescale conflict.
Abstract: The observed lifetimes of gaseous protoplanetary discs place strong constraints on gas and ice giant formation in the core accretion scenario. The approximately 10-Earth-mass solid core responsible for the attraction of the gaseous envelope has to form before gas dissipation in the protoplanetary disc is completed within 1–10 million years. Building up the core by collisions between km-sized planetesimals fails to meet this timescale constraint, especially at wide stellar separations. Nonetheless, gas-giant planets are detected by direct imaging at wide orbital distances. In this paper, we numerically study the growth of cores by the accretion of cm-sized pebbles loosely coupled to the gas. We measure the accretion rate onto seed masses ranging from a large planetesimal to a fully grown 10-Earth-mass core and test different particle sizes. The numerical results are in good agreement with our analytic expressions, indicating the existence of two accretion regimes, one set by the azimuthal and radial particle drift for the lower seed masses and the other, for higher masses, by the velocity at the edge of the Hill sphere. In the former, the optimally accreted particle size increases with core mass, while in the latter the optimal size is centimeters, independent of core mass. We discuss the implications for rapid core growth of gas-giant and ice-giant cores. We conclude that pebble accretion can resolve the long-standing core accretion timescale conflict. This requires a near-unity dust-to-gas ratio in the midplane, particle growth to mm and cm and the formation of massive planetesimals or low radial pressure support. The core growth timescale is shortened by a factor 30–1000 at 5 AU and by a factor 100–10 000 at 50 AU, compared to the gravitationally focused accretion of, respectively, low-scale-height planetesimal fragments or standard km-sized planetesimals.

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Nobuyuki Hamajima, Kaoru Hirose, K. Tajima, T E Rohan1  +289 moreInstitutions (81)
TL;DR: The effects of menarche and menopause on breast cancer risk might not be acting merely by lengthening women's total number of reproductive years, and endogenous ovarian hormones are more relevant for oestrogen receptor-positive disease than for ostrogens receptor-negative disease and for lobular than for ductal tumours.
Abstract: BACKGROUND:Menarche and menopause mark the onset and cessation, respectively, of ovarian activity associated with reproduction, and affect breast cancer risk. Our aim was to assess the strengths of their effects and determine whether they depend on characteristics of the tumours or the affected women.METHODS:Individual data from 117 epidemiological studies, including 118 964 women with invasive breast cancer and 306 091 without the disease, none of whom had used menopausal hormone therapy, were included in the analyses. We calculated adjusted relative risks (RRs) associated with menarche and menopause for breast cancer overall, and by tumour histology and by oestrogen receptor expression.FINDINGS:Breast cancer risk increased by a factor of 1·050 (95% CI 1·044-1·057; p<0·0001) for every year younger at menarche, and independently by a smaller amount (1·029, 1·025-1·032; p<0·0001), for every year older at menopause. Premenopausal women had a greater risk of breast cancer than postmenopausal women of an identical age (RR at age 45-54 years 1·43, 1·33-1·52, p<0·001). All three of these associations were attenuated by increasing adiposity among postmenopausal women, but did not vary materially by women's year of birth, ethnic origin, childbearing history, smoking, alcohol consumption, or hormonal contraceptive use. All three associations were stronger for lobular than for ductal tumours (p<0·006 for each comparison). The effect of menopause in women of an identical age and trends by age at menopause were stronger for oestrogen receptor-positive disease than for oestrogen receptor-negative disease (p<0·01 for both comparisons).INTERPRETATION:The effects of menarche and menopause on breast cancer risk might not be acting merely by lengthening women's total number of reproductive years. Endogenous ovarian hormones are more relevant for oestrogen receptor-positive disease than for oestrogen receptor-negative disease and for lobular than for ductal tumours.

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Robert A. Scott, Vasiliki Lagou1, Ryan P. Welch2, Eleanor Wheeler3  +213 moreInstitutions (67)
TL;DR: Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations and further functional analysis of these newly discovered loci will further improve the understanding of glycemic control.
Abstract: Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.

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24 May 2012-Nature
TL;DR: In this paper, the authors compared phenology (the timing of recurring life history events) in observational studies and warming experiments spanning four continents and 1,634 plant species using a common measure of temperature sensitivity (change in days per degree Celsius).
Abstract: Warming experiments are increasingly relied on to estimate plant responses to global climate change. For experiments to provide meaningful predictions of future responses, they should reflect the empirical record of responses to temperature variability and recent warming, including advances in the timing of flowering and leafing. We compared phenology (the timing of recurring life history events) in observational studies and warming experiments spanning four continents and 1,634 plant species using a common measure of temperature sensitivity (change in days per degree Celsius). We show that warming experiments underpredict advances in the timing of flowering and leafing by 8.5-fold and 4.0-fold, respectively, compared with long-term observations. For species that were common to both study types, the experimental results did not match the observational data in sign or magnitude. The observational data also showed that species that flower earliest in the spring have the highest temperature sensitivities, but this trend was not reflected in the experimental data. These significant mismatches seem to be unrelated to the study length or to the degree of manipulated warming in experiments. The discrepancy between experiments and observations, however, could arise from complex interactions among multiple drivers in the observational data, or it could arise from remediable artefacts in the experiments that result in lower irradiance and drier soils, thus dampening the phenological responses to manipulated warming. Our results introduce uncertainty into ecosystem models that are informed solely by experiments and suggest that responses to climate change that are predicted using such models should be re-evaluated.

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21 Jun 2012-Nature
TL;DR: Spectroscopic metallicities of the host stars of 226 small exoplanet candidates discovered by NASA's Kepler mission are reported, finding that planets with radii less than four Earth radii form around host stars with a wide range of metallicities (but on average a metallicity close to that of the Sun), whereas large planets preferentially form around stars with higher metallicities.
Abstract: The abundance of heavy elements (metallicity) in the photospheres of stars similar to the Sun provides a 'fossil' record of the chemical composition of the initial protoplanetary disk. Metal-rich stars are much more likely to harbour gas giant planets(1-4), supporting the model that planets form by accumulation of dust and ice particles(5). Recent ground-based surveys suggest that this correlation is weakened for Neptunian-sized planets(4,6-9). However, how the relationship between size and metallicity extends into the regime of terrestrial-sized exoplanets is unknown. Here we report spectroscopic metallicities of the host stars of 226 small exoplanet candidates discovered by NASA's Kepler mission(10), including objects that are comparable in size to the terrestrial planets in the Solar System. We find that planets with radii less than four Earth radii form around host stars with a wide range of metallicities (but on average a metallicity close to that of the Sun), whereas large planets preferentially form around stars with higher metallicities. This observation suggests that terrestrial planets may be widespread in the disk of the Galaxy, with no special requirement of enhanced metallicity for their formation.

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TL;DR: This article proposed an Early-Middle Holocene Boundary at 8200 a BP and a Middle-Late Holocene boundary at 4200 aBP, each of which is linked to a Global Stratotype Section and Point (GSSP) to ensure consistency in stratigraphic terminology.
Abstract: This discussion paper, by a Working Group of INTIMATE (Integration of ice-core, marine and terrestrial records) and the Subcommision on Quaternary Stratigraphy (SQS) of the International Commission on Stratigraphy (ICS), considers the prospects for a formal subdivision of the Holocene Series/Epoch. Although previous attempts to subdivide the Holocene have proved inconclusive, recent developments in Quaternary stratigraphy, notably the definition of the Pleistocene-Holocene boundary and the emergence of formal subdivisions of the Pleistocene Series/ Epoch, mean that it may be timely to revisit this matter. The Quaternary literature reveals a widespread but variable informal usage of a tripartite division of the Holocene ('early', 'middle' or 'mid', and 'late'), and we argue that this de facto subdivision should now be formalized to ensure consistency in stratigraphic terminology. We propose an Early-Middle Holocene Boundary at 8200 a BP and a Middle-Late Holocene Boundary at 4200 a BP, each of which is linked to a Global Stratotype Section and Point (GSSP). Should the proposal find a broad measure of support from the Quaternary community, a submission will be made to the International Union of Geological Sciences (IUGS), via the SQS and the ICS, for formal ratification of this subdivision of the Holocene Series/Epoch. Copyright# 2012 John Wiley & Sons, Ltd.

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TL;DR: Evidence supports the notion to include immunological biomarkers, implemented as a tool for the prediction of prognosis and response to therapy, into traditional classification of cancer, designated TNM-I (TNM-Immune), and introduction of this parameter as a biomarker to classify cancers will facilitate clinical decision-making.
Abstract: Prediction of clinical outcome in cancer is usually achieved by histopathological evaluation of tissue samples obtained during surgical resection of the primary tumor. Traditional tumor staging (AJCC/UICC-TNM classification) summarizes data on tumor burden (T), presence of cancer cells in draining and regional lymph nodes (N) and evidence for metastases (M). However, it is now recognized that clinical outcome can significantly vary among patients within the same stage. The current classification provides limited prognostic information, and does not predict response to therapy. Recent literature has alluded to the importance of the host immune system in controlling tumor progression. Thus, evidence supports the notion to include immunological biomarkers, implemented as a tool for the prediction of prognosis and response to therapy. Accumulating data, collected from large cohorts of human cancers, has demonstrated the impact of immune-classification, which has a prognostic value that may add to the significance of the AJCC/UICC TNM-classification. It is therefore imperative to begin to incorporate the 'Immunoscore' into traditional classification, thus providing an essential prognostic and potentially predictive tool. Introduction of this parameter as a biomarker to classify cancers, as part of routine diagnostic and prognostic assessment of tumors, will facilitate clinical decision-making including rational stratification of patient treatment. Equally, the inherent complexity of quantitative immunohistochemistry, in conjunction with protocol variation across laboratories, analysis of different immune cell types, inconsistent region selection criteria, and variable ways to quantify immune infiltration, all underline the urgent requirement to reach assay harmonization. In an effort to promote the Immunoscore in routine clinical settings, an international task force was initiated. This review represents a follow-up of the announcement of this initiative, and of the J Transl Med. editorial from January 2012. Immunophenotyping of tumors may provide crucial novel prognostic information. The results of this international validation may result in the implementation of the Immunoscore as a new component for the classification of cancer, designated TNM-I (TNM-Immune).

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TL;DR: Temperature-dependent angle-resolved photoelectron spectroscopy demonstrates that the narrow-gap semiconductor Pb(1-x)Sn(x)Se is a TCI, a new class of topological insulators in which crystalline symmetry replaces the role of time-reversal symmetry in ensuring topological protection.
Abstract: Topological insulators are a class of quantum materials in which time-reversal symmetry, relativistic effects and an inverted band structure result in the occurrence of electronic metallic states on the surfaces of insulating bulk crystals. These helical states exhibit a Dirac-like energy dispersion across the bulk bandgap, and they are topologically protected. Recent theoretical results have suggested the existence of topological crystalline insulators (TCIs), a class of topological insulators in which crystalline symmetry replaces the role of time-reversal symmetry in ensuring topological protection. In this study we show that the narrow-gap semiconductor Pb(1-x)Sn(x)Se is a TCI for x = 0.23. Temperature-dependent angle-resolved photoelectron spectroscopy demonstrates that the material undergoes a temperature-driven topological phase transition from a trivial insulator to a TCI. These experimental findings add a new class to the family of topological insulators, and we anticipate that they will lead to a considerable body of further research as well as detailed studies of topological phase transitions.

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TL;DR: The molecular subtypes cut across pathologic classification, and class-defining gene signatures show coordinated expression irrespective of pathologic stage and grade, suggesting the molecular phenotypes as intrinsic properties of the tumors.
Abstract: Purpose Even though urothelial cancer is the fourth most common tumor type among males, progress in treatment has been scarce. A problem in day-to-day clinical practice is that precise assessment of individual tumors is still fairly uncertain; consequently efforts have been undertaken to complement tumor evaluation with molecular biomarkers. An extension of this approach would be to base tumor classification primarily on molecular features. Here, we present a molecular taxonomy for urothelial carcinoma based on integrated genomics. Experimental design We use gene expression profiles from 308 tumor cases to define five major urothelial carcinoma subtypes: urobasal A, genomically unstable, urobasal B, squamous cell carcinoma like, and an infiltrated class of tumors. Tumor subtypes were validated in three independent publically available data sets. The expression of 11 key genes was validated at the protein level by immunohistochemistry. Results The subtypes show distinct clinical outcomes and differ with respect to expression of cell-cycle genes, receptor tyrosine kinases particularly FGFR3, ERBB2, and EGFR, cytokeratins, and cell adhesion genes, as well as with respect to FGFR3, PIK3CA, and TP53 mutation frequency. The molecular subtypes cut across pathologic classification, and class-defining gene signatures show coordinated expression irrespective of pathologic stage and grade, suggesting the molecular phenotypes as intrinsic properties of the tumors. Available data indicate that susceptibility to specific drugs is more likely to be associated with the molecular stratification than with pathologic classification. Conclusions We anticipate that the molecular taxonomy will be useful in future clinical investigations.