Showing papers by "University of Warwick published in 2018"

The Mixed Methods Appraisal Tool (MMAT) Version 2018 for Information Professionals and Researchers.

Abstract: INTRODUCTION: Appraising the quality of studies included in systematic reviews combining qualitative and quantitative evidence is challenging. To address this challenge, a critical appraisal tool was developed: the Mixed Methods Appraisal Tool (MMAT). The aim of this paper is to present the enhancements made to the MMAT. DEVELOPMENT: The MMAT was initially developed in 2006 based on a literature review on systematic reviews combining qualitative and quantitative evidence. It was subject to pilot and interrater reliability testing. A revised version of the MMAT was developed in 2018 based on the results from usefulness testing, a literature review on critical appraisal tools and a modified e-Delphi study with methodological experts to identify core criteria. TOOL DESCRIPTION: The MMAT assesses the quality of qualitative, quantitative, and mixed methods studies. It focuses on methodological criteria and includes five core quality criteria for each of the following five categories of study designs: (a) qualitative, (b) randomized controlled, (c) nonrandomized, (d) quantitative descriptive, and (e) mixed methods. CONCLUSION: The MMAT is a unique tool that can be used to appraise the quality of different study designs. Also, by limiting to core criteria, the MMAT can provide a more efficient appraisal.

Comparison of an Oral Factor Xa Inhibitor With Low Molecular Weight Heparin in Patients With Cancer With Venous Thromboembolism: Results of a Randomized Trial (SELECT-D)

Abstract: PurposeVenous thromboembolism (VTE) is common in patients with cancer. Long-term daily subcutaneous low molecular weight heparin has been standard treatment for such patients. The purpose of this study was to assess if an oral factor Xa inhibitor, rivaroxaban, would offer an alternative treatment for VTE in patients with cancer.Patient and MethodsIn this multicenter, randomized, open-label, pilot trial in the United Kingdom, patients with active cancer who had symptomatic pulmonary embolism (PE), incidental PE, or symptomatic lower-extremity proximal deep vein thrombosis (DVT) were recruited. Allocation was to dalteparin (200 IU/kg daily during month 1, then 150 IU/kg daily for months 2-6) or rivaroxaban (15 mg twice daily for 3 weeks, then 20 mg once daily for a total of 6 months). The primary outcome was VTE recurrence over 6 months. Safety was assessed by major bleeding and clinically relevant nonmajor bleeding (CRNMB). A sample size of 400 patients would provide estimates of VTE recurrence to within ±...

Speed breeding is a powerful tool to accelerate crop research and breeding

Abstract: The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand1. This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called ‘speed breeding’, which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2–3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.

Enterotypes in the landscape of gut microbial community composition

Abstract: Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.

Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci

Abstract: Genome-wide association studies (GWAS) and fine-mapping efforts to date have identified more than 100 prostate cancer (PrCa)-susceptibility loci. We meta-analyzed genotype data from a custom high-density array of 46,939 PrCa cases and 27,910 controls of European ancestry with previously genotyped data of 32,255 PrCa cases and 33,202 controls of European ancestry. Our analysis identified 62 novel loci associated (P C, p.Pro1054Arg) in ATM and rs2066827 (OR = 1.06; P = 2.3 × 10−9; T>G, p.Val109Gly) in CDKN1B. The combination of all loci captured 28.4% of the PrCa familial relative risk, and a polygenic risk score conferred an elevated PrCa risk for men in the ninetieth to ninety-ninth percentiles (relative risk = 2.69; 95% confidence interval (CI): 2.55–2.82) and first percentile (relative risk = 5.71; 95% CI: 5.04–6.48) risk stratum compared with the population average. These findings improve risk prediction, enhance fine-mapping, and provide insight into the underlying biology of PrCa1. A large meta-analysis combining genome-wide and custom high-density genotyping array data identifies 63 new susceptibility loci for prostate cancer, enhancing fine-mapping efforts and providing insights into the underlying biology.

Composition Loss for Counting, Density Map Estimation and Localization in Dense Crowds

Abstract: With multiple crowd gatherings of millions of people every year in events ranging from pilgrimages to protests, concerts to marathons, and festivals to funerals; visual crowd analysis is emerging as a new frontier in computer vision. In particular, counting in highly dense crowds is a challenging problem with far-reaching applicability in crowd safety and management, as well as gauging political significance of protests and demonstrations. In this paper, we propose a novel approach that simultaneously solves the problems of counting, density map estimation and localization of people in a given dense crowd image. Our formulation is based on an important observation that the three problems are inherently related to each other making the loss function for optimizing a deep CNN decomposable. Since localization requires high-quality images and annotations, we introduce UCF-QNRF dataset that overcomes the shortcomings of previous datasets, and contains 1.25 million humans manually marked with dot annotations. Finally, we present evaluation measures and comparison with recent deep CNNs, including those developed specifically for crowd counting. Our approach significantly outperforms state-of-the-art on the new dataset, which is the most challenging dataset with the largest number of crowd annotations in the most diverse set of scenes.

A Survey of the State-of-the-Art Localization Techniques and Their Potentials for Autonomous Vehicle Applications

Abstract: For an autonomous vehicle to operate safely and effectively, an accurate and robust localization system is essential. While there are a variety of vehicle localization techniques in literature, there is a lack of effort in comparing these techniques and identifying their potentials and limitations for autonomous vehicle applications. Hence, this paper evaluates the state-of-the-art vehicle localization techniques and investigates their applicability on autonomous vehicles. The analysis starts with discussing the techniques which merely use the information obtained from on-board vehicle sensors. It is shown that although some techniques can achieve the accuracy required for autonomous driving but suffer from the high cost of the sensors and also sensor performance limitations in different driving scenarios (e.g., cornering and intersections) and different environmental conditions (e.g., darkness and snow). This paper continues the analysis with considering the techniques which benefit from off-board information obtained from V2X communication channels, in addition to vehicle sensory information. The analysis shows that augmenting off-board information to sensory information has potential to design low-cost localization systems with high accuracy and robustness, however, their performance depends on penetration rate of nearby connected vehicles or infrastructure and the quality of network service.

A Survey of Channel Modeling for UAV Communications

Abstract: Unmanned aerial vehicles (UAVs) have attracted great interest in rapid deployment for both civil and military applications. UAV communication has its own distinctive channel characteristics compared to the widely used cellular or satellite systems. Accurate channel characterization is crucial for the performance optimization and design of efficient UAV communication. However, several challenges exist in UAV channel modeling. For example, the propagation characteristics of UAV channels are under explored for spatial and temporal variations in non–stationary channels. Additionally, airframe shadowing has not yet been investigated for small size rotary UAVs. This paper provides an extensive survey of the measurement methods proposed for UAV channel modeling that use low altitude platforms and discusses various channel characterization efforts. We also review from a contemporary perspective of UAV channel modeling approaches, and outline future research challenges in this domain.

ESHRE guideline: recurrent pregnancy loss.

Abstract: Study question What is the recommended management of women with recurrent pregnancy loss (RPL) based on the best available evidence in the literature? Summary answer The guideline development group formulated 77 recommendations answering 18 key questions on investigations and treatments for RPL, and on how care should be organized. What is known already A previous guideline for the investigation and medical treatment of recurrent miscarriage was published in 2006 and is in need of an update. Study design size duration The guideline was developed according to the structured methodology for development of ESHRE guidelines. After formulation of key questions by a group of experts, literature searches and assessments were performed. Papers published up to 31 March 2017 and written in English were included. Cumulative live birth rate, live birth rate and pregnancy loss rate (or miscarriage rate) were considered the critical outcomes. Participants/materials setting methods Based on the collected evidence, recommendations were formulated and discussed until consensus was reached within the guideline group. A stakeholder review was organized after finalization of the draft. The final version was approved by the guideline group and the ESHRE Executive Committee. Main results and the role of chance The guideline provides 38 recommendations on risk factors, prevention and investigations in couples with RPL, and 39 recommendations on treatments. These include 60 evidence-based recommendations - of which 31 were formulated as strong recommendations and 29 as conditional - and 17 good practice points. The evidence supporting investigations and treatment of couples with RPL is limited and of moderate quality. Of the evidence-based recommendations, only 10 (16.3%) were supported by moderate quality evidence. The remaining recommendations were supported by low (35 recommendations: 57.4%), or very low quality evidence (16 recommendations: 26.2%). There were no recommendations based on high quality evidence. Owing to the lack of evidence-based investigations and treatments in RPL care, the guideline also clearly mentions investigations and treatments that should not be used for couples with RPL. Limitations reasons for caution Several investigations and treatments are offered to couples with RPL, but most of them are not well studied. For most of these investigations and treatments, a recommendation against the intervention or treatment was formulated based on insufficient evidence. Future studies may require these recommendations to be revised. Wider implications of the findings The guideline provides clinicians with clear advice on best practice in RPL, based on the best evidence available. In addition, a list of research recommendations is provided to stimulate further studies in RPL. One of the most important consequences of the limited evidence is the absence of evidence for a definition of RPL. Study funding/competing interests The guideline was developed and funded by ESHRE, covering expenses associated with the guideline meetings, with the literature searches and with the dissemination of the guideline. The guideline group members did not receive payment. J.E. reports position funding from CARE Fertility. S.L. reports position funding from SpermComet Ltd. S.M. reports research grants, consulting and speaker's fees from GSK, BMS/Pfizer, Sanquin, Aspen, Bayer and Daiichi Sankyo. S.Q. reports speaker's fees from Ferring. The other authors report no conflicts of interest.ESHRE Pages are not externally peer reviewed. This article has been approved by the Executive Committee of ESHRE.

Detection and Resolution of Rumours in Social Media: A Survey

Abstract: Despite the increasing use of social media platforms for information and news gathering, its unmoderated nature often leads to the emergence and spread of rumours, i.e., items of information that are unverified at the time of posting. At the same time, the openness of social media platforms provides opportunities to study how users share and discuss rumours, and to explore how to automatically assess their veracity, using natural language processing and data mining techniques. In this article, we introduce and discuss two types of rumours that circulate on social media: long-standing rumours that circulate for long periods of time, and newly emerging rumours spawned during fast-paced events such as breaking news, where reports are released piecemeal and often with an unverified status in their early stages. We provide an overview of research into social media rumours with the ultimate goal of developing a rumour classification system that consists of four components: rumour detection, rumour tracking, rumour stance classification, and rumour veracity classification. We delve into the approaches presented in the scientific literature for the development of each of these four components. We summarise the efforts and achievements so far toward the development of rumour classification systems and conclude with suggestions for avenues for future research in social media mining for the detection and resolution of rumours.

GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens

Abstract: Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.

Guidelines for Inclusion of Patient-Reported Outcomes in Clinical Trial Protocols: The SPIRIT-PRO Extension.

Abstract: Importance Patient-reported outcome (PRO) data from clinical trials can provide valuable evidence to inform shared decision making, labeling claims, clinical guidelines, and health policy; however, the PRO content of clinical trial protocols is often suboptimal. The SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) statement was published in 2013 and aims to improve the completeness of trial protocols by providing evidence-based recommendations for the minimum set of items to be addressed, but it does not provide PRO-specific guidance. Objective To develop international, consensus-based, PRO-specific protocol guidance (the SPIRIT-PRO Extension). Design, Setting, and Participants The SPIRIT-PRO Extension was developed following the Enhancing Quality and Transparency of Health Research (EQUATOR) Network’s methodological framework for guideline development. This included (1) a systematic review of existing PRO-specific protocol guidance to generate a list of potential PRO-specific protocol items (published in 2014); (2) refinements to the list and removal of duplicate items by the International Society for Quality of Life Research (ISOQOL) Protocol Checklist Taskforce; (3) an international stakeholder survey of clinical trial research personnel, PRO methodologists, health economists, psychometricians, patient advocates, funders, industry representatives, journal editors, policy makers, ethicists, and researchers responsible for evidence synthesis (distributed by 38 international partner organizations in October 2016); (4) an international Delphi exercise (n = 137 invited; October 2016 to February 2017); and (5) consensus meeting (n = 30 invited; May 2017). Prior to voting, consensus meeting participants were informed of the results of the Delphi exercise and given data from structured reviews evaluating the PRO protocol content of 3 defined samples of trial protocols. Results The systematic review identified 162 PRO-specific protocol recommendations from 54 sources. The ISOQOL Taskforce (n = 21) reduced this to 56 items, which were considered by 138 international stakeholder survey participants and 99 Delphi panelists. The final wording of the SPIRIT-PRO Extension was agreed on at a consensus meeting (n = 29 participants) and reviewed by external group of experts during a consultation period. Eleven extensions and 5 elaborations to the SPIRIT 2013 checklist were recommended for inclusion in clinical trial protocols in which PROs are a primary or key secondary outcome. Extension items focused on PRO-specific issues relating to the trial rationale, objectives, eligibility criteria, concepts used to evaluate the intervention, time points for assessment, PRO instrument selection and measurement properties, data collection plan, translation to other languages, proxy completion, strategies to minimize missing data, and whether PRO data will be monitored during the study to inform clinical care. Conclusions and Relevance The SPIRIT-PRO guidelines provide recommendations for items that should be addressed and included in clinical trial protocols in which PROs are a primary or key secondary outcome. Improved design of clinical trials including PROs could help ensure high-quality data that may inform patient-centered care.

Introduction-Platforms and Infrastructures in the Digital Age

Abstract: In the last few years, leading-edge research from information systems, strategic management, and economics have separately informed our understanding of platforms and infrastructures in the digital age. Our motivation for undertaking this special issue rests in the conviction that it is significant to discuss platforms and infrastructures concomitantly, while enabling knowledge from diverse disciplines to cross-pollinate to address critical, pressing policy challenges and inform strategic thinking across both social and business spheres. In this editorial, we review key insights from the literature on digital infrastructures and platforms, present emerging research themes, highlight the contributions developed from each of the six articles in this special issue, and conclude with suggestions for further research.

Minimum information reporting in bio-nano experimental literature.

Abstract: Studying the interactions between nanoengineered materials and biological systems plays a vital role in the development of biological applications of nanotechnology and the improvement of our fundamental understanding of the bio-nano interface. A significant barrier to progress in this multidisciplinary area is the variability of published literature with regards to characterizations performed and experimental details reported. Here, we suggest a 'minimum information standard' for experimental literature investigating bio-nano interactions. This standard consists of specific components to be reported, divided into three categories: material characterization, biological characterization and details of experimental protocols. Our intention is for these proposed standards to improve reproducibility, increase quantitative comparisons of bio-nano materials, and facilitate meta analyses and in silico modelling.

A genomic overview of the population structure of Salmonella.

Abstract: For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Abstract: Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.

Search for dark matter and other new phenomena in events with an energetic jet and large missing transverse momentum using the ATLAS detector

Abstract: Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses proton-proton collision data corresponding to an integrated luminosity of 36.1 fb−1 at a centre-of-mass energy of 13 TeV collected in 2015 and 2016 with the ATLAS detector at the Large Hadron Collider. Events are required to have at least one jet with a transverse momentum above 250 GeV and no leptons (e or μ). Several signal regions are considered with increasing requirements on the missing transverse momentum above 250 GeV. Good agreement is observed between the number of events in data and Standard Model predictions. The results are translated into exclusion limits in models with pair-produced weakly interacting dark-matter candidates, large extra spatial dimensions, and supersymmetric particles in several compressed scenarios.

Mapping interactions between the sustainable development goals: lessons learned and ways forward

Abstract: Pursuing integrated research and decision-making to advance action on the sustainable development goals (SDGs) fundamentally depends on understanding interactions between the SDGs, both negative ones (“trade-offs”) and positive ones (“co-benefits”). This quest, triggered by the 2030 Agenda, has however pointed to a gap in current research and policy analysis regarding how to think systematically about interactions across the SDGs. This paper synthesizes experiences and insights from the application of a new conceptual framework for mapping and assessing SDG interactions using a defined typology and characterization approach. Drawing on results from a major international research study applied to the SDGs on health, energy and the ocean, it analyses how interactions depend on key factors such as geographical context, resource endowments, time horizon and governance. The paper discusses the future potential, barriers and opportunities for applying the approach in scientific research, in policy making and in bridging the two through a global SDG Interactions Knowledge Platform as a key mechanism for assembling, systematizing and aggregating knowledge on interactions.

Biologically Targeted Magnetic Hyperthermia: Potential and Limitations.

Abstract: Hyperthermia, the mild elevation of temperature to 40-43°C, can induce cancer cell death and enhance the effects of radiotherapy and chemotherapy. However, achievement of its full potential as a clinically relevant treatment modality has been restricted by its inability to effectively and preferentially heat malignant cells. The limited spatial resolution may be circumvented by the intravenous administration of cancer-targeting magnetic nanoparticles that accumulate in the tumor, followed by the application of an alternating magnetic field to raise the temperature of the nanoparticles located in the tumor tissue. This targeted approach enables preferential heating of malignant cancer cells whilst sparing the surrounding normal tissue, potentially improving the effectiveness and safety of hyperthermia. Despite promising results in preclinical studies, there are numerous challenges that must be addressed before this technique can progress to the clinic. This review discusses these challenges and highlights the current understanding of targeted magnetic hyperthermia.

UAV Trajectory Optimization for Data Offloading at the Edge of Multiple Cells

Abstract: In future mobile networks, it is difficult for static base stations (BSs) to support the rapidly increasing data services, especially for cell-edge users. Unmanned aerial vehicle (UAV) is a promising method that can assist BSs to offload the data traffic, due to its high mobility and flexibility. In this correspondence, we focus on the UAV trajectory at the edges of three adjacent cells to offload traffic for BSs. In the proposed scheme, the sum rate of UAV-served edge users is maximized subject to the rate requirements for all the users, by optimizing the UAV trajectory in each flying cycle. The optimization is a mixed-integer nonconvex problem, which is difficult to solve. Thus, it is transformed into two convex problems, and an iterative algorithm is proposed to solve it by optimizing the UAV trajectory and edge user scheduling alternately. Simulation results are presented to show the effectiveness of the proposed scheme.

Optimum Placement of UAV as Relays

Abstract: Unmanned aerial vehicles (UAVs) as aerial base stations or relays are becoming increasingly important in communications. In this letter, the optimum placement of a relaying UAV for maximum reliability is studied. The total power loss, the overall outage, and the overall bit error rate are derived as reliability measures. The optimum altitude is investigated for both static and mobile UAVs. Numerical results show that different reliability measures have slightly different optimum altitudes and that decode-and-forward is better than amplify-and-forward.

Caching UAV Assisted Secure Transmission in Hyper-Dense Networks Based on Interference Alignment

Abstract: Unmanned aerial vehicles (UAVs) can help small-cell base stations (SBSs) offload traffic via wireless backhaul to improve coverage and increase rate. However, the capacity of backhaul is limited. In this paper, UAV assisted secure transmission for scalable videos in hyper-dense networks via caching is studied. In the proposed scheme, UAVs can act as SBSs to provide videos to mobile users in some small cells. To reduce the pressure of wireless backhaul, UAVs and SBSs are both equipped with caches to store videos at off-peak time. To facilitate UAVs, a single antenna is equipped at each UAV and thus, only the precoding matrices of SBSs should be cooperatively designed to manage interference by exploiting the principle of interference alignment. On the other hand, the SBSs replaced by UAVs will be idle. Thus, in order to guarantee secure transmission, the idle SBSs can be further exploited to generate jamming signal to disrupt eavesdropping. The jamming signal is zero-forced at the legitimate users through the precoding of the idle SBSs, without affecting the legitimate transmission. The feasibility conditions of the proposed scheme are derived, and the secrecy performance is analyzed. Finally, simulation results are presented to verify the effectiveness of the proposed scheme.