scispace - formally typeset
Search or ask a question

Showing papers by "University College Dublin published in 2014"


Journal ArticleDOI
Keith A. Olive1, Kaustubh Agashe2, Claude Amsler3, Mario Antonelli  +222 moreInstitutions (107)
TL;DR: The review as discussed by the authors summarizes much of particle physics and cosmology using data from previous editions, plus 3,283 new measurements from 899 Japers, including the recently discovered Higgs boson, leptons, quarks, mesons and baryons.
Abstract: The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,283 new measurements from 899 Japers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as heavy neutrinos, supersymmetric and technicolor particles, axions, dark photons, etc. 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 Supersymmetry, Extra Dimensions, Particle Detectors, Probability, and Statistics. Among the 112 reviews are many that are new or heavily revised including those on: Dark Energy, Higgs Boson Physics, Electroweak Model, Neutrino Cross Section Measurements, Monte Carlo Neutrino Generators, Top Quark, Dark Matter, Dynamical Electroweak Symmetry Breaking, Accelerator Physics of Colliders, High-Energy Collider Parameters, Big Bang Nucleosynthesis, Astrophysical Constants and Cosmological Parameters.

7,337 citations


Journal ArticleDOI
Roel Aaij, Bernardo Adeva1, Marco Adinolfi2, A. Affolder3  +698 moreInstitutions (50)
TL;DR: The value of the ratio of branching fractions for the dilepton invariant mass squared range 1 < q(2) < 6 GeV(2)/c(4) is measured to be 0.745(-0.074)(+0.090)(stat) ± 0.036(syst).
Abstract: A measurement of the ratio of the branching fractions of the B+→K+μ+μ− and B+→K+e+e− decays is presented using proton-proton collision data, corresponding to an integrated luminosity of 3.0 fb−1, recorded with the LHCb experiment at center-of-mass energies of 7 and 8 TeV. The value of the ratio of branching fractions for the dilepton invariant mass squared range 1

1,017 citations


Book ChapterDOI
TL;DR: Clustal Omega is a completely rewritten and revised version of the widely used Clustal series of programs for multiple sequence alignment that can deal with very large numbers of DNA/RNA or protein sequences due to its use of the mBED algorithm for calculating guide trees.
Abstract: Clustal Omega is a completely rewritten and revised version of the widely used Clustal series of programs for multiple sequence alignment. It can deal with very large numbers (many tens of thousands) of DNA/RNA or protein sequences due to its use of the mBED algorithm for calculating guide trees. This algorithm allows very large alignment problems to be tackled very quickly, even on personal computers. The accuracy of the program has been considerably improved over earlier Clustal programs, through the use of the HHalign method for aligning profile hidden Markov models. The program currently is used from the command line or can be run on line.

998 citations


Journal ArticleDOI
28 Mar 2014-Science
TL;DR: It is found that disadvantaged children randomly assigned to treatment have significantly lower prevalence of risk factors for cardiovascular and metabolic diseases in their mid-30s, and the evidence is especially strong for males.
Abstract: High-quality early childhood programs have been shown to have substantial benefits in reducing crime, raising earnings, and promoting education. Much less is known about their benefits for adult health. We report on the long-term health effects of one of the oldest and most heavily cited early childhood interventions with long-term follow-up evaluated by the method of randomization: the Carolina Abecedarian Project (ABC). Using recently collected biomedical data, we find that disadvantaged children randomly assigned to treatment have significantly lower prevalence of risk factors for cardiovascular and metabolic diseases in their mid-30s. The evidence is especially strong for males. The mean systolic blood pressure among the control males is 143 millimeters of mercury (mm Hg), whereas it is only 126 mm Hg among the treated. One in four males in the control group is affected by metabolic syndrome, whereas none in the treatment group are affected. To reach these conclusions, we address several statistical challenges. We use exact permutation tests to account for small sample sizes and conduct a parallel bootstrap confidence interval analysis to confirm the permutation analysis. We adjust inference to account for the multiple hypotheses tested and for nonrandom attrition. Our evidence shows the potential of early life interventions for preventing disease and promoting health.

885 citations


Journal ArticleDOI
TL;DR: Stable isotope mixing models are increasingly used to quantify consumer diets, but may be misused and misinter- preted, and major challenges to their effective application are addressed.
Abstract: Stable isotope mixing models are increasingly used to quantify consumer diets, but may be misused and misinter- preted. We address major challenges to their effective application. Mixing models have increased rapidly in sophistication. Current models estimate probability distributions of source contributions, have user-friendly interfaces, and incorporate com- plexities such as variability in isotope signatures, discrimination factors, hierarchical variance structure, covariates, and con- centration dependence. For proper implementation of mixing models, we offer the following suggestions. First, mixing models can only be as good as the study and data. Studies should have clear questions, be informed by knowledge of the system, and have strong sampling designs to effectively characterize isotope variability of consumers and resources on proper spatio-temporal scales. Second, studies should use models appropriate for the question and recognize their assumptions and limitations. Decisions about source grouping or incorporation of concentration dependence can influence results. Third, studies should be careful about interpretation of model outputs. Mixing models generally estimate proportions of assimilated resources with substantial uncertainty distributions. Last, common sense, such as graphing data before analyzing, is essential to maximize usefulness of these tools. We hope these suggestions for effective implementation of stable isotope mixing models will aid continued development and application of this field.

857 citations


Journal ArticleDOI
Dalila Pinto1, Elsa Delaby2, Elsa Delaby3, Elsa Delaby4, Daniele Merico5, Mafalda Barbosa1, Alison K. Merikangas6, Lambertus Klei7, Bhooma Thiruvahindrapuram5, Xiao Xu1, Robert Ziman5, Zhuozhi Wang5, Jacob A. S. Vorstman8, Ann P. Thompson9, Regina Regan10, Regina Regan11, Marion Pilorge4, Marion Pilorge3, Marion Pilorge2, Giovanna Pellecchia5, Alistair T. Pagnamenta12, Bárbara Oliveira13, Bárbara Oliveira14, Christian R. Marshall5, Tiago R. Magalhaes11, Tiago R. Magalhaes10, Jennifer K. Lowe15, Jennifer L. Howe5, Anthony J. Griswold16, John R. Gilbert16, Eftichia Duketis17, Beth A. Dombroski18, Maretha de Jonge8, Michael L. Cuccaro16, Emily L. Crawford19, Catarina Correia14, Catarina Correia13, Judith Conroy20, Inȇs C. Conceição13, Inȇs C. Conceição14, Andreas G. Chiocchetti17, Jillian P. Casey10, Jillian P. Casey11, Guiqing Cai1, Christelle Cabrol4, Christelle Cabrol3, Christelle Cabrol2, Nadia Bolshakova6, Elena Bacchelli21, Richard Anney6, Steven Gallinger5, Michelle Cotterchio22, Graham Casey23, Lonnie Zwaigenbaum24, Kerstin Wittemeyer25, Kirsty Wing12, Simon Wallace12, Herman van Engeland8, Ana Tryfon26, Susanne Thomson19, Latha Soorya27, Bernadette Rogé, Wendy Roberts5, Fritz Poustka17, Susana Mouga28, Nancy J. Minshew7, L. Alison McInnes29, Susan G. McGrew19, Catherine Lord30, Marion Leboyer, Ann Le Couteur31, Alexander Kolevzon1, Patricia Jiménez González, Suma Jacob32, Suma Jacob33, Richard Holt12, Stephen J. Guter32, Jonathan Green, Andrew Green10, Andrew Green11, Christopher Gillberg34, Bridget A. Fernandez35, Frederico Duque28, Richard Delorme, Geraldine Dawson36, Pauline Chaste, Cátia Café, Sean Brennan6, Thomas Bourgeron37, Patrick Bolton38, Patrick Bolton39, Sven Bölte17, Raphael Bernier40, Gillian Baird38, Anthony J. Bailey12, Evdokia Anagnostou5, Joana Almeida, Ellen M. Wijsman40, Veronica J. Vieland41, Astrid M. Vicente14, Astrid M. Vicente13, Gerard D. Schellenberg18, Margaret A. Pericak-Vance16, Andrew D. Paterson5, Jeremy R. Parr31, Guiomar Oliveira28, John I. Nurnberger42, Anthony P. Monaco43, Anthony P. Monaco12, Elena Maestrini21, Sabine M. Klauck44, Hakon Hakonarson18, Jonathan L. Haines19, Daniel H. Geschwind15, Christine M. Freitag17, Susan E. Folstein16, Sean Ennis10, Sean Ennis11, Hilary Coon45, Agatino Battaglia, Peter Szatmari9, James S. Sutcliffe19, Joachim Hallmayer46, Michael Gill6, Edwin H. Cook32, Joseph D. Buxbaum1, Bernie Devlin7, Louise Gallagher6, Catalina Betancur3, Catalina Betancur2, Catalina Betancur4, Stephen W. Scherer5 
TL;DR: For example, the authors analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability.
Abstract: Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.

833 citations


Journal ArticleDOI
TL;DR: The requirements and the methodological issues to be addressed for using ABPM in clinical practice are addressed, the clinical indications for ABPM suggested by the available studies are outlined in detail, and the place of home measurement of blood pressure in relation to ABPM is discussed.
Abstract: Given the increasing use of ambulatory blood pressure monitoring (ABPM) in both clinical practice and hypertension research, a group of scientists, participating in the European Society of Hypertension Working Group on blood pressure monitoring and cardiovascular variability, in year 2013 published a comprehensive position paper dealing with all aspects of the technique, based on the available scientific evidence for ABPM. The present work represents an updated schematic summary of the most important aspects related to the use of ABPM in daily practice, and is aimed at providing recommendations for proper use of this technique in a clinical setting by both specialists and practicing physicians. The present article details the requirements and the methodological issues to be addressed for using ABPM in clinical practice, The clinical indications for ABPM suggested by the available studies, among which white-coat phenomena, masked hypertension, and nocturnal hypertension, are outlined in detail, and the place of home measurement of blood pressure in relation to ABPM is discussed. The role of ABPM in pharmacological, epidemiological, and clinical research is also briefly mentioned. Finally, the implementation of ABPM in practice is considered in relation to the situation of different countries with regard to the reimbursement and the availability of ABPM in primary care practices, hospital clinics, and pharmacies.

786 citations


Journal ArticleDOI
TL;DR: Curious wave phenomena that occur in optical fibres due to the interplay of instability and nonlinear effects are reviewed in this article, where the authors propose a method to detect such phenomena.
Abstract: Curious wave phenomena that occur in optical fibres due to the interplay of instability and nonlinear effects are reviewed.

735 citations


Journal ArticleDOI
TL;DR: The risk of the primary composite end point of death or a complication related to pulmonary arterial hypertension was significantly lower with selexipag than with placebo and there was no significant difference in mortality between the two study groups.
Abstract: BackgroundIn a phase 2 trial, selexipag, an oral selective IP prostacyclin-receptor agonist, was shown to be beneficial in the treatment of pulmonary arterial hypertension. MethodsIn this event-driven, phase 3, randomized, double-blind, placebo-controlled trial, we randomly assigned 1156 patients with pulmonary arterial hypertension to receive placebo or selexipag in individualized doses (maximum dose, 1600 μg twice daily). Patients were eligible for enrollment if they were not receiving treatment for pulmonary arterial hypertension or if they were receiving a stable dose of an endothelin-receptor antagonist, a phosphodiesterase type 5 inhibitor, or both. The primary end point was a composite of death from any cause or a complication related to pulmonary arterial hypertension up to the end of the treatment period (defined for each patient as 7 days after the date of the last intake of selexipag or placebo). ResultsA primary end-point event occurred in 397 patients — 41.6% of those in the placebo group and...

713 citations


Journal ArticleDOI
TL;DR: The first definition of palliative care in dementia based on evidence and consensus is provided, a framework to provide guidance for clinical practice, policy and research.
Abstract: Background: Dementia is a life-limiting disease without curative treatments. Patients and families may need palliative care specific to dementia. Aim: To define optimal palliative care in dementia. Methods: Five-round Delphi study. Based on literature, a core group of 12 experts from 6 countries drafted a set of core domains with salient recommendations for each domain. We invited 89 experts from 27 countries to evaluate these in a two-round online survey with feedback. Consensus was determined according to predefined criteria. The fourth round involved decisions by the core team, and the fifth involved input from the European Association for Palliative Care. Results: A total of 64 (72%) experts from 23 countries evaluated a set of 11 domains and 57 recommendations. There was immediate and full consensus on the following eight domains, including the recommendations: person-centred care, communication and shared decision-making; optimal treatment of symptoms and providing comfort (these two identified as central to care and research); setting care goals and advance planning; continuity of care; psychosocial and spiritual support; family care and involvement; education of the health care team; and societal and ethical issues. After revision, full consensus was additionally reached for prognostication and timely recognition of dying. Recommendations on nutrition and dehydration (avoiding overly aggressive, burdensome or futile treatment) and on dementia stages in relation to care goals (applicability of palliative care) achieved moderate consensus. Conclusion: We have provided the first definition of palliative care in dementia based on evidence and consensus, a framework to provide guidance for clinical practice, policy and research.

709 citations


Journal ArticleDOI
TL;DR: Females were at a higher risk of sustaining an ankle sprain compared with males and children compared with adolescents and adults, with indoor and court sports the highest risk activity and Ankle sprain prevalence period estimates were similar across sub-groups.
Abstract: Ankle sprain is one of the most common musculoskeletal injuries, yet a contemporary review and meta-analysis of prospective epidemiological studies investigating ankle sprain does not exist. Our aim is to provide an up-to-date account of the incidence rate and prevalence period of ankle sprain injury unlimited by timeframe or context activity. We conducted a systematic review and meta-analyses of English articles using relevant computerised databases. Search terms included Medical Search Headings for the ankle joint, injury and epidemiology. The following inclusion criteria were used: the study must report epidemiology findings of injuries sustained in an observed sample; the study must report ankle sprain injury with either incidence rate or prevalence period among the surveyed sample, or provide sufficient data from which these figures could be calculated; the study design must be prospective. Independent extraction of articles was performed by two authors using pre-determined data fields. One-hundred and eighty-one prospective epidemiology studies from 144 separate papers were included. The average rating of all the included studies was 6.67/11, based on an adapted version of the STROBE (STrengthening the Reporting of OBservational studies in Epidemiology) guidelines for rating observational studies. 116 studies were considered high quality and 65 were considered low quality. The main findings of the meta-analysis demonstrated a higher incidence of ankle sprain in females compared with males (13.6 vs 6.94 per 1,000 exposures), in children compared with adolescents (2.85 vs 1.94 per 1,000 exposures) and adolescents compared with adults (1.94 vs 0.72 per 1,000 exposures). The sport category with the highest incidence of ankle sprain was indoor/court sports, with a cumulative incidence rate of 7 per 1,000 exposures or 1.37 per 1,000 athlete exposures and 4.9 per 1,000 h. Low-quality studies tended to underestimate the incidence of ankle sprain when compared with high-quality studies (0.54 vs 11.55 per 1,000 exposures). Ankle sprain prevalence period estimates were similar across sub-groups. Lateral ankle sprain was the most commonly observed type of ankle sprain. Females were at a higher risk of sustaining an ankle sprain compared with males and children compared with adolescents and adults, with indoor and court sports the highest risk activity. Studies at a greater risk of bias were more likely to underestimate the risk of ankle sprain. Participants were at a significantly higher risk of sustaining a lateral ankle sprain compared with syndesmotic and medial ankle sprains.

Journal ArticleDOI
21 Aug 2014-Nature
TL;DR: Improved accelerator mass spectrometry 14C techniques are applied to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, showing that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.
Abstract: The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

Journal ArticleDOI
TL;DR: A 5,000-year transect of human genomes sampled from petrous bones giving consistently excellent endogenous DNA yields are analysed, suggesting genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability.
Abstract: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

Journal ArticleDOI
S. Chatrchyan, Khachatryan1, Albert M. Sirunyan, Armen Tumasyan  +2384 moreInstitutions (207)
26 May 2014
TL;DR: In this paper, a description of the software algorithms developed for the CMS tracker both for reconstructing charged-particle trajectories in proton-proton interactions and for using the resulting tracks to estimate the positions of the LHC luminous region and individual primary-interaction vertices is provided.
Abstract: A description is provided of the software algorithms developed for the CMS tracker both for reconstructing charged-particle trajectories in proton-proton interactions and for using the resulting tracks to estimate the positions of the LHC luminous region and individual primary-interaction vertices. Despite the very hostile environment at the LHC, the performance obtained with these algorithms is found to be excellent. For tt events under typical 2011 pileup conditions, the average track-reconstruction efficiency for promptly-produced charged particles with transverse momenta of p_T > 0.9GeV is 94% for pseudorapidities of |η| < 0.9 and 85% for 0.9 < |η| < 2.5. The inefficiency is caused mainly by hadrons that undergo nuclear interactions in the tracker material. For isolated muons, the corresponding efficiencies are essentially 100%. For isolated muons of p_T = 100GeV emitted at |η| < 1.4, the resolutions are approximately 2.8% in p_T, and respectively, 10μm and 30μm in the transverse and longitudinal impact parameters. The position resolution achieved for reconstructed primary vertices that correspond to interesting pp collisions is 10–12μm in each of the three spatial dimensions. The tracking and vertexing software is fast and flexible, and easily adaptable to other functions, such as fast tracking for the trigger, or dedicated tracking for electrons that takes into account bremsstrahlung.

Journal ArticleDOI
TL;DR: This work confirms that the salience network drives the switching between default mode and central executive networks and that the novel technique is repeatable.

Journal ArticleDOI
TL;DR: In this paper, the authors presented the results of a project with the European Research Council and EPLANET (European Union) with the objective of supporting the development of a research network in the field of nuclear energy.
Abstract: Austrian Federal Ministry of Science and Research and the Austrian Science Fund; the Belgian Fonds de la Recherche Scientifique and Fonds voor Wetenschappelijk Onderzoek; the Brazilian Funding Agencies (CNPq, CAPES, FAPERJ, and FAPESP); the Bulgarian Ministry of Education and Science; CERN; the Chinese Academy of Sciences, Ministry of Science and Technology, and National Natural Science Foundation of China; the Colombian Funding Agency (COLCIENCIAS); the Croatian Ministry of Science, Education and Sport, and the Croatian Science Foundation; the Research Promotion Foundation, Cyprus; the Ministry of Education and Research, Recurrent Financing Contract No. SF0690030s09 and European Regional Development Fund, Estonia; the Academy of Finland, Finnish Ministry of Education and Culture, and Helsinki Institute of Physics; the Institut National de Physique Nucleaire et de Physique des Particules/CNRS and Commissariat a l’Energie Atomique et aux Energies Alternatives/CEA, France; the Bundesministerium fur Bildung und Forschung, Deutsche Forschungsgemeinschaft, and Helmholtz-Gemeinschaft Deutscher Forschungszentren, Germany; the General Secretariat for Research and Technology, Greece; the National Scientific Research Foundation and National Innovation Office, Hungary; the Department of Atomic Energy and the Department of Science and Technology, India; the Institute for Studies in Theoretical Physics and Mathematics, Iran; the Science Foundation, Ireland; the Istituto Nazionale di Fisica Nucleare, Italy; the Korean Ministry of Education, Science and Technology and the World Class University program of NRF, Republic of Korea; the Lithuanian Academy of Sciences; the Mexican Funding Agencies (CINVESTAV, CONACYT, SEP, and UASLP-FAI); the Ministry of Business, Innovation and Employment, New Zealand; the Pakistan Atomic Energy Commission; the Ministry of Science and Higher Education and the National Science Centre, Poland; the Fundacao para a Ciencia e a Tecnologia, Portugal; JINR, Dubna, the Ministry of Education and Science of the Russian Federation, the Federal Agency of Atomic Energy of the Russian Federation, Russian Academy of Sciences, and the Russian Foundation for Basic Research; the Ministry of Education, Science and Technological Development of Serbia; the Secretaria de Estado de Investigacion, Desarrollo e Innovacion and Programa Consolider-Ingenio 2010, Spain; the Swiss Funding Agencies (ETH Board, ETH Zurich, PSI, SNF, UniZH, Canton Zurich, and SER); the National Science Council, Taipei; the Thailand Center of Excellence in Physics, the Institute for the Promotion of Teaching Science and Technology of Thailand, Special Task Force for Activating Research and the National Science and Technology Development Agency of Thailand; the Scientific and Technical Research Council of Turkey and the Turkish Atomic Energy Authority; the Science and Technology Facilities Council, United Kingdom; the U.S. Department of Energy and the U.S. National Science Foundation.Individuals have received support from the Marie-Curie program and the European Research Council and EPLANET (European Union); the Leventis Foundation; the A. P. Sloan Foundation; the Alexander von Humboldt Foundation; the Belgian Federal Science Policy Office; the Fonds pour la Formation a la Recherche dans l’Industrie et dans l’Agriculture (FRIA-Belgium); the Agentschap voor Innovatie door Wetenschap en Technologie (IWT-Belgium); the Ministry of Education, Youth and Sports (MEYS) of the Czech Republic; the Council of Science and Industrial Research, India; the Compagnia di San Paolo (Torino); the HOMING PLUS programme of Foundation for Polish Science, cofinanced by EU, Regional Development Fund; and the Thalis and Aristeia programmes cofinanced by EU-ESF and the Greek NSRF.

Journal ArticleDOI
TL;DR: Clustal Omega as mentioned in this paper is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately, which is a complete upgrade and rewrite of earlier Clustal programs.
Abstract: Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment. © 2014 by John Wiley & Sons, Inc. Keywords: Clustal Omega; multiple sequence alignment; iteration; HMM; hidden Markov model

Journal ArticleDOI
TL;DR: In this paper, the diphoton decay mode of the recently discovered Higgs boson and measurement of some of its properties are reported using the entire dataset collected by the CMS experiment in proton-proton collisions during the 2011 and 2012 LHC running periods.
Abstract: Observation of the diphoton decay mode of the recently discovered Higgs boson and measurement of some of its properties are reported. The analysis uses the entire dataset collected by the CMS experiment in proton-proton collisions during the 2011 and 2012 LHC running periods. The data samples correspond to integrated luminosities of 5.1 inverse femtobarns at sqrt(s) = 7 TeV and 19.7 inverse femtobarns at 8 TeV. A clear signal is observed in the diphoton channel at a mass close to 125 GeV with a local significance of 5.7 sigma, where a significance of 5.2 sigma is expected for the standard model Higgs boson. The mass is measured to be 124.70 +/- 0.34 GeV = 124.70 +/- 0.31 (stat) +/- 0.15 (syst) GeV, and the best-fit signal strength relative to the standard model prediction is 1.14 +0.26/-0.23 = 1.14 +/- 0.21 (stat) +0.09/-0.05 (syst) +0.13/-0.09 (theo). Additional measurements include the signal strength modifiers associated with different production mechanisms, and hypothesis tests between spin-0 and spin-2 models.

Journal ArticleDOI
TL;DR: In line with the results obtained with the same PS NPs in several human cell lines, also in sea urchin embryos, differences in surface charges and aggregation in seawater strongly affect their embryotoxicity.
Abstract: Nanoplastic debris, resulted from runoff and weathering breakdown of macro- and microplastics, represents an emerging concern for marine ecosystems. The aim of the present study was to investigate disposition and toxicity of polystyrene nanoparticles (NPs) in early development of sea urchin embryos (Paracentrotus lividus). NPs with two different surface charges where chosen, carboxylated (PS-COOH) and amine (PS-NH2) polystyrene, the latter being a less common variant, known to induce cell death in several in vitro cell systems. NPs stability in natural seawater (NSW) was measured while disposition and embryotoxicity were monitored within 48 h of postfertilization (hpf). Modulation of genes involved in cellular stress response (cas8, 14-3-3e, p-38 MAPK, Abcb1, Abcc5) was investigated. PS-COOH forms microaggregates (PDI > 0.4) in NSW, whereas PS-NH2 results are better dispersed (89 ± 2 nm) initially, though they also aggregated partially with time. Their respectively anionic and cationic nature was confirmed by ζ-potential measurements. No embryotoxicity was observed for PS-COOH up to 50 μg mL(-1) whereas PS-NH2 caused severe developmental defects (EC50 3.85 μg mL(-1) 24 hpf and EC50 2.61 μg mL(-1) 48 hpf). PS-COOH accumulated inside embryo's digestive tract while PS-NH2 were more dispersed. Abcb1 gene resulted up-regulated at 48 hpf by PS-COOH whereas PS-NH2 induced cas8 gene at 24 hpf, suggesting an apoptotic pathway. In line with the results obtained with the same PS NPs in several human cell lines, also in sea urchin embryos, differences in surface charges and aggregation in seawater strongly affect their embryotoxicity.

Journal ArticleDOI
TL;DR: A critical review of the literature in the field of demand response can be found in this article, where the authors provide an overview of the benefits and challenges of the demand response resource, including the ability to balance fluctuations in renewable generation and facilitate higher penetrations of renewable resources on the power system.
Abstract: Advances in IT, control and forecasting capabilities have made demand response a viable, and potentially attractive, option to increase power system flexibility. This paper presents a critical review of the literature in the field of demand response, providing an overview of the benefits and challenges of demand response. These benefits include the ability to balance fluctuations in renewable generation and consequently facilitate higher penetrations of renewable resources on the power system, an increase in economic efficiency through the implementation of real-time pricing, and a reduction in generation capacity requirements. Nevertheless, demand response is not without its challenges. The key challenges for demand response centre around establishing reliable control strategies and market frameworks so that the demand response resource can be used optimally. One of the greatest challenges for demand response is the lack of experience, and the consequent need to employ extensive assumptions when modelling and evaluating this resource. This paper concludes with an examination of these assumptions, which range from assuming a fixed linear price–demand relationship for price responsive demand, to modelling the highly diverse, distributed and uncertain demand response resource as a single, centralised negative generator, adopting fixed characteristics and constraints.


Journal ArticleDOI
TL;DR: This paper provides an overview of cold plasma theory, equipment and summarises recent advances in the modification of polymeric food packaging materials along with potential applications in the food industry.
Abstract: Cold plasma technology is an emerging, green process offering many potential applications for food packaging. While it was originally developed to increase the surface energy of polymers, enhancing adhesion and printability, it has recently emerged as a powerful tool for surface decontamination of both foodstuffs and food packaging materials. New trends aim to develop in-package decontamination, offering non-thermal treatment of foods post-packaging. This paper provides an overview of cold plasma theory, equipment and summarises recent advances in the modification of polymeric food packaging materials along with potential applications in the food industry.

Journal ArticleDOI
Roel Aaij, Bernardo Adeva1, Marco Adinolfi2, A. A. Affolder3  +710 moreInstitutions (63)
TL;DR: In this article, the authors measured the isospin asymmetries of the B (0) -> K ( 0) mu (+) mu (-), B (1) → K (1)-m (+) m mu (-) and B (2)→ K (2)-m (-) m (-), respectively.
Abstract: The isospin asymmetries of B -> K mu (+) mu (-) and B -> K (*) mu (+) mu (-) decays and the partial branching fractions of the B (0) -> K (0) mu (+) mu (-), B (+) -> K (+) mu (+) mu (-) and B (+) -> K (*+) mu (+) mu (-) decays are measured as functions of the dimuon mass squared, q (2). The data used correspond to an integrated luminosity of 3 fb(-1) from proton-proton collisions collected with the LHCb detector at centre-of-mass energies of 7 TeV and 8 TeV in 2011 and 2012, respectively. The isospin asymmetries are both consistent with the Standard Model expectations. The three measured branching fractions favour lower values than their respective theoretical predictions, however they are all individually consistent with the Standard Model.

Journal ArticleDOI
Roel Aaij, Bernardo Adeva1, Marco Adinolfi2, A. A. Affolder3  +695 moreInstitutions (49)
TL;DR: The observed evolution of the Z(4430)^{-} amplitude with the ψ^{ fb^{-1} mass establishes the resonant nature of this particle.
Abstract: Resonant structures in B-0 -> psi'pi K--(+) decays are analyzed by performing a four-dimensional fit of the decay amplitude, using pp collision data corresponding to 3 fb(-1) collected with the LHCb detector. The data cannot be described with K+pi(-) resonances alone, which is confirmed with a model-independent approach. A highly significant Z(4430)(-) -> psi'pi(-) component is required, thus confirming the existence of this state. The observed evolution of the Z(4430)(-) amplitude with the psi'pi(-) mass establishes the resonant nature of this particle. The mass and width measurements are substantially improved. The spin parity is determined unambiguously to be 1(+).

Journal ArticleDOI
TL;DR: In this article, the authors presented the updated set of spectral analyses of gamma-ray bursts (GRBs) detected by the Fermi Gamma-Ray Burst Monitor during its first four years of operation.
Abstract: In this catalog we present the updated set of spectral analyses of gamma-ray bursts (GRBs) detected by the Fermi Gamma-Ray Burst Monitor during its first four years of operation. It contains two types of spectra, time-integrated spectral fits and spectral fits at the brightest time bin, from 943 triggered GRBs. Four different spectral models were fitted to the data, resulting in a compendium of more than 7500 spectra. The analysis was performed similarly but not identically to Goldstein et al. All 487 GRBs from the first two years have been re-fitted using the same methodology as that of the 456 GRBs in years three and four. We describe, in detail, our procedure and criteria for the analysis and present the results in the form of parameter distributions both for the observer-frame and rest-frame quantities. The data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center.

Journal ArticleDOI
16 Jan 2014-Immunity
TL;DR: In this paper, the authors investigated the contribution of neutrophils and respiratory burst to inflammatory hypoxia and effective inflammatory resolution in a colitis model using HIF-inducible factor (HIF) mice.

Journal ArticleDOI
TL;DR: In this article, the authors combine theory and practice to develop an integrated supply chain resilience framework by investigating the interdependencies between the strategic literature based concept of supply-chain resilience and operational practitioner-based disaster management processes.
Abstract: Purpose – This study aims to combine theory and practice to develop an integrated supply chain resilience framework by investigating the inter-dependencies between the strategic literature based concept of supply chain resilience and operational practitioner based disaster management processes. Design/methodology/approach – Utilising an in-depth qualitative case of a collaborative agency, this study identifies best practices within disaster management for insights on the operationalisation of supply chain resilience. Findings – The empirical data leads to the development of an integrated supply chain resilience framework capturing the interplay of disaster management processes and capabilities required to build supply chain resilience. The critical importance of mitigation processes in building supply chain resilience is highlighted. Practical implications – The generic supply chain resilience framework represents a valuable guide for managers when directing resources and planning for building the capabil...

Journal ArticleDOI
14 Aug 2014-Nature
TL;DR: By identifying the vulnerability factors underlying individual differences in alcohol misuse, these models shed light on the aetiology of alcohol misuse and suggest targets for prevention.
Abstract: Many factors have been proposed as contributors to risk of alcohol abuse, but quantifying their influence has been difficult; here a longitudinal study of a large sample of adolescents and machine learning are used to generate models of predictors of current and future alcohol abuse, assessing the relative contribution of many factors, including life history, individual personality differences, brain structure and genotype. Many factors have been identified as contributors to risk of alcohol abuse but their relative importance has been difficult to quantify. Robert Whelan et al. constructed models of current and future adolescent binge drinking using data from the IMAGEN project, a study of risk-taking behaviour in more than 2,000 teenagers recruited at age 14 from the United Kingdom, Ireland, France and Germany. The authors used machine learning to generate models of predictors of current and future alcohol abuse, assessing the contribution of many factors including life history, individual personality differences, brain structure and genotype. A key finding of the study was that personality factors were, surprisingly, not particularly useful predictors of future alcohol misuse. In contrast, neurodevelopmental immaturity, certain structural and functional indicators in the brain, sexual experience and prenatal alcohol exposure were associated with current and future binge drinking. A comprehensive account of the causes of alcohol misuse must accommodate individual differences in biology, psychology and environment, and must disentangle cause and effect. Animal models1 can demonstrate the effects of neurotoxic substances; however, they provide limited insight into the psycho-social and higher cognitive factors involved in the initiation of substance use and progression to misuse. One can search for pre-existing risk factors by testing for endophenotypic biomarkers2 in non-using relatives; however, these relatives may have personality or neural resilience factors that protect them from developing dependence3. A longitudinal study has potential to identify predictors of adolescent substance misuse, particularly if it can incorporate a wide range of potential causal factors, both proximal and distal, and their influence on numerous social, psychological and biological mechanisms4. Here we apply machine learning to a wide range of data from a large sample of adolescents (n = 692) to generate models of current and future adolescent alcohol misuse that incorporate brain structure and function, individual personality and cognitive differences, environmental factors (including gestational cigarette and alcohol exposure), life experiences, and candidate genes. These models were accurate and generalized to novel data, and point to life experiences, neurobiological differences and personality as important antecedents of binge drinking. By identifying the vulnerability factors underlying individual differences in alcohol misuse, these models shed light on the aetiology of alcohol misuse and suggest targets for prevention.

Journal ArticleDOI
TL;DR: Three physical-chemical properties of GBMs have been defined by the GRAPHENE Flagship Project of the European Union for the unequivocal classification of these materials (see grid).
Abstract: Graphing graphene: Because the naming of graphene-based materials (GBMs) has led to confusion and inconsistency, a classification approach is necessary. Three physical-chemical properties of GBMs have been defined by the GRAPHENE Flagship Project of the European Union for the unequivocal classification of these materials (see grid).

Journal ArticleDOI
Vardan Khachatryan1, Albert M. Sirunyan1, Armen Tumasyan1, Wolfgang Adam  +2121 moreInstitutions (139)
TL;DR: In this paper, searches for the direct electroweak production of supersymmetric charginos, neutralinos, and sleptons in a variety of signatures with leptons and W, Z, and Higgs bosons are presented.
Abstract: Searches for the direct electroweak production of supersymmetric charginos, neutralinos, and sleptons in a variety of signatures with leptons and W, Z, and Higgs bosons are presented. Results are based on a sample of proton-proton collision data collected at center-of-mass energy sqrt(s) = 8 TeV with the CMS detector in 2012, corresponding to an integrated luminosity of 19.5 inverse femtobarns. The observed event rates are in agreement with expectations from the standard model. These results probe charginos and neutralinos with masses up to 720 GeV, and sleptons up to 260 GeV, depending on the model details.