University of Bristol
  • Bristol, United Kingdom
Recent publications
System identification of engineering structures is an established area in the structural dynamics research community. It is often used to characterise certain physical properties of a structure using the data measured from it. For structures exhibiting nonlinear behaviour, physics-based approaches are used where a form of nonlinearity is synthesised and parameters are estimated using the data, or probabilistic approaches are investigated to tackle the model uncertainty of structures. However, to build reliable models, the estimated parameters from the measurement data must reflect the true underlying physics of the structure. Therefore, Reduced-Order Models (ROMs) can be used as the surrogate models, where the nonlinear parameters of the ROMs are having a meaningful relation with the physical parameters of the system. In this work, we propose nonlinear system identification in the context of using some recently developed ROMs which account for the kinetic energy of unmodelled modes. It is shown how ROMs may be used to represent low-order, accurate models for system identification. Identification of a nonlinear system with strong modal coupling is demonstrated, using simulated data, while the estimated ROM response shows good convergence with that of full order system. Similarly, the estimated parameters match with those of directly computed ROM.
Self-excited vibrations can be found in many engineering applications such as flutter of aerofoils, stick-slip vibrations in drill strings, and wheel shimmy. These self-excited vibrations are generally unwanted since they can cause serious damage to the system. To avoid such phenomena, an accurate mathematical model of the system is crucial. Self-excited systems are typically modelled as dynamical systems with Hopf bifurcations. The identification of such non-linear dynamical system from data is much more challenging compared to linear systems. In this research, we propose two different mathematical model identification methods for self-excited systems that use experimental bifurcation analysis data. The first method considers an empirical mathematical model whose coefficients are identified to fit the measured bifurcation diagram. The second approach considers a fundamental Hopf normal form model and learns a data-driven coordinate transformation mapping the normal form state-space to physical coordinates. The approaches developed are applied to bifurcation data collected on a two degree-of-freedom flutter rig and the two methods show promising results. The advantages and disadvantages of the methods are discussed.
This paper presents an investigation of complex mode shape analysis caused by non-linear damping. Nowadays, most academics are accustomed to complex mode shapes, which are a characteristic of most axisymmetric structures. The topic was deeply investigated during the 1980s, sparking the sharpest debates about their physical existence or not. However, after nearly three decades, one question still stands, do we know all about complex mode shapes? This paper takes the dust off this topic again and explores how complex eigenvectors arise when the percentage frequency separation between two mode shapes is the same order of magnitude as the percentage damping. The difference between the past and present investigations relates to the non-linear damping that might arise from joint dynamics under various vibration amplitudes. Hence, the new research question is about the investigation of amplitude-dependent damping on the modal complexity. Why bother? There are several engineering applications in both space and aerospace where axisymmetric structures and joint dynamics can impair the numerical analysis that is currently performed. This paper does not offer any solutions but does expand the research on an unsolved challenge by identifying the questions posed.
A parameter study is presented to determine effects of planet gear design parameters on the global modal behaviour of planetary geared rotor systems. The modal sensitivity analysis is conducted using a three-dimensional dynamic model of a planetary geared rotor system for the number of planet gears, planet mistuning, mass of planet gears, gear mesh stiffness and planet gear speed. These parameters have varying impacts on both natural frequencies and mode shapes, therefore the sensitivity of the planetary geared rotor vibration modes to the planet gear parameters is determined by computing the frequency shifts and comparing the mode shapes. The results show that the mass and mesh stiffness of planet gears have a larger influence on the global dynamic response. Torsional modes and coupled torsional-axial modes are more sensitive to gear mesh stiffness whereas lateral vibration modes are more sensitive to gearbox mass. Planet mistuning results in coupling between lateral and torsional vibrations. The planetary gearbox becomes more rigid in the torsional-axial modes and more flexible in the lateral modes with an increase in the number of planet gears. Planet gears are also found to be having significant gyroscopic effects inside the planetary gearbox. The main original findings in this study can be directly used as initial guidelines for planetary geared rotor design.
Background: The eating habits of children and adults have been impacted by the COVID-19 pandemic, with evidence of increases in snacking and emotional eating, including eating to relieve boredom. We explored the experiences of families with children aged 4-8 years who had recently participated in a healthy eating pilot trial when the first national lockdown began in England. Methods: Eleven mothers were interviewed in April and May 2020. Interview questions were developed based on the COM-B model of behaviour. Four main themes were constructed using inductive thematic analysis. Results: The first theme related to an initial panic phase, in which having enough food was the primary concern. The second related to ongoing challenges during the lockdown, with sub-themes including difficulties accessing food, managing children's food requests and balancing home and work responsibilities. The perception that energy-dense foods met families' needs during this time led to increased purchasing of (and thus exposure to) energy-dense foods. In the third theme, families described a turning point, with a desire to eat a healthier diet than they had in the early stages of the lockdown. Finally, in the fourth theme, families reported a number of strategies for adapting and encouraging a balanced diet with their children. Conclusions: Our results suggest that even if parents have the capability (e.g. knowledge) and motivation to provide a healthy diet for their family, opportunity challenges (e.g. time, access to resources, environmental stressors) mean this is not always practical. Healthy eating interventions should not assume parents lack motivation and should be sensitive to the context within which parents make feeding decisions.
Autophagosome formation involves the sequential actions of conserved ATG proteins to coordinate the lipidation of the ubiquitin-like modifier Atg8-family proteins at the nascent phagophore membrane. Although the molecular steps driving this process are well understood, the source of membranes for the expanding phagophore and their mode of delivery are only now beginning to be revealed. Here, we have used quantitative SILAC-based proteomics to identify proteins that associate with the ATG12-ATG5 conjugate, a crucial player during Atg8-family protein lipidation. Our datasets reveal a strong enrichment of regulators of clathrin-mediated vesicular trafficking, including clathrin heavy and light chains, and several clathrin adaptors. Also identified were PIK3C2A (a phosphoinositide 3-kinase involved in clathrin-mediated endocytosis) and HIP1R (a component of clathrin vesicles), and the absence of either of these proteins alters autophagic flux in cell-based starvation assays. To determine whether the ATG12-ATG5 conjugate reciprocally influences trafficking within the endocytic compartment, we captured the cell surface proteomes of autophagy-competent and autophagy-incompetent mouse embryonic fibroblasts under fed and starved conditions. We report changes in the relative proportions of individual cell surface proteins and show that cell surface levels of the SLC7A5-SLC3A2 amino acid transporter are influenced by autophagy capability. Our data provide evidence for direct regulatory coupling between the ATG12-ATG5 conjugate and the clathrin membrane trafficking system and suggest candidate membrane proteins whose trafficking within the cell may be modulated by the autophagy machinery. Abbreviations: ATG, autophagy related; BafA1, bafilomycin A1; GFP, green fluorescent protein; HIP1R, huntingtin interacting protein 1 related; MEF, mouse embryo fibroblast; PIK3C2A, phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha; SILAC, stable isotope labelling with amino acids in culture; SQSTM1, sequestosome 1; STRING, search tool for the retrieval of interacting genes/proteins.
Background: Understanding the course of post-traumatic stress disorder (PTSD) and the factors that impact this is essential to inform decisions about when and for whom screening and intervention are likely to be beneficial. Objective: To provide meta-analytic evidence of the course of recovery from PTSD in the first year following trauma, and the factors that influence that recovery. Method: We conducted a meta-analysis of observational studies of adult PTSD prevalence which included at least two assessments within the first 12 months following trauma exposure, examining prevalence statistics through to 2 years post-trauma. We examined trauma intentionality (intentional or non-intentional), PTSD assessment method (clinician or self-report), sample sex distribution, and age as moderators of PTSD prevalence over time. Results: We identified 78 eligible studies including 16,484 participants. Pooled prevalence statistics indicated that over a quarter of individuals presented with PTSD at 1 month post-trauma, with this proportion reducing by a third between 1 and 3 months. Beyond 3 months, any prevalence changes were detected over longer intervals and were small in magnitude. Intentional trauma, younger age, and female sex were associated with higher PTSD prevalence at 1 month. In addition, higher proportions of females, intentional trauma exposure, and higher baseline PTSD prevalence were each associated with larger reductions in prevalence over time. Conclusions: Recovery from PTSD following acute trauma exposure primarily occurs in the first 3 months post-trauma. Screening measures and intervention approaches offered at 3 months may better target persistent symptoms than those conducted prior to this point.
Background: Social cognitive impairments, specifically in facial emotion processing and mental state attribution, are common in post-traumatic stress disorder. However few studies so far have examined whether social cognitive ability impacts on PTSD recovery. Objective: To examine whether baseline social cognitive abilities are associated with treatment outcomes following trauma-focused therapy for PTSD. Method: This is a cohort study that will relate treatment outcomes post-discharge to baseline measures of social cognition (five tasks: Emotion Odd-One-Out Task (Oddity), Reading the Mind in the Eyes Task (RMET), Social Shapes Test (SST), Spontaneous Theory of Mind Protocol (STOMP), and Reflective Functioning Questionnaire (RFQ-8)) in people starting a course of psychological therapy for PTSD (target N = 60). The primary outcome will be pre- to post-treatment change in PTSD symptom severity (assessed using the PTSD Checklist for DSM-5). Secondary outcomes include functional impairment (assessed using the Work and Social Adjustment Scale), drop-out rate, and analyses differentiating participants with DSM-5 PTSD and ICD-11 PTSD and CPTSD. Regression models will be used to examine associations between baseline social cognitive performance and outcome measures while adjusting for potential confounders. Two pilot studies informed the development of our study protocol. The first involved qualitative analysis of interviews with nine participants with lived experience of mental health problems to inform our research questions and study protocol. The second involved trialling social cognitive tasks on 20 non-clinical participants to refine our test battery. Discussion: This study will address a gap in the literature about whether abilities in social cognition in people living with PTSD are associated with treatment-related recovery. Highlights: Impairments in social cognition are recognised in people with PTSD.Few studies have examined whether social cognitive ability is associated with recovery from PTSD.We present a study protocol, developed after pilot testing, to address this question.
Background: Self-stigma refers to the internalisation of negative societal views and stereotypes. Self-stigma has been well-characterised in the context of mental disorders such as schizophrenia but has received little attention in relation to post-traumatic stress disorder (PTSD). Objective: This work aimed to determine the prevalence of self-stigma in a sample of adults with PTSD and to establish factors associated with the internalisation of stigma in this population. Method: Participants were 194 adults (mean age 46.07 (SD = 12.39); 64.4% female; 96.6% white Caucasian; residing in the UK), who self-reported a diagnosis of PTSD and currently screened positive for the disorder according to the PTSD Checklist for DSM-5 (PCL-5). Structured interviews and validated self-report questionnaires were used to ascertain clinical and sociodemographic information for analysis. Results: The prevalence of self-stigma measured by the Internalized Stigma of Mental Illness Scale (ISMIS) was 41.2% (95% CI 34.24-48.22). There was no evidence of an association between self-stigma and gender (β = -2.975 (95% CI -7.046-1.097) p = .151), age (β = 0.007 (95% CI -0.152-0.165) p = .953), sexual trauma (β = 0.904 (95% CI -3.668-5.476) p = .697), military trauma (β = -0.571 (95% CI -4.027-7.287) p = .571). Self-stigma was associated with lower income and higher levels of anxiety (β = 5.722 (95% CI 2.922-8.522) p = <.001), depression (β = 6.937 (95% CI 4.287-9.588) p = <.000), and traumatic stress symptoms (β = 3.880 (95% CI 1.401-6.359) p = .002). Conclusions: The results indicate that self-stigma may be a significant issue among people with a diagnosis of PTSD. Further work is needed to understand the long-term impact and to develop interventions to address the internalisation of stigma in this population. Highlights: The prevalence of self-stigma among a sample of participants with PTSD was 41.2%.There was no evidence of an association between self-stigma and gender, age or sexual / military trauma.Self-stigma was associated with lower income and higher levels of anxiety, depression, and traumatic stress symptoms.
The Large Hadron Collider beauty (LHCb) experiment at CERN is undergoing an upgrade in preparation for the Run 3 data collection period at the Large Hadron Collider (LHC). As part of this upgrade, the trigger is moving to a full software implementation operating at the LHC bunch crossing rate. We present an evaluation of a CPU-based and a GPU-based implementation of the first stage of the high-level trigger. After a detailed comparison, both options are found to be viable. This document summarizes the performance and implementation details of these options, the outcome of which has led to the choice of the GPU-based implementation as the baseline.
Background Epigenetic clocks are biomarkers of ageing derived from DNA methylation levels at a subset of CpG sites. The difference between age predicted by these clocks and chronological age, termed “epigenetic age acceleration”, has been shown to predict age-related disease and mortality. We aimed to assess the prognostic value of epigenetic age acceleration and a DNA methylation-based mortality risk score with all-cause mortality in a prospective clinical cohort of individuals with head and neck cancer: Head and Neck 5000. We investigated two markers of intrinsic epigenetic age acceleration ( IEAAHorvath and IEAAHannum ), one marker of extrinsic epigenetic age acceleration ( EEAA ), one optimised to predict physiological dysregulation ( AgeAccelPheno ), one optimised to predict lifespan ( AgeAccelGrim ) and a DNA methylation-based predictor of mortality ( ZhangScore ). Cox regression models were first used to estimate adjusted hazard ratios (HR) and 95% confidence intervals (CI) for associations of epigenetic age acceleration with all-cause mortality in people with oropharyngeal cancer ( n = 408; 105 deaths). The added prognostic value of epigenetic markers compared to a clinical model including age, sex, TNM stage and HPV status was then evaluated. Results IEAAHannum and AgeAccelGrim were associated with mortality risk after adjustment for clinical and lifestyle factors (HRs per standard deviation [SD] increase in age acceleration = 1.30 [95% CI 1.07, 1.57; p = 0.007] and 1.40 [95% CI 1.06, 1.83; p = 0.016], respectively). There was weak evidence that the addition of AgeAccelGrim to the clinical model improved 3-year mortality prediction (area under the receiver operating characteristic curve: 0.80 vs. 0.77; p value for difference = 0.069). Conclusion In the setting of a large, clinical cohort of individuals with head and neck cancer, our study demonstrates the potential of epigenetic markers of ageing to enhance survival prediction in people with oropharyngeal cancer, beyond established prognostic factors. Our findings have potential uses in both clinical and non-clinical contexts: to aid treatment planning and improve patient stratification.
Background and objective Spontaneous pneumothorax is a common pathology but optimal initial treatment regime is not well defined. Treatment options including conservative management, needle aspiration (NA) or insertion of a small-bore chest drain. Recent large randomised controlled trials may change the treatment paradigm: comparing conservative and ambulatory management to standard care, but current guidelines need to be updated. The aim of this study was to assess the current “state of play” in the management of pneumothorax in the UK. Methods Physicians and respiratory healthcare staff were invited to complete an online survey on the initial and subsequent management of pneumothorax. Results This study is the first survey of pneumothorax practice across the UK, which highlights variation in practice: 50% would manage a large primary pneumothorax with minimal symptoms conservatively, compared to only 3% if there were significant symptoms; 64% use suction if the pneumothorax had not resolved after > 2 days, 15% always clamp the chest drain prior to removal; whereas 30% never do. NICE guidance recommends the use of digital suction but this has not translated into widespread usage: only 23% use digital suction to check for resolution of air leak). Conclusion Whilst there has always been allowance for individual clinician preference in guidelines, there needs to be consensus on the optimum management strategy. The challenge the new guidelines face is to design a simple and pragmatic approach, using this new evidence base.
Mendelian randomization (MR) is a term that applies to the use of genetic variation to address causal questions about how modifiable exposures influence different outcomes. The principles of MR are based on Mendel’s laws of inheritance and instrumental variable estimation methods, which enable the inference of causal effects in the presence of unobserved confounding. In this Primer, we outline the principles of MR, the instrumental variable conditions underlying MR estimation and some of the methods used for estimation. We go on to discuss how the assumptions underlying an MR study can be assessed and describe methods of estimation that are robust to certain violations of these assumptions. We give examples of a range of studies in which MR has been applied, the limitations of current methods of analysis and the outlook for MR in the future. The differences between the assumptions required for MR analysis and other forms of epidemiological studies means that MR can be used as part of a triangulation across multiple sources of evidence for causal inference. Mendelian randomization is a technique for using genetic variation to examine the causal effect of a modifiable exposure on an outcome such as disease status. This Primer by Sanderson et al. explains the concepts of and the conditions required for Mendelian randomization analysis, describes key examples of its application and looks towards applying the technique to growing genomic datasets.
There are many factors that contribute to the reproducibility and replicability of scientific research. There is a need to understand the research ecosystem, and improvements will require combined efforts across all parts of this ecosystem. National structures can play an important role in coordinating these efforts, working collaboratively with researchers, institutions, funders, publishers, learned societies and other sectoral organisations, and providing a monitoring and reporting function. Whilst many new ways of working and emerging innovations hold a great deal of promise, it will be important to invest in meta-research activity to ensure that these approaches are evidence based, work as intended, and do not have unintended consequences. Addressing reproducibility will require working collaboratively across the research ecosystem to share best practice and to make the most effective use of resources. The UK Reproducibility Network (UKRN) brings together Local Networks of researchers, Institutions, and External Stakeholders (funders, publishers, learned societies and other sectoral organisations), to coordinate action on reproducibility and work to ensure the UK retains its place as a centre for world-leading research. This activity is coordinated by the UKRN Steering Group. We consider this structure as valuable, bringing together a range of voices at a range of levels to support the combined efforts required to enact change.
Africa has seen an upsurge in diagnostic imaging utilization, with benefits of efficient and accurate diagnosis, but these could easily be offset by undesirable effects attributed to unjustified, unoptimized imaging and poor quality examinations. This paper aims to present Africa’s position regarding quality and safety in imaging, give reasons for the rising interest in quality and safety, define quality and safety from an African context, list drivers for quality and safety in Africa, discuss the impact of COVID-19 on quality and safety, and review Africa’s progress using the Bonn Call for Action framework while proposing a way forward for imaging quality and safety in Africa. In spite of a healthcare setting characterized by meagre financial, human and technology resources, a rapidly widening disease-burden spectrum, growing proportion of non-communicable diseases and resurgence of tropical and global infections, Africa has over the last ten years made significant strides in quality and safety for imaging. These include raising radiation-safety awareness, interest and application of evidence-based radiation safety recommendations and guidance tools, establishing facility and national diagnostic reference levels (DRLs) and strengthening end-user education and training. Major challenges are: limited human resource, low prioritization of imaging in relation to other health services, low level of integration of imaging into the entire health service delivery, insufficient awareness for radiation safety awareness, a radiation safety culture which is emerging, insufficient facilities and opportunities for education and training. Solutions to these challenges should target the entire hierarchy of health service delivery from prioritization, policy, planning, processes to procedures.
Background Physical activity (PA) declines during childhood. Important sources of PA are active travel, organised sport and physical education (PE), but it is unclear how these domain-specific PA sources contribute to (changes in) daily moderate-to-vigorous PA (MVPA) in young people. This study aimed to examine (1) the cross-sectional association between domain-specific physical activity (i.e., active travel, organised sport and PE) and daily minutes in accelerometer-assessed MVPA; and (2) the longitudinal association between domain-specific physical activity at baseline and change in daily minutes in MVPA. Methods Participants (baseline age 11.3 ± .1.2 years) were drawn from three studies in the International Children’s Accelerometry Database. The contribution of self-reported standardised active travel, organised sport and PE to accelerometer-measured daily minutes in MVPA was examined using linear regression. In cross-sectional analyses, MVPA was regressed on each PA domain in separate models, adjusted for study, age, sex, maternal education, season, and monitor wear time. In longitudinal analyses, change in MVPA was regressed on each of the baseline PA domains, additionally adjusting for changes in season and wear time, follow-up duration, and baseline MVPA. R-squared was used to compare variance explained by each PA domain. Results In the cross-sectional analyses ( n = 3871), organised sport (standardised β = 3.81, 95% confidence interval [95%CI] = 3.06, 4.56) and active travel (β = 3.46, 95%CI = 2.73, 4.19) contributed more to daily MVPA than PE (β = 0.82, 95%CI = -0.02, 1.66). Compared to the base model which included only covariates (R ² = 21.5%), organised sport (absolute change: + 1.9%) and active travel (+ 1.7%) models explained more of the variance than the PE model (± < 0.1%). Associations followed a similar pattern in the longitudinal analyses ( n = 2302), but none of the PA domains predicted change in MVPA (organised sport: standardised β = 0.85, 95%CI = -0.03, 1.72; active travel: β = 0.68, 95%CI = -0.14, 1.50; PE: β = 0.02, 95%CI = -0.87, 0.91). Conclusions A multi-sectoral approach covering a wide range of PA domains should be promoted to minimise the age-related decline in MVPA during childhood.
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Anastasios Sextos
  • Department of Civil Engineering
Sanjay Rawat
  • Department of Computer Science
Daniel Fudulu
  • School of Clinical Sciences
Jonathan Ives
  • Centre for Ethics in Medicine
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Woodland Road, BS8 1TH, Bristol, United Kingdom
Head of institution
Professor Hugh Redmond Brady
Website
www.bristol.ac.uk