Peacock Bundles: Bundle Coloring for Graphs with Globality-Locality Trade-off

Bundling of graph edges (node-to-node connections) is a common technique to enhance visibility of overall trends in the edge structure of a large graph layout, and a large variety of bundling algorithms have been proposed. However, with strong bundling, it becomes hard to identify origins and destinations of individual edges. We propose a solution: we optimize edge coloring to differentiate bundled edges. We quantify strength of bundling in a flexible pairwise fashion between edges, and among bundled edges, we quantify how dissimilar their colors should be by dissimilarity of their origins and destinations. We solve the resulting nonlinear optimization, which is also interpretable as a novel dimensionality reduction task. In large graphs the necessary compromise is whether to differentiate colors sharply between locally occurring strongly bundled edges ("local bundles"), or also between the weakly bundled edges occurring globally over the graph ("global bundles"); we allow a user-set global-local tradeoff. We call the technique "peacock bundles". Experiments show the coloring clearly enhances comprehensibility of graph layouts with edge bundling.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Incidence of 'low-risk but not no-risk' features of cancer prior to high-risk feature occurrence: An observational cohort study in primary care.

This is the final version. Available from MDPI via the DOI in this record. Data Availability Statement: The anonymised participant data from this study are not available, in line with the CPRD’s data security policy. CPRD code libraries are available from the authors on request.Diagnosing cancer may be expedited by decreasing referral risk threshold. Clinical Practice Research Datalink participants (≥40 years) had a positive predictive value (PPV) ≥3% feature for breast, lung, colorectal, oesophagogastric, pancreatic, renal, bladder, prostatic, ovarian, endometrial or laryngeal cancer in 2016. The numbers of participants with features representing a 1-1.99% or 2-2.99% PPV for same cancer in the previous year were reported, alongside the time difference between meeting the ≥3% criteria and the lower threshold criteria. A total of 8616 participants had a PPV ≥3% feature, of whom 365 (4.2%) and 1147 (13.3%), respectively, met 2-2.99% and 1-1.99% criteria in the preceding year. The median time difference was 131 days (Interquartile Range (IQR) 27 to 256) for the 2-2.99% band and 179 days (IQR 58 to 289) for the 1-1.99% band. Results were heterogeneous across cancer sites. For some cancers, participants may progress from presenting lower- to higher-risk features before meeting urgent referral criteria; however, this was not usually the case. The details of specific features across multiple cancer sites will allow for a tailored approach to future reductions in referral thresholds, potentially improving the efficiency of urgent cancer referrals for the benefit both of individuals and the National Health Service (NHS).National Institute for Health ResearchNational Institute for Health Researc

Supporting Weight Management during COVID-19: A Randomized Controlled Trial of a Web-Based, ACT-Based, Guided Self-Help Intervention

Introduction: Adults with overweight and obesity are vulnerable to weight gain and mental health deterioration during the COVID-19 pandemic. We developed a web-based, guided self-help intervention based on Acceptance and Commitment Therapy (ACT) that aims to support adults with overweight and obesity to prevent weight gain by helping them to manage their eating behaviours, be more physically active, and protect their emotional wellbeing (“SWiM-C”). SWiM-C is a guided self-help programme using non-specialist guides to enhance scalability and population reach while minimizing cost. This study evaluated the effect of SWiM-C on bodyweight, eating behaviour, physical activity, and mental wellbeing in adults with overweight and obesity over 4 months during the COVID-19 pandemic in the UK. Methods: We randomized adults (BMI ≥25 kg/m2) to SWiM-C or to a wait-list standard advice group. Participants completed outcome assessments online at baseline and 4 months. The primary outcome was self-measured weight; secondary outcomes were eating behaviour, physical activity, experiential avoidance/psychological flexibility, depression, anxiety, stress, and wellbeing. We estimated differences between study groups in change in outcomes from baseline to 4 months using linear regression, adjusted for outcome at baseline and the randomization stratifiers (BMI, sex). The trial was pre-registered (ISRCTN12107048). Results: 486 participants were assessed for eligibility; 388 participants were randomized (196 standard advice, 192 SWiM-C), and 324 were analysed. The adjusted difference in weight between SWiM-C and standard advice was −0.60 kg (−1.67 to 0.47, p = 0.27). SWiM-C led to improvements in uncontrolled eating (−3.61 [−5.94 to −1.28]), cognitive restraint (5.28 [2.81–7.75]), experiential avoidance (−3.39 [−5.55 to −1.23]), and wellbeing (0.13 [0.07–0.18]). Conclusions: SWiM-C improved several psychological determinants of successful weight management and had a protective effect on wellbeing during the pandemic. However, differences in weight and some other outcomes were compatible with no effect of the intervention, suggesting further refinement of the intervention is needed

Reducing Constraints in a Higher Dimensional Extension of the Randall and Sundrum Model

In order to investigate the phenomenological implications of warped spaces in more than five dimensions, we consider a $4+1+\delta$ dimensional extension to the Randall and Sundrum model in which the space is warped with respect to a single direction by the presence of an anisotropic bulk cosmological constant. The Einstein equations are solved, giving rise to a range of possible spaces in which the $\delta$ additional spaces are warped. Here we consider models in which the gauge fields are free to propagate into such spaces. After carrying out the Kaluza Klein (KK) decomposition of such fields it is found that the KK mass spectrum changes significantly depending on how the $\delta$ additional dimensions are warped. We proceed to compute the lower bound on the KK mass scale from electroweak observables for models with a bulk $SU(2)\times U(1)$ gauge symmetry and models with a bulk $SU(2)_R\times SU(2)_L\times U(1)$ gauge symmetry. It is found that in both cases the most favourable bounds are approximately $M_{KK}\gtrsim 2$ TeV, corresponding to a mass of the first gauge boson excitation of about 4-6 TeV. Hence additional warped dimensions offer a new way of reducing the constraints on the KK scale.Comment: 27 pages, 15 figures, v3: Additional comments in sections 1, 2 and 4. New appendix added. Five additional figures. References adde

Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection.

Many single-stranded, positive-sense RNA viruses regulate assembly of their infectious virions by forming multiple, cognate coat protein (CP)-genome contacts at sites termed Packaging Signals (PSs). We have determined the secondary structures of the bacteriophage MS2 ssRNA genome (gRNA) frozen in defined states using constraints from X-ray synchrotron footprinting (XRF). Comparison of the footprints from phage and transcript confirms the presence of multiple PSs in contact with CP dimers in the former. This is also true for a virus-like particle (VLP) assembled around the gRNA in vitro in the absence of the single-copy Maturation Protein (MP) found in phage. Since PS folds are present at many sites across gRNA transcripts, it appears that this genome has evolved to facilitate this mechanism of assembly regulation. There are striking differences between the gRNA-CP contacts seen in phage and the VLP, suggesting that the latter are inappropriate surrogates for aspects of phage structure/function. Roughly 50% of potential PS sites in the gRNA are not in contact with the protein shell of phage. However, many of these sit adjacent to, albeit not in contact with, PS-binding sites on CP dimers. We hypothesize that these act as PSs transiently during assembly but subsequently dissociate. Combining the XRF data with PS locations from an asymmetric cryo-EM reconstruction suggests that the genome positions of such dissociations are non-random and may facilitate infection. The loss of many PS-CP interactions towards the 3′ end of the gRNA would allow this part of the genome to transit more easily through the narrow basal body of the pilus extruding machinery. This is the known first step in phage infection. In addition, each PS-CP dissociation event leaves the protein partner trapped in a non-lowest free-energy conformation. This destabilizes the protein shell which must disassemble during infection, further facilitating this stage of the life-cycle

Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid

Using RNA-coat protein crosslinking we have shown that the principal RNA recognition surface on the interior of infectious MS2 virions overlaps with the known peptides that bind the high affinity translational operator, TR, within the phage genome. The data also reveal the sequences of genomic fragments in contact with the coat protein shell. These show remarkable overlap with previous predictions based on the hypothesis that virion assembly is mediated by multiple sequences-specific contacts at RNA sites termed Packaging Signals (PSs). These PSs are variations on the TR stem-loop sequence and secondary structure. They act co-operatively to regulate the dominant assembly pathway and ensure cognate RNA encapsidation. In MS2, they also trigger conformational change in the dimeric capsomere creating the A/B quasi-conformer, 60 of which are needed to complete the T=3 capsid. This is the most compelling demonstration to date that this ssRNA virus, and by implications potentially very many of them, assemble via a PS-mediated assembly mechanism

Effectiveness and cost-effectiveness of referral to a commercial open group behavioural weight management programme in adults with overweight and obesity: 5-year follow-up of the WRAP randomised controlled trial

Background There is evidence that commercially available behavioural weight management programmes can lead to short-term weight loss and reductions in glycaemia. Here, we aimed to provide the 5-year impact and cost-effectiveness of these interventions compared with a brief intervention. Methods WRAP was a non-blinded, parallel-group randomised controlled trial (RCT). We recruited from primary care practices in England and randomly assigned participants to one of three interventions (brief intervention, 12-week open-group behavioural programme [WW, formerly Weight Watchers], or a 52-week open-group WW behavioural programme) in an uneven (2:5:5) allocation. Participants were followed up 5 years after randomisation using data from measurement visits at primary care practices or a research centre, review of primary care electronic medical notes, and self-report questionnaires. The primary outcome was change in weight at 5 years follow-up, assessed using analysis of covariance. We also estimated cost-effectiveness of the intervention. This study is registered at Current Controlled Trials, ISRCTN64986150. Findings Between Oct 18, 2012, and Feb 10, 2014, we recruited 1269 eligible participants (two participants were randomly assigned but not eligible and therefore excluded) and 1040 (82%) consented to be approached about additional follow-up and to have their medical notes reviewed at 5 years. The primary outcome (weight) was ascertained for 871 (69%) of 1267 eligible participants. Mean duration of follow-up was 5·1 (SD 0·3) years. Mean weight change from baseline to 5 years was −0·46 (SD 8·31) kg in the brief intervention group, −1·95 (9·55) kg in the 12-week programme group, and −2·67 (9·81) kg in the 52-week programme. The adjusted difference in weight change was –1·76 (95% CI –3·68 to 0·17) kg between the 52-week programme and the brief intervention; –0·80 (–2·13 to 0·54) kg between the 52-week and the 12-week programme; and –0·96 (–2·90 to 0·97) kg between the 12-week programme and the brief intervention. During the trial, the 12-week programme incurred the lowest cost and produced the highest quality-adjusted life-years (QALY). Simulations beyond 5 years suggested that the 52-week programme would deliver the highest QALYs at the lowest cost and would be the most cost-effective. No participants reported adverse events related to the intervention. Interpretation Although the difference in weight change between groups was not statistically significant, some weight loss was maintained at 5 years after an open-group behavioural weight management programme. Health economic modelling suggests that this could have important implications to reduce the incidence of weight-related disease and these interventions might be cost-saving. Funding The UK National Institute for Health and Care Research Programme Grants for Applied Research and the Medical Research Council

Using formative research to develop CHANGE! : a curriculum-based physical activity promoting intervention

Background : Low childhood physical activity levels are currently one of the most pressing public health concerns. Numerous school-based physical activity interventions have been conducted with varied success. Identifying effective child-based physical activity interventions are warranted. The purpose of this formative study was to elicit subjective views of children, their parents, and teachers about physical activity to inform the design of the CHANGE! (Children\u27s Health, Activity, and Nutrition: Get Educated!) intervention programme. Methods : Semi-structured mixed-gender interviews (group and individual) were conducted in 11 primary schools, stratified by socioeconomic status, with 60 children aged 9-10 years (24 boys, 36 girls), 33 parents (4 male, 29 female) and 10 teachers (4 male, 6 female). Questions for interviews were structured around the PRECEDE stage of the PRECEDE-PROCEDE model and addressed knowledge, attitudes and beliefs towards physical activity, as well as views on barriers to participation. All data were transcribed verbatim. Pen profiles were constructed from the transcripts in a deductive manner using the Youth Physical Activity Promotion Model framework. The profiles represented analysis outcomes via a diagram of key emergent themes. Results : Analyses revealed an understanding of the relationship between physical activity and health, although some children had limited understanding of what constitutes physical activity. Views elicited by children and parents were generally consistent. Fun, enjoyment and social support were important predictors of physical activity participation, though several barriers such as lack of parental support were identified across all group interviews. The perception of family invested time was positively linked to physical activity engagement. Conclusions : Families have a powerful and important role in promoting health-enhancing behaviours. Involvement of parents and the whole family is a strategy that could be significant to increase children\u27s physical activity levels. Addressing various perceived barriers to such behaviours therefore, remains imperative. <br /

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO