Showing papers by "University of Warwick published in 2015"

UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age

Abstract: Cathie Sudlow and colleagues describe the UK Biobank, a large population-based prospective study, established to allow investigation of the genetic and non-genetic determinants of the diseases of middle and old age.

Combined Measurement of the Higgs Boson Mass in pp Collisions at √s=7 and 8 TeV with the ATLAS and CMS Experiments

Abstract: A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4l decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is mH=125.09±0.21 (stat)±0.11 (syst) GeV.

Anvi'o: an advanced analysis and visualization platform for 'omics data.

Abstract: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.

Contemporary particle-in-cell approach to laser-plasma modelling

Abstract: Particle-in-cell (PIC) methods have a long history in the study of laser-plasma interactions. Early electromagnetic codes used the Yee staggered grid for field variables combined with a leapfrog EM-field update and the Boris algorithm for particle pushing. The general properties of such schemes are well documented. Modern PIC codes tend to add to these high-order shape functions for particles, Poisson preserving field updates, collisions, ionisation, a hybrid scheme for solid density and high-field QED effects. In addition to these physics packages, the increase in computing power now allows simulations with real mass ratios, full 3D dynamics and multi-speckle interaction. This paper presents a review of the core algorithms used in current laser-plasma specific PIC codes. Also reported are estimates of self-heating rates, convergence of collisional routines and test of ionisation models which are not readily available elsewhere. Having reviewed the status of PIC algorithms we present a summary of recent applications of such codes in laser-plasma physics, concentrating on SRS, short-pulse laser-solid interactions, fast-electron transport, and QED effects.

Service Research Priorities in a Rapidly Changing Context

Abstract: The context in which service is delivered and experienced has, in many respects, fundamentally changed. For instance, advances in technology, especially information technology, are leading to a proliferation of revolutionary services and changing how customers serve themselves before, during, and after purchase. To understand this changing landscape, the authors engaged in an international and interdisciplinary research effort to identify research priorities that have the potential to advance the service field and benefit customers, organizations, and society. The priority-setting process was informed by roundtable discussions with researchers affiliated with service research centers and networks located around the world and resulted in the following 12 service research priorities: • stimulating service innovation, • facilitating servitization, service infusion, and solutions, • understanding organization and employee issues relevant to successful service, • developing service networks and systems, • leveraging service design, • using big data to advance service, • understanding value creation, • enhancing the service experience, • improving well-being through transformative service, • measuring and optimizing service performance and impact, • understanding service in a global context, and • leveraging technology to advance service. For each priority, the authors identified important specific service topics and related research questions. Then, through an online survey, service researchers assessed the subtopics’ perceived importance and the service field’s extant knowledge about them. Although all the priorities and related topics were deemed important, the results show that topics related to transformative service and measuring and optimizing service performance are particularly important for advancing the service field along with big data, which had the largest gap between importance and current knowledge of the field. The authors present key challenges that should be addressed to move the field forward and conclude with a discussion of the need for additional interdisciplinary research.

LHCb detector performance

Abstract: The LHCb detector is a forward spectrometer at the Large Hadron Collider (LHC) at CERN. The experiment is designed for precision measurements of CP violation and rare decays of beauty and charm hadrons. In this paper the performance of the various LHCb sub-detectors and the trigger system are described, using data taken from 2010 to 2012. It is shown that the design criteria of the experiment have been met. The excellent performance of the detector has allowed the LHCb collaboration to publish a wide range of physics results, demonstrating LHCb's unique role, both as a heavy flavour experiment and as a general purpose detector in the forward region.

The stepped wedge cluster randomised trial: rationale, design, analysis, and reporting

Abstract: The stepped wedge cluster randomised trial is a novel research study design that is increasingly being used in the evaluation of service delivery type interventions. The design involves random and sequential crossover of clusters from control to intervention until all clusters are exposed. It is a pragmatic study design which can reconcile the need for robust evaluations with political or logistical constraints. While not exclusively for the evaluation of service delivery interventions, it is particularly suited to evaluations that do not rely on individual patient recruitment. As in all cluster trials, stepped wedge trials with individual recruitment and without concealment of allocation (or blinding of the intervention) are at risk of selection biases. In a stepped wedge design more clusters are exposed to the intervention towards the end of the study than in its early stages. This implies that the effect of the intervention might be confounded with any underlying temporal trend. A result that initially might seem suggestive of an effect of the intervention may therefore transpire to be the result of a positive underlying temporal trend. Sample size calculations and analysis must make allowance for both the clustered nature of the design and the confounding effect of time. The stepped wedge cluster randomised trial is an alternative to traditional parallel cluster studies, in which the intervention is delivered in only half the clusters with the remainder functioning as controls. When the clusters are relatively homogeneous (that is, the intra-cluster correlation is small), parallel studies tend to deliver better statistical performance than a stepped wedge trial. However, if substantial cluster-level effects are present (that is, larger intra-cluster correlations) or the clusters are large, the stepped wedge design will be more powerful than a parallel design, even one in which the intervention is preceded by a period of baseline control observations.

Observation of $J/\psi p$ Resonances Consistent with Pentaquark States in $\Lambda_b^0 \to J/\psi K^- p$ Decays

Abstract: Observations of exotic structures in the J/ψp channel, that we refer to as pentaquark-charmonium states, in Λ0b→J/ψK−p decays are presented. The data sample corresponds to an integrated luminosity of 3/fb acquired with the LHCb detector from 7 and 8 TeV pp collisions. An amplitude analysis is performed on the three-body final-state that reproduces the two-body mass and angular distributions. To obtain a satisfactory fit of the structures seen in the J/ψp mass spectrum, it is necessary to include two Breit-Wigner amplitudes that each describe a resonant state. The significance of each of these resonances is more than 9 standard deviations. One has a mass of 4380±8±29 MeV and a width of 205±18±86 MeV, while the second is narrower, with a mass of 4449.8±1.7±2.5 MeV and a width of 39±5±19 MeV. The preferred JP assignments are of opposite parity, with one state having spin 3/2 and the other 5/2.

The global threat of antimicrobial resistance: science for intervention

Abstract: In the last decade we have witnessed a dramatic increase in the proportion and absolute number of bacterial pathogens resistant to multiple antibacterial agents. Multidrug-resistant bacteria are currently considered as an emergent global disease and a major public health problem. The B-Debate meeting brought together renowned experts representing the main stakeholders (i.e. policy makers, public health authorities, regulatory agencies, pharmaceutical companies and the scientific community at large) to review the global threat of antibiotic resistance and come up with a coordinated set of strategies to fight antimicrobial resistance in a multifaceted approach. We summarize the views of the B-Debate participants regarding the current situation of antimicrobial resistance in animals and the food chain, within the community and the healthcare setting as well as the role of the environment and the development of novel diagnostic and therapeutic strategies, providing expert recommendations to tackle the global threat of antimicrobial resistance.

A positive-negative mode of population covariation links brain connectivity, demographics and behavior

Abstract: We investigated the relationship between individual subjects' functional connectomes and 280 behavioral and demographic measures in a single holistic multivariate analysis relating imaging to non-imaging data from 461 subjects in the Human Connectome Project. We identified one strong mode of population co-variation: subjects were predominantly spread along a single 'positive-negative' axis linking lifestyle, demographic and psychometric measures to each other and to a specific pattern of brain connectivity.

Common genetic variants influence human subcortical brain structures.

Abstract: The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

Discovery of microbial natural products by activation of silent biosynthetic gene clusters.

Abstract: Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.

What are the main drivers of the Bitcoin price? Evidence from wavelet coherence analysis

Abstract: The Bitcoin has emerged as a fascinating phenomenon in the Financial markets. Without any central authority issuing the currency, the Bitcoin has been associated with controversy ever since its popularity, accompanied by increased public interest, reached high levels. Here, we contribute to the discussion by examining the potential drivers of Bitcoin prices, ranging from fundamental sources to speculative and technical ones, and we further study the potential influence of the Chinese market. The evolution of relationships is examined in both time and frequency domains utilizing the continuous wavelets framework, so that we not only comment on the development of the interconnections in time but also distinguish between short-term and long-term connections. We find that the Bitcoin forms a unique asset possessing properties of both a standard financial asset and a speculative one.

The Top 10 oomycete pathogens in molecular plant pathology

Abstract: Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Mendelian randomization of blood lipids for coronary heart disease

Abstract: AIMS: To investigate the causal role of high-density lipoprotein cholesterol (HDL-C) and triglycerides in coronary heart disease (CHD) using multiple instrumental variables for Mendelian randomization. METHODS AND RESULTS: We developed weighted allele scores based on single nucleotide polymorphisms (SNPs) with established associations with HDL-C, triglycerides, and low-density lipoprotein cholesterol (LDL-C). For each trait, we constructed two scores. The first was unrestricted, including all independent SNPs associated with the lipid trait identified from a prior meta-analysis (threshold P < 2 × 10(-6)); and the second a restricted score, filtered to remove any SNPs also associated with either of the other two lipid traits at P ≤ 0.01. Mendelian randomization meta-analyses were conducted in 17 studies including 62,199 participants and 12,099 CHD events. Both the unrestricted and restricted allele scores for LDL-C (42 and 19 SNPs, respectively) associated with CHD. For HDL-C, the unrestricted allele score (48 SNPs) was associated with CHD (OR: 0.53; 95% CI: 0.40, 0.70), per 1 mmol/L higher HDL-C, but neither the restricted allele score (19 SNPs; OR: 0.91; 95% CI: 0.42, 1.98) nor the unrestricted HDL-C allele score adjusted for triglycerides, LDL-C, or statin use (OR: 0.81; 95% CI: 0.44, 1.46) showed a robust association. For triglycerides, the unrestricted allele score (67 SNPs) and the restricted allele score (27 SNPs) were both associated with CHD (OR: 1.62; 95% CI: 1.24, 2.11 and 1.61; 95% CI: 1.00, 2.59, respectively) per 1-log unit increment. However, the unrestricted triglyceride score adjusted for HDL-C, LDL-C, and statin use gave an OR for CHD of 1.01 (95% CI: 0.59, 1.75). CONCLUSION: The genetic findings support a causal effect of triglycerides on CHD risk, but a causal role for HDL-C, though possible, remains less certain.

Introduction to Tropical Geometry

Abstract: Tropical islands Building blocks Tropical varieties Tropical rain forest Tropical garden Toric connections Bibliography Index

Happiness and Productivity

Abstract: Some firms say they care about the well-being and “happiness” of their employees. But are such claims hype or scientific good sense? We provide evidence, for a classic piece rate setting, that happ...

Ion channels enable electrical communication in bacterial communities

Abstract: The study of bacterial ion channels has provided fundamental insights into the structural basis of neuronal signalling; however, the native role of ion channels in bacteria has remained elusive. Here we show that ion channels conduct long-range electrical signals within bacterial biofilm communities through spatially propagating waves of potassium. These waves result from a positive feedback loop, in which a metabolic trigger induces release of intracellular potassium, which in turn depolarizes neighbouring cells. Propagating through the biofilm, this wave of depolarization coordinates metabolic states among cells in the interior and periphery of the biofilm. Deletion of the potassium channel abolishes this response. As predicted by a mathematical model, we further show that spatial propagation can be hindered by specific genetic perturbations to potassium channel gating. Together, these results demonstrate a function for ion channels in bacterial biofilms, and provide a prokaryotic paradigm for active, long-range electrical signalling in cellular communities.

Measurement of the Ratio of Branching Fractions B (B ¯ 0 →d∗+τ- ν ¯ τ) / B (B ¯ 0 →d∗+μ- ν ¯ μ)

Abstract: The branching fraction ratio R(D-*) = B((B) over bar (0) -> D-*(+)tau(-)(nu) over bar (tau))/B((B) over bar (0) -> D-*(+)mu(-)(nu) over bar (mu)) is measured using a sample of proton-proton collision data corresponding to 3.0 fb(-1) of integrated luminosity recorded by the LHCb experiment during 2011 and 2012. The tau lepton is identified in the decay mode tau(-) -> mu(-)(nu) over bar (mu)nu(tau). The semitauonic decay is sensitive to contributions from non-standard-model particles that preferentially couple to the third generation of fermions, in particular, Higgs-like charged scalars. A multidimensional fit to kinematic distributions of the candidate (B) over bar (0) decays gives R(D-*) = 0.336 +/- 0.027(stat) +/- 0.030(syst). This result, which is the first measurement of this quantity at a hadron collider, is 2.1 standard deviations larger than the value expected from lepton universality in the standard model.

Modeling infectious disease dynamics in the complex landscape of global health.

Abstract: Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health.

Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces

Abstract: We present a molecular dynamics scheme which combines first-principles and machine-learning (ML) techniques in a single information-efficient approach. Forces on atoms are either predicted by Bayesian inference or, if necessary, computed by on-the-fly quantum-mechanical (QM) calculations and added to a growing ML database, whose completeness is, thus, never required. As a result, the scheme is accurate and general, while progressively fewer QM calls are needed when a new chemical process is encountered for the second and subsequent times, as demonstrated by tests on crystalline and molten silicon.

Smart hybrid materials by conjugation of responsive polymers to biomacromolecules

Abstract: The chemical structure and function of biomacromolecules has evolved to fill many essential roles in biological systems. More specifically, proteins, peptides, nucleic acids and polysaccharides serve as vital structural components, and mediate chemical transformations and energy/information storage processes required to sustain life. In many cases, the properties and applications of biological macromolecules can be further expanded by attaching synthetic macromolecules. The modification of biomacromolecules by attaching a polymer that changes its properties in response to environmental variations, thus affecting the properties of the biomacromolecule, has led to the emergence of a new family of polymeric biomaterials. Here, we summarize techniques for conjugating responsive polymers to biomacromolecules and highlight applications of these bioconjugates reported so far. In doing so, we aim to show how advances in synthetic tools could lead to rapid expansion in the variety and uses of responsive bioconjugates.

NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain

Abstract: Here we present NeuroVault — a web based repository that allows researchers to store, share, visualize, and decode statistical maps of the human brain. NeuroVault is easy to use and employs modern web technologies to provide informative visualization of data without the need to install additional software. In addition, it leverages the power of the Neurosynth database to provide cognitive decoding of deposited maps. The data are exposed through a public REST API enabling other services and tools to take advantage of it. NeuroVault is a new resource for researchers interested in conducting meta- and coactivation analyses.

SME innovation, exporting and growth: A review of existing evidence

Abstract: This article summarises and synthesises the evidence on SME innovation, exporting and growth, paying particular attention to internal and external (eco-system) enablers, and for the interplay between innovation and exporting in SME growth. We highlight those areas for which the evidence base is secure and where the evidence base remains limited, and develop policy suggestions and an agenda for further research.

Observation of the rare B-s(0)->mu(+)mu(-) decay from the combined analysis of CMS and LHCb data

Abstract: The standard model of particle physics describes the fundamental particles and their interactions via the strong, electromagnetic and weak forces. It provides precise predictions for measurable quantities that can be tested experimentally. The probabilities, or branching fractions, of the strange B meson (B-s(0)) and the B-0 meson decaying into two oppositely charged muons (mu(+) and mu(-)) are especially interesting because of their sensitivity to theories that extend the standard model. The standard model predicts that the B-s(0)->mu(+)mu(-) and B-0 ->mu(+)mu(-) decays are very rare, with about four of the former occurring for every billion B-s(0) mesons produced, and one of the latter occurring for every ten billion B-0 mesons(1). A difference in the observed branching fractions with respect to the predictions of the standard model would provide a direction in which the standard model should be extended. Before the Large Hadron Collider (LHC) at CERN2 started operating, no evidence for either decay mode had been found. Upper limits on the branching fractions were an order of magnitude above the standard model predictions. The CMS (Compact Muon Solenoid) and LHCb(Large Hadron Collider beauty) collaborations have performed a joint analysis of the data from proton-proton collisions that they collected in 2011 at a centre-of-mass energy of seven teraelectronvolts and in 2012 at eight teraelectronvolts. Here we report the first observation of the B-s(0)->mu(+)mu(-) decay, with a statistical significance exceeding six standard deviations, and the best measurement so far of its branching fraction. Furthermore, we obtained evidence for the B-0 ->mu(+)mu(-) decay with a statistical significance of three standard deviations. Both measurements are statistically compatible with standard model predictions and allow stringent constraints to be placed on theories beyond the standard model. The LHC experiments will resume taking data in 2015, recording proton-proton collisions at a centre-of-mass energy of 13 teraelectronvolts, which will approximately double the production rates of B-s(0) and B-0 mesons and lead to further improvements in the precision of these crucial tests of the standard model.

A giant comet-like cloud of hydrogen escaping the warm Neptune-mass exoplanet GJ 436b

Abstract: In the ultraviolet spectrum, the Neptune-mass exoplanet GJ 436b is shown to have transit depths far greater than those seen in the optical spectrum, indicating that it is surrounded and trailed by a large cloud composed mainly of hydrogen atoms. Observations of the Neptune-mass exoplanet GJ 436b in the ultraviolet reveal a transit signature that is much deeper and longer than in the optical spectrum, an indication that it is surrounded and trailed by a large cloud of gas escaping from the planetary atmosphere. Numerical simulations indicate that in the ultraviolet GJ 436b looks like a giant comet. The authors propose that the gaseous 'tail' is composed mainly of hydrogen atoms and suggest that the exoplanet may have lost 10% of its atmosphere in its early life. Exoplanets orbiting close to their parent stars may lose some fraction of their atmospheres because of the extreme irradiation1,2,3,4,5,6. Atmospheric mass loss primarily affects low-mass exoplanets, leading to the suggestion that hot rocky planets7,8,9 might have begun as Neptune-like10,11,12,13,14,15,16, but subsequently lost all of their atmospheres; however, no confident measurements have hitherto been available. The signature of this loss could be observed in the ultraviolet spectrum, when the planet and its escaping atmosphere transit the star, giving rise to deeper and longer transit signatures than in the optical spectrum17. Here we report that in the ultraviolet the Neptune-mass exoplanet GJ 436b (also known as Gliese 436b) has transit depths of 56.3 ± 3.5% (1σ), far beyond the 0.69% optical transit depth. The ultraviolet transits repeatedly start about two hours before, and end more than three hours after the approximately one hour optical transit, which is substantially different from one previous claim6 (based on an inaccurate ephemeris). We infer from this that the planet is surrounded and trailed by a large exospheric cloud composed mainly of hydrogen atoms. We estimate a mass-loss rate in the range of about 108–109 grams per second, which is far too small to deplete the atmosphere of a Neptune-like planet in the lifetime of the parent star, but would have been much greater in the past.

Long-term effects of bullying

Abstract: Bullying is the systematic abuse of power and is defined as aggressive behaviour or intentional harm-doing by peers that is carried out repeatedly and involves an imbalance of power. Being bullied is still often wrongly considered as a ‘normal rite of passage’. This review considers the importance of bullying as a major risk factor for poor physical and mental health and reduced adaptation to adult roles including forming lasting relationships, integrating into work and being economically independent. Bullying by peers has been mostly ignored by health professionals but should be considered as a significant risk factor and safeguarding issue.