Showing papers by "University of Amsterdam published in 2012"
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
Daniel J. Klionsky1, Fábio Camargo Abdalla2, Hagai Abeliovich3, Robert T. Abraham4 +1284 more•Institutions (463)
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
Wellcome Trust Sanger Institute1, Broad Institute2, University of Groningen3, University of Pittsburgh4, Cedars-Sinai Medical Center5, Yale University6, University of Cambridge7, University of Chicago8, Harvard University9, Katholieke Universiteit Leuven10, University of Liège11, King's College London12, Université de Montréal13, New Jersey Institute of Technology14, Cleveland Clinic15, Peninsula College of Medicine and Dentistry16, Université libre de Bruxelles17, Aarhus University18, University of Adelaide19, University of Kiel20, Flinders University21, McGill University22, Ludwig Maximilian University of Munich23, Charité24, Icahn School of Medicine at Mount Sinai25, University of Bonn26, Karolinska Institutet27, Torbay Hospital28, University of Auckland29, Christchurch Hospital30, Imperial College London31, Queen's University32, University of Oslo33, Lithuanian University of Health Sciences34, Emory University35, Casa Sollievo della Sofferenza36, Ghent University37, University of Western Australia38, University of Edinburgh39, Queensland Health40, Newcastle University41, University of Dundee42, University of Manchester43, University of Amsterdam44, University of Maribor45, Royal Hospital for Sick Children46, Guy's and St Thomas' NHS Foundation Trust47, QIMR Berghofer Medical Research Institute48, Norfolk and Norwich University Hospital49, Leiden University50, Technische Universität München51, University of Toronto52, University of Pennsylvania53, Johns Hopkins University54, University of Queensland55
TL;DR: A meta-analysis of Crohn’s disease and ulcerative colitis genome-wide association scans is undertaken, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls.
Abstract: Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
4,094 citations
TL;DR: Six weeks after infusion of microbiota from lean donors, insulin sensitivity of recipients increased along with levels of butyrate-producing intestinal microbiota, and intestinal microbiota might be developed as therapeutic agents to increase insulin sensitivity in humans.
2,304 citations
Harvard University1, University of Cambridge2, Mayo Clinic3, Okayama University4, Technische Universität München5, Dalhousie University6, University of Amsterdam7, Southampton General Hospital8, Tokyo Metropolitan Komagome Hospital9, Shinshu University10, Kanazawa University11, Kanazawa Medical University12, Kansai Medical University13, Seoul National University14, University College London15, Sapporo Medical University16, University of Verona17
TL;DR: This statement proposes a terminology scheme for the diagnosis of IgG4-related disease that is based primarily on the morphological appearance on biopsy, and advocates the use of strict criteria for accepting newly proposed entities or sites as components of the IgG 4- related disease spectrum.
2,041 citations
TL;DR: A fixed-dose regimen of rivaroxaban alone was noninferior to standard therapy for the initial and long-term treatment of pulmonary embolism and had a potentially improved benefit-risk profile.
Abstract: A b s t r ac t Background A fixed-dose regimen of rivaroxaban, an oral factor Xa inhibitor, has been shown to be as effective as standard anticoagulant therapy for the treatment of deep-vein thrombosis, without the need for laboratory monitoring. This approach may also simplify the treatment of pulmonary embolism. Methods In a randomized, open-label, event-driven, noninferiority trial involving 4832 patients who had acute symptomatic pulmonary embolism with or without deep-vein thrombosis, we compared rivaroxaban (15 mg twice daily for 3 weeks, followed by 20 mg once daily) with standard therapy with enoxaparin followed by an adjusted-dose vitamin K antagonist for 3, 6, or 12 months. The primary efficacy outcome was symptomatic recurrent venous thromboembolism. The principal safety outcome was major or clinically relevant nonmajor bleeding. Results Rivaroxaban was noninferior to standard therapy (noninferiority margin, 2.0; P = 0.003) for the primary efficacy outcome, with 50 events in the rivaroxaban group (2.1%) versus 44 events in the standard-therapy group (1.8%) (hazard ratio, 1.12; 95% confidence interval [CI], 0.75 to 1.68). The principal safety outcome occurred in 10.3% of patients in the rivaroxaban group and 11.4% of those in the standardtherapy group (hazard ratio, 0.90; 95% CI, 0.76 to 1.07; P = 0.23). Major bleeding was observed in 26 patients (1.1%) in the rivaroxaban group and 52 patients (2.2%) in the standard-therapy group (hazard ratio, 0.49; 95% CI, 0.31 to 0.79; P = 0.003). Rates of other adverse events were similar in the two groups. Conclusions A fixed-dose regimen of rivaroxaban alone was noninferior to standard therapy for the initial and long-term treatment of pulmonary embolism and had a potentially improved benefit–risk profile. (Funded by Bayer HealthCare and Janssen Phar maceuticals; EINSTEIN-PE ClinicalTrials.gov number, NCT00439777.)
1,932 citations
Andrew P. Morris1, Benjamin F. Voight2, Benjamin F. Voight3, Tanya M. Teslovich4 +229 more•Institutions (53)
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
University of Louisville1, Rush University Medical Center2, University of North Carolina at Chapel Hill3, University of Amsterdam4, University of Pennsylvania5, Mayo Clinic6, University of Göttingen7, Columbia University Medical Center8, University of Cambridge9, Stavanger University Hospital10, Autonomous University of Barcelona11, Ikerbasque12, Newcastle University13, Istanbul University14
TL;DR: These diagnostic criteria will support future research efforts to identify at the earliest stage those PD patients at increased risk of progressive cognitive decline and dementia who may benefit from clinical interventions at a predementia stage.
Abstract: Mild cognitive impairment is common in nondemented Parkinson's disease (PD) patients and may be a harbinger of dementia. In view of its importance, the Movement Disorder Society commissioned a task force to delineate diagnostic criteria for mild cognitive impairment in PD. The proposed diagnostic criteria are based on a literature review and expert consensus. This article provides guidelines to characterize the clinical syndrome and methods for its diagnosis. The criteria will require validation, and possibly refinement, as additional research improves our understanding of the epidemiology, presentation, neurobiology, assessment, and long-term course of this clinical syndrome. These diagnostic criteria will support future research efforts to identify at the earliest stage those PD patients at increased risk of progressive cognitive decline and dementia who may benefit from clinical interventions at a predementia stage.
1,867 citations
TL;DR: More than 70% of all massive stars will exchange mass with a companion, leading to a binary merger in one-third of the cases, greatly exceed previous estimates and imply that binary interaction dominates the evolution of massive stars, with implications for populations ofmassive stars and their supernovae.
Abstract: The presence of a nearby companion alters the evolution of massive stars in binary systems, leading to phenomena such as stellar mergers, x-ray binaries, and gamma-ray bursts. Unambiguous constraints on the fraction of massive stars affected by binary interaction were lacking. We simultaneously measured all relevant binary characteristics in a sample of Galactic massive O stars and quantified the frequency and nature of binary interactions. More than 70% of all massive stars will exchange mass with a companion, leading to a binary merger in one-third of the cases. These numbers greatly exceed previous estimates and imply that binary interaction dominates the evolution of massive stars, with implications for populations of massive stars and their supernovae.
1,779 citations
Columbia University1, University of Amsterdam2, University of California, Los Angeles3, University of Coimbra4, University of Zurich5, University of Mainz6, University of Münster7, University of Nantes8, Weizmann Institute of Science9, Shanghai Jiao Tong University10, University of Bologna11, Max Planck Society12, Purdue University13, Rice University14
TL;DR: A search for particle dark matter with the XENON100 experiment, operated at the Laboratori Nazionali del Gran Sasso for 13 months during 2011 and 2012, has yielded no evidence for dark matter interactions.
Abstract: We report on a search for particle dark matter with the XENON100 experiment, operated at the Laboratori Nazionali del Gran Sasso (LNGS) for 13 months during 2011 and 2012. XENON100 features an ultra-low electromagnetic background of (5.3\pm0.6)\times10^-3 events (kg day keVee)^-1 in the energy region of interest. A blind analysis of 224.6 live days \times 34 kg exposure has yielded no evidence for dark matter interactions. The two candidate events observed in the pre-defined nuclear recoil energy range of 6.6-30.5 keVnr are consistent with the background expectation of (1.0 \pm 0.2) events. A Profile Likelihood analysis using a 6.6-43.3 keVnr energy range sets the most stringent limit on the spin-independent elastic WIMP-nucleon scattering cross section for WIMP masses above 8 GeV/c^2, with a minimum of 2 \times 10^-45 cm^2 at 55 GeV/c^2 and 90% confidence level.
1,624 citations
University of Amsterdam1, Ghent University2, University of Chicago3, University of Pennsylvania4, Auckland City Hospital5, University of Antwerp6, University of New South Wales7, Katholieke Universiteit Leuven8, St Thomas' Hospital9, University of Nottingham10, University of Zagreb11, Northwestern University12, Medical University of Łódź13, University of Aberdeen14, Innsbruck Medical University15, Medical University of South Carolina16, University of Southampton17, Children's Hospital of Philadelphia18, University of São Paulo19, National University of Singapore20, Flinders University21, University of Adelaide22
TL;DR: The European Position Paper on Rhinosinusitis and Nasal Polyps 2012 as discussed by the authors is the update of similar evidence-based position papers published in 2005 and 2007, it contains chapters on definitions and classification, we now also proposed definitions for difficult to treat rhinositis, control of disease, and better definitions for rhinosinitis in children.
Abstract: The European Position Paper on Rhinosinusitis and Nasal Polyps 2012 is the update of similar evidence based position papers published in 2005 and 2007. The document contains chapters on definitions and classification, we now also proposed definitions for difficult to treat rhinosinusitis, control of disease and better definitions for rhinosinusitis in children. More emphasis is placed on the diagnosis and treatment of acute rhinosinusitis. Throughout the document the terms chronic rhinosinusitis without nasal polyps (CRSsNP) and chronic rhinosinusitis with nasal polyps (CRSwNP) are used to further point out differences in pathophysiology and treatment of these two entities. There are extensive chapters on epidemiology and predisposing factors, inflammatory mechanisms, (differential) diagnosis of facial pain, genetics, cystic fibrosis, aspirin exacerbated respiratory disease, immunodeficiencies, allergic fungal rhinosinusitis and the relationship between upper and lower airways. The chapters on paediatric acute and chronic rhinosinusitis are totally rewritten. Last but not least all available evidence for management of acute rhinosinusitis and chronic rhinosinusitis with or without nasal polyps in adults and children is analyzed and presented and management schemes based on the evidence are proposed. This executive summary for otorhinolaryngologists focuses on the most important changes and issues for otorhinolaryngologists. The full document can be downloaded for free on the website of this journal: http://www.rhinologyjournal.com.
Wellcome Trust Sanger Institute1, Wellcome Trust2, Katholieke Universiteit Leuven3, University of East Anglia4, Guy's and St Thomas' NHS Foundation Trust5, Academia Sinica6, Singapore General Hospital7, Netherlands Cancer Institute8, University of Queensland9, University of British Columbia10, Erasmus University Rotterdam11, Harvard University12, University of Cambridge13, Claude Bernard University Lyon 114, Curie Institute15, Royal Brisbane and Women's Hospital16, University of Amsterdam17, Université libre de Bruxelles18, The Breast Cancer Research Foundation19, Cambridge University Hospitals NHS Foundation Trust20, Oslo University Hospital21
TL;DR: Strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade are found, and multiple mutational signatures are observed, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides.
Abstract: All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.
German Cancer Research Center1, Heidelberg University2, McGill University3, Montreal Children's Hospital4, University of Düsseldorf5, University of Tübingen6, Virginia Commonwealth University7, Augsburg College8, Boston Children's Hospital9, University of Colorado Denver10, Cincinnati Children's Hospital Medical Center11, University of Würzburg12, Martin Luther University of Halle-Wittenberg13, Hannover Medical School14, Medical University of Łódź15, Memorial Hospital of South Bend16, Semmelweis University17, University of Debrecen18, University of Toronto19, University of Amsterdam20, Henry Ford Health System21, University of Texas MD Anderson Cancer Center22, University of Cambridge23
TL;DR: It is demonstrated that each H3F3A mutation defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and that they are mutually exclusive with IDH1 mutations, which characterize a third mutation-defined subgroup.
TL;DR: In this paper, the metal-organic framework Fe2(dobdc) was demonstrated to exhibit excellent performance characteristics for separation of ethylene/ethane and propylene/propane mixtures at 318 kelvin.
Abstract: The energy costs associated with large-scale industrial separation of light hydrocarbons by cryogenic distillation could potentially be lowered through development of selective solid adsorbents that operate at higher temperatures. Here, the metal-organic framework Fe2(dobdc) (dobdc4- : 2,5-dioxido-1,4-benzenedicarboxylate) is demonstrated to exhibit excellent performance characteristics for separation of ethylene/ethane and propylene/propane mixtures at 318 kelvin. Breakthrough data obtained for these mixtures provide experimental validation of simulations, which in turn predict high selectivities and capacities of this material for the fractionation of methane/ethane/ethylene/acetylene mixtures, removal of acetylene impurities from ethylene, and membrane-based olefin/paraffin separations. Neutron powder diffraction data confirm a side-on coordination of acetylene, ethylene, and propylene at the iron(II) centers, while also providing solid-state structural characterization of the much weaker interactions of ethane and propane with the metal.
TL;DR: Evidence is accumulating that vesicles are cargo containers used by eukaryotic cells to exchange biomolecules as transmembrane receptors and genetic information, and they have a myriad of potential clinical applications, ranging from biomarkers to anticancer therapy.
Abstract: Both eukaryotic and prokaryotic cells release small, phospholipid-enclosed vesicles into their environment. Why do cells release vesicles? Initial studies showed that eukaryotic vesicles are used to remove obsolete cellular molecules. Although this release of vesicles is beneficial to the cell, the vesicles can also be a danger to their environment, for instance in blood, where vesicles can provide a surface supporting coagulation. Evidence is accumulating that vesicles are cargo containers used by eukaryotic cells to exchange biomolecules as transmembrane receptors and genetic information. Because also bacteria communicate to each other via extracellular vesicles, the intercellular communication via extracellular cargo carriers seems to be conserved throughout evolution, and therefore vesicles are likely to be a highly efficient, robust, and economic manner of exchanging information between cells. Furthermore, vesicles protect cells from accumulation of waste or drugs, they contribute to physiology and pathology, and they have a myriad of potential clinical applications, ranging from biomarkers to anticancer therapy. Because vesicles may pass the blood-brain barrier, they can perhaps even be considered naturally occurring liposomes. Unfortunately, pathways of vesicle release and vesicles themselves are also being used by tumors and infectious diseases to facilitate spreading, and to escape from immune surveillance. In this review, the different types, nomenclature, functions, and clinical relevance of vesicles will be discussed.
TL;DR: It is proposed that frequency-specific neuronal correlations in large-scale cortical networks may be 'fingerprints' of canonical neuronal computations underlying cognitive processes.
Abstract: Cognition results from interactions among functionally specialized but widely distributed brain regions; however, neuroscience has so far largely focused on characterizing the function of individual brain regions and neurons therein. Here we discuss recent studies that have instead investigated the interactions between brain regions during cognitive processes by assessing correlations between neuronal oscillations in different regions of the primate cerebral cortex. These studies have opened a new window onto the large-scale circuit mechanisms underlying sensorimotor decision-making and top-down attention. We propose that frequency-specific neuronal correlations in large-scale cortical networks may be 'fingerprints' of canonical neuronal computations underlying cognitive processes.
La Trobe University1, Harvard University2, German Cancer Research Center3, Yale University4, Morehouse School of Medicine5, Autonomous University of Barcelona6, University of Massachusetts Medical School7, Semmelweis University8, Cardiff University9, Ikerbasque10, Karolinska Institutet11, Pohang University of Science and Technology12, Allahabad University13, Ghent University14, University of Melbourne15, London Metropolitan University16, Erasmus University Rotterdam17, University of Mainz18, National University of Singapore19, University of Oslo20, University of Gothenburg21, University of Valencia22, Umeå University23, University of Freiburg24, University of Amsterdam25, Utrecht University26, Johns Hopkins University27, Mayo Clinic28, Ohio State University29, University of Cambridge30, University of Zurich31, Curie Institute32, Michigan State University33, Autonomous University of Madrid34, University of Helsinki35, Aalborg University36, University of Louisville37, Carlos III Health Institute38, Centre national de la recherche scientifique39, Heidelberg University40
TL;DR: Vesiclepedia is a community-annotated compendium of molecular data on extracellular vesicles that aims to provide a single authoritative source for information on vesicle structure and function.
Abstract: Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.
Karol Estrada1, Unnur Styrkarsdottir, Evangelos Evangelou2, Yi-Hsiang Hsu3 +187 more•Institutions (69)
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.
TL;DR: Although the very public problems experienced by psychology over this 2-year period are embarrassing to those of us working in the field, some have found comfort in the fact that, over the same period, similar concerns have been arising across the scientific landscape.
Abstract: Is there currently a crisis of confidence in psychological science reflecting an unprecedented level of doubt among practitioners about the reliability of research findings in the field? It would certainly appear that there is. These doubts emerged and grew as a series of unhappy events unfolded in 2011: the Diederik Stapel fraud case (see Stroebe, Postmes, & Spears, 2012, this issue), the publication in a major social psychology journal of an article purporting to show evidence of extrasensory perception (Bem, 2011) followed by widespread public mockery (see Galak, LeBoeuf, Nelson, & Simmons, in press; Wagenmakers, Wetzels, Borsboom, & van der Maas, 2011), reports by Wicherts and colleagues that psychologists are often unwilling or unable to share their published data for reanalysis (Wicherts, Bakker, & Molenaar, 2011; see also Wicherts, Borsboom, Kats, & Molenaar, 2006), and the publication of an important article in Psychological Science showing how easily researchers can, in the absence of any real effects, nonetheless obtain statistically significant differences through various questionable research practices (QRPs) such as exploring multiple dependent variables or covariates and only reporting these when they yield significant results (Simmons, Nelson, & Simonsohn, 2011). For those psychologists who expected that the embarrassments of 2011 would soon recede into memory, 2012 offered instead a quick plunge from bad to worse, with new indications of outright fraud in the field of social cognition (Simonsohn, 2012), an article in Psychological Science showing that many psychologists admit to engaging in at least some of the QRPs examined by Simmons and colleagues (John, Loewenstein, & Prelec, 2012), troubling new meta-analytic evidence suggesting that the QRPs described by Simmons and colleagues may even be leaving telltale signs visible in the distribution of p values in the psychological literature (Masicampo & Lalande, in press; Simonsohn, 2012), and an acrimonious dust-up in science magazines and blogs centered around the problems some investigators were having in replicating well-known results from the field of social cognition (Bower, 2012; Yong, 2012). Although the very public problems experienced by psychology over this 2-year period are embarrassing to those of us working in the field, some have found comfort in the fact that, over the same period, similar concerns have been arising across the scientific landscape (triggered by revelations that will be described shortly). Some of the suspected causes of unreplicability, such as publication bias (the tendency to publish only positive findings) have been discussed for years; in fact, the phrase file-drawer problem was first coined by a distinguished psychologist several decades ago (Rosenthal, 1979). However, many have speculated that these problems have been exacerbated in recent years as academia reaps the harvest of a hypercompetitive academic climate and an incentive scheme that provides rich rewards for overselling one’s work and few rewards at all for caution and circumspection (see Giner-Sorolla, 2012, this issue). Equally disturbing, investigators seem to be replicating each others’ work even less often than they did in the past, again presumably reflecting an incentive scheme gone askew (a point discussed in several articles in this issue, e.g., Makel, Plucker, & Hegarty, 2012). The frequency with which errors appear in the psychological literature is not presently known, but a number of facts suggest it might be disturbingly high. Ioannidis (2005) has shown through simple mathematical modeling that any scientific field that ignores replication can easily come to the miserable state wherein (as the title of his most famous article puts it) “most published research findings are false” (see also Ioannidis, 2012, this issue, and Pashler & Harris, 2012, this issue). Meanwhile, reports emerging from cancer research have made such grim scenarios seem more plausible: In 2012, several large pharmaceutical companies revealed that their efforts to replicate exciting preclinical findings from published academic studies in cancer biology were only rarely verifying the original results (Begley & Ellis, 2012; see also Osherovich, 2011; Prinz, Schlange, & Asadullah, 2011).
TL;DR: The nature of the stability of miRNAs that circulate in the bloodstream are discussed and the available evidence regarding the possible function of these circulating mi RNAs in distant cell-to-cell communication is discussed.
Abstract: In the past few years, the crucial role of different micro-RNAs (miRNAs) in the cardiovascular system has been widely recognized. Recently, it was discovered that extracellular miRNAs circulate in the bloodstream and that such circulating miRNAs are remarkably stable. This has raised the possibility that miRNAs may be probed in the circulation and can serve as novel diagnostic markers. Although the precise cellular release mechanisms of miRNAs remain largely unknown, the first studies revealed that these circulating miRNAs may be delivered to recipient cells, where they can regulate translation of target genes. In this review, we will discuss the nature of the stability of miRNAs that circulate in the bloodstream and discuss the available evidence regarding the possible function of these circulating miRNAs in distant cell-to-cell communication. Furthermore, we summarize and discuss the usefulness of circulating miRNAs as biomarkers for a wide range of cardiovascular diseases such as myocardial infarction, heart failure, atherosclerosis, hypertension, and type 2 diabetes mellitus.
TL;DR: This article conducted a meta-analysis of 116 empirical studies of intragroup conflict (n = 8,880 groups) and its relationship with group outcomes, finding that task conflict and group performance were more positively related among studies where the association between task and relationship conflict was relatively weak, in studies conducted among top management teams rather than non-top management teams.
Abstract: Since the meta-analysis by De Dreu and Weingart (2003b) on the effects of intragroup conflict on group outcomes, more than 80 new empirical studies of conflict have been conducted, often investigating more complex, moderated relationships between conflict and group outcomes, as well as new types of intragroup conflict, such as process conflict. To explore the trends in this new body of literature, we conducted a meta-analysis of 116 empirical studies of intragroup conflict (n = 8,880 groups) and its relationship with group outcomes. To address the heterogeneity across the studies included in the meta-analysis, we also investigated a number of moderating variables. Stable negative relationships were found between relationship and process conflict and group outcomes. In contrast to the results of De Dreu and Weingart, we did not find a strong and negative association between task conflict and group performance. Analyses of main effects as well as moderator analyses revealed a more complex picture. Task conflict and group performance were more positively related among studies where the association between task and relationship conflict was relatively weak, in studies conducted among top management teams rather than non-top management teams, and in studies where performance was measured in terms of financial performance or decision quality rather than overall performance.
TL;DR: It is shown that the systemic response to ischaemic injury aggravates chronic atherosclerosis and provides a novel therapeutic opportunity to mitigate disease progression.
Abstract: During progression of atherosclerosis, myeloid cells destabilize lipid-rich plaques in the arterial wall and cause their rupture, thus triggering myocardial infarction and stroke. Survivors of acute coronary syndromes have a high risk of recurrent events for unknown reasons. Here we show that the systemic response to ischaemic injury aggravates chronic atherosclerosis. After myocardial infarction or stroke, Apoe-/- mice developed larger atherosclerotic lesions with a more advanced morphology. This disease acceleration persisted over many weeks and was associated with markedly increased monocyte recruitment. Seeking the source of surplus monocytes in plaques, we found that myocardial infarction liberated haematopoietic stem and progenitor cells from bone marrow niches via sympathetic nervous system signalling. The progenitors then seeded the spleen, yielding a sustained boost in monocyte production. These observations provide new mechanistic insight into atherogenesis and provide a novel therapeutic opportunity to mitigate disease progression.
German Cancer Research Center1, University Hospital Heidelberg2, University of Toronto3, Stanford University4, University of Amsterdam5, VU University Amsterdam6, Newcastle University7, University of Bonn8, University of Hamburg9, Manchester Academic Health Science Centre10, University of Cambridge11, Karolinska Institutet12, Medical University of Vienna13, Curie Institute14, Paris Descartes University15, Harvard University16
TL;DR: A meta-analysis of all molecular and clinical data of 550 medulloblastomas brought together from seven independent studies shows how distinct the molecular subtypes are with respect to their transcriptome, DNA copy-number aberrations, demographics, and survival.
Abstract: Medulloblastoma is the most common malignant brain tumor in childhood. Molecular studies from several groups around the world demonstrated that medulloblastoma is not one disease but comprises a collection of distinct molecular subgroups. However, all these studies reported on different numbers of subgroups. The current consensus is that there are only four core subgroups, which should be termed WNT, SHH, Group 3 and Group 4. Based on this, we performed a meta-analysis of all molecular and clinical data of 550 medulloblastomas brought together from seven independent studies. All cases were analyzed by gene expression profiling and for most cases SNP or array-CGH data were available. Data are presented for all medulloblastomas together and for each subgroup separately. For validation purposes, we compared the results of this meta-analysis with another large medulloblastoma cohort (n = 402) for which subgroup information was obtained by immunohistochemistry. Results from both cohorts are highly similar and show how distinct the molecular subtypes are with respect to their transcriptome, DNA copy-number aberrations, demographics, and survival. Results from these analyses will form the basis for prospective multi-center studies and will have an impact on how the different subgroups of medulloblastoma will be treated in the future.
Ruhr University Bochum1, Leiden University2, National Autonomous University of Mexico3, University of Córdoba (Spain)4, Rikshospitalet–Radiumhospitalet5, University of Amsterdam6, University of Paris7, University of Leeds8, Eötvös Loránd University9, Hamad Medical Corporation10, University of Toronto11, Case Western Reserve University12, University of Helsinki13, University of Alberta14, Charles University in Prague15, Erciyes University16, VU University Amsterdam17
TL;DR: This first update of the ASAS/EULAR recommendations on the management of ankylosing spondylitis is based on the original paper, a systematic review of existing recommendations and the literature since 2005 and the discussion and agreement among 21 international experts, 2 patients and 2 physiotherapists in a meeting in February 2010.
TL;DR: In this paper, the authors highlight the use of non-innocent redox active ligands in catalysis and highlight four main application strategies of redox-active ligands: oxidation/reduction of the ligand to tune the electronic properties (i.e., Lewis acidity/basicity) of the metal.
Abstract: In this (tutorial overview) perspective we highlight the use of “redox non-innocent” ligands in catalysis. Two main types of reactivity in which the redox non-innocent ligand is involved can be specified: (A) The redox active ligand participates in the catalytic cycle only by accepting/donating electrons, and (B) the ligand actively participates in the formation/breaking of substrate covalent bonds. On the basis of these two types of behavior, four main application strategies of redox-active ligands in catalysis can be distinguished: The first strategy (I) involves oxidation/reduction of the ligand to tune the electronic properties (i.e., Lewis acidity/basicity) of the metal. In the second approach (II) the ligand is used as an electron reservoir. This allows multiple-electron transformations for metal complexes that are reluctant to such transformations otherwise (e.g., because the metal would need to accommodate an uncommon, high-energy oxidation state). This includes examples of (first row) transition ...
TL;DR: It is argued that a biological approach to psychiatry based on 'neurocognitive endophenotypes', whereby changes in behavioural or cognitive processes are associated with discrete deficits in defined neural systems, has important implications for the future classification of psychiatric disorders, genetics and therapeutics.
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.
German Cancer Research Center1, European Bioinformatics Institute2, Max Planck Society3, Stanford University4, Broad Institute5, Heidelberg University6, University of Amsterdam7, Ludwig Maximilian University of Munich8, Saarland University9, Boston Children's Hospital10, McGill University11, University of Hamburg12, Royal Victoria Infirmary13, University of Cambridge14, Manchester Academic Health Science Centre15, University of Düsseldorf16, Harvard University17
TL;DR: An integrative deep-sequencing analysis of 125 tumour–normal pairs enhances the understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provides several potential targets for new therapeutics, especially for Group 3 and 4 patients.
Abstract: Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.
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.
TL;DR: Among patients without ARDS, protective ventilation with lower tidal volumes was associated with better clinical outcomes, and was significant only in randomized trials for pulmonary infection and only in nonrandomized trials for mortality.
Abstract: Context Lung-protective mechanical ventilation with the use of lower tidal volumes has been found to improve outcomes of patients with acute respiratory distress syndrome (ARDS). It has been suggested that use of lower tidal volumes also benefits patients who do not have ARDS. Objective To determine whether use of lower tidal volumes is associated with improved outcomes of patients receiving ventilation who do not have ARDS.