Feasibility of MR-Based Body Composition Analysis in Large Scale Population Studies

Introduction Quantitative and accurate measurements of fat and muscle in the body are important for prevention and diagnosis of diseases related to obesity and muscle degeneration. Manually segmenting muscle and fat compartments in MR body-images is laborious and time-consuming, hindering implementation in large cohorts. In the present study, the feasibility and success-rate of a Dixon-based MR scan followed by an intensity-normalised, non-rigid, multi-atlas based segmentation was investigated in a cohort of 3,000 subjects. Materials and Methods 3,000 participants in the in-depth phenotyping arm of the UK Biobank imaging study underwent a comprehensive MR examination. All subjects were scanned using a 1.5 T MR-scanner with the dual-echo Dixon Vibe protocol, covering neck to knees. Subjects were scanned with six slabs in supine position, without localizer. Automated body composition analysis was performed using the AMRA Profiler™ system, to segment and quantify visceral adipose tissue (VAT), abdominal subcutaneous adipose tissue (ASAT) and thigh muscles. Technical quality assurance was performed and a standard set of acceptance/rejection criteria was established. Descriptive statistics were calculated for all volume measurements and quality assurance metrics. Results Of the 3,000 subjects, 2,995 (99.83%) were analysable for body fat, 2,828 (94.27%) were analysable when body fat and one thigh was included, and 2,775 (92.50%) were fully analysable for body fat and both thigh muscles. Reasons for not being able to analyse datasets were mainly due to missing slabs in the acquisition, or patient positioned so that large parts of the volume was outside of the field-of-view. Discussion and Conclusions In conclusion, this study showed that the rapid UK Biobank MR-protocol was well tolerated by most subjects and sufficiently robust to achieve very high success-rate for body composition analysis. This research has been conducted using the UK Biobank Resource.

Optimising power take-off of an oscillating wave surge converter using high fidelity numerical simulations

Oscillating wave surge converters are a promising technology to harvest ocean wave energy in the near shore region. Although research has been going on for many years, the characteristics of the wave action on the structure and especially the phase relation between the driving force and wave quantities like velocity or surface elevation have not been investigated in detail. The main reason for this is the lack of suitable methods. Experimental investigations using tank tests do not give direct access to overall hydrodynamic loads, only damping torque of a power take off system can be measured directly. Non-linear computational fluid dynamics methods have only recently been applied in the research of this type of devices. This paper presents a new metric named wave torque, which is the total hydrodynamic torque minus the still water pitch stiffness at any given angle of rotation. Changes in characteristics of that metric over a wave cycle and for different power take off settings are investigated using computational fluid dynamics methods. Firstly, it is shown that linearised methods cannot predict optimum damping in typical operating states of OWSCs. We then present phase relationships between main kinetic parameters for different damping levels. Although the flap seems to operate close to resonance, as predicted by linear theory, no obvious condition defining optimum damping is found.

Secrecy Capacity Analysis Over κ–μ Fading Channels: Theory and Applications

In this paper, we consider the transmission of confidential information over a κ-μ fading channel in the presence of an eavesdropper who also experiences κ-μ fading. In particular, we obtain novel analytical solutions for the probability of strictly positive secrecy capacity (SPSC) and a lower bound of secure outage probability (SOPL) for independent and non-identically distributed channel coefficients without parameter constraints. We also provide a closed-form expression for the probability of SPSC when the μ parameter is assumed to take positive integer values. Monte-Carlo simulations are performed to verify the derived results. The versatility of the κ-μ fading model means that the results presented in this paper can be used to determine the probability of SPSC and SOPL for a large number of other fading scenarios, such as Rayleigh, Rice (Nakagamin), Nakagami-m, One-Sided Gaussian, and mixtures of these common fading models. In addition, due to the duality of the analysis of secrecy capacity and co-channel interference (CCI), the results presented here will have immediate applicability in the analysis of outage probability in wireless systems affected by CCI and background noise (BN). To demonstrate the efficacy of the novel formulations proposed here, we use the derived equations to provide a useful insight into the probability of SPSC and SOPL for a range of emerging wireless applications, such as cellular device-to-device, peer-to-peer, vehicle-to-vehicle, and body centric communications using data obtained from real channel measurements.

Three-dimensional simulations of gravitationally confined detonations compared to observations of SN 1991T

The gravitationally confined detonation (GCD) model has been proposed as a possible explosion mechanism for Type Ia supernovae in the single-degenerate evolution channel. It starts with ignition of a deflagration in a single off-centre bubble in a near-Chandrasekhar-mass white dwarf. Driven by buoyancy, the deflagration flame rises in a narrow cone towards the surface. For the most part, the main component of the flow of the expanding ashes remains radial, but upon reaching the outer, low-pressure layers of the white dwarf, an additional lateral component develops. This causes the deflagration ashes to converge again at the opposite side, where the compression heats fuel and a detonation may be launched. We first performed five three-dimensional hydrodynamic simulations of the deflagration phase in 1.4 M⊙ carbon/oxygen white dwarfs at intermediate-resolution (2563computational zones). We confirm that the closer the initial deflagration is ignited to the centre, the slower the buoyant rise and the longer the deflagration ashes takes to break out and close in on the opposite pole to collide. To test the GCD explosion model, we then performed a high-resolution (5123 computational zones) simulation for a model with an ignition spot offset near the upper limit of what is still justifiable, 200 km. This high-resolution simulation met our deliberately optimistic detonation criteria, and we initiated a detonation. The detonation burned through the white dwarf and led to its complete disruption. For this model, we determined detailed nucleosynthetic yields by post-processing 106 tracer particles with a 384 nuclide reaction network, and we present multi-band light curves and time-dependent optical spectra. We find that our synthetic observables show a prominent viewing-angle sensitivity in ultraviolet and blue wavelength bands, which contradicts observed SNe Ia. The strong dependence on the viewing angle is caused by the asymmetric distribution of the deflagration ashes in the outer ejecta layers. Finally, we compared our model to SN 1991T. The overall flux level of the model is slightly too low, and the model predicts pre-maximum light spectral features due to Ca, S, and Si that are too strong. Furthermore, the model chemical abundance stratification qualitatively disagrees with recent abundance tomography results in two key areas: our model lacks low-velocity stable Fe and instead has copious amounts of high-velocity 56Ni and stable Fe. We therefore do not find good agreement of the model with SN 1991T.

Dietary exposure assessments for children in Europe (the EXPOCHI project): rationale, methods and design

[EN]The number of dietary exposure assessment studies focussing on children is very limited. Children are however a vulnerable group due to their higher food consumption level per kg body weight. Therefore, the EXPOCHI project aims [1] to create a relational network of individual food consumption databases in children, covering different geographical areas within Europe, and [2] to use these data to assess the usual intake of lead, chromium, selenium and food colours.

Methods for Hypothesis Testing in Animal Carcinogenicity Experiments

Thesis (Ph.D.)--University of Washington, 2016-08

Objective Methods for Characterizing Physical Exposures which may contribute to Work-related Musculoskeletal Disorders in Agricultural Workers

Thesis (Ph.D.)--University of Washington, 2016-08

Load balancing for aspect ratio in adaptive finite element simulations

In parallel adaptive finite element simulations the work load on the individual processors may change frequently. To (re)distribute the load evenly over the processors a load balancing heuristic is needed. Common strategies try to minimise subdomain dependencies by optimising the cutsize of the partitioning. However for certain solvers cutsize only plays a minor role, and their convergence is highly dependent on the subdomain shapes. Degenerated subdomain shapes cause them to need significantly more iterations to converge. In this work a new parallel load balancing strategy is introduced which directly addresses the problem of generating and conserving reasonably good subdomain shapes in a dynamically changing Finite Element Simulation. Geometric data is used to formulate several cost functions to rate elements in terms of their suitability to be migrated. The well known diffusive method which calculates the necessary load flow is enhanced by weighting the subdomain edges with the help of these cost functions. The proposed methods have been tested and results are presented.

Resting energy expenditure, macronutrient utilization, and body composition in term infants after corrective surgery of major congenital anomalies: a case-study

Introduction - Knowledge on the metabolic changes and nutritional needs during the postsurgical anabolic phase in infants is scarce. This analysis explores the associations of resting energy expenditure (REE) and macronutrient utilization with body composition of full-term infants, during catch-up growth after corrective surgery of major congenital anomalies. Methods - A cohort of full-term appropriate for-gestational-age neonates subjected to corrective surgery of major congenital anomalies were recruited after gaining weight for at least one week. REE and macronutrient utilization, measured by respiratory quotient (RQ), were assessed by indirect calorimetry using the Deltatrac II Metabolic Monitor ®. Body composition, expressed as fat-free mass (FFM), fat mass (FM) and adiposity defined as percentage of FM (% FM), was measured by air displacement plethysmography using the Pea Pod ®. Results - Four infants were included at 3 to 5 postnatal weeks. Recommended energy and macronutrient intakes for healthy term infants were provided. Through the study, the median (min-max) REE (Kcal/Kg FFM/d) was 70.8 (60.6-96.1) and RQ was 0.99 (0.72-1.20). Steady increases in both body weight and FFM were associated with initial decrease in FM and adiposity followed by their increase. Low RQ preceded decrease in adiposity. Conclusion - The marked adiposity depletion, not expected during steady weight gain in the postsurgical period, prompts us to report this finding. The subsequent adiposity catch-up was associated with relatively high REE and RQ, suggesting preferential oxidation of carbohydrates and preservation of lipids for fat storage.

Specimen generation approaches for DEM simulations.

Discrete Element Method (DEM) simulations ofelement tests cam provide significant insight into the micro-mechanics of soil response. It is well established that soil behaviour is strongly dependant on the initial density. Generation of particulate assemblies for three-dimensional DEM analyses must therefore allow for void ratio control. In this paper, different specimen generation approaches for DEM analyses are discussed. A methodology for the generation of assemblies of spherical particles with a specified initial density and stress state is presented. The effects of the different preparation methods on the specimen fabric are then considered in detail. For isotropic consolidation, it is shown that varying the coefficient of inter-particle friction allows control of the specimen void ratio at a specified confining stress. Simulations of anisotropic consolidation, from an initial isotropic stress state, to a final state where sigma(3) = K(0)sigma(1) indicated that the specimen void ratio and fabric are relatively insensitive to the intermediate stress path, provided an intermediate stress along the K(0) line was attained.

Evolution of soil fabric and its interpretation using different methods.

Different methods to study the evolution of fabric anisotropy are presented. DEM simulations on assemblies of spheres subjected to different stress paths using a three-dimensional periodic cell are used for the analysis of these methods. The links between soil fabric and macro-scale behaviour are also discussed.

Analysis of Molecular Dynamics Simulations of Protein Folding

Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics over many milliseconds will become available. Since these timescales match the physiological timescales over which many small proteins fold, all atom MD simulations of protein folding are now becoming popular. To distill features of such large folding trajectories, we must develop methods that can both compress trajectory data to enable visualization, and that can yield themselves to further analysis, such as the finding of collective coordinates and reduction of the dynamics. Conventionally, clustering has been the most popular MD trajectory analysis technique, followed by principal component analysis (PCA). Simple clustering used in MD trajectory analysis suffers from various serious drawbacks, namely, (i) it is not data driven, (ii) it is unstable to noise and change in cutoff parameters, and (iii) since it does not take into account interrelationships amongst data points, the separation of data into clusters can often be artificial. Usually, partitions generated by clustering techniques are validated visually, but such validation is not possible for MD trajectories of protein folding, as the underlying structural transitions are not well understood. Rigorous cluster validation techniques may be adapted, but it is more crucial to reduce the dimensions in which MD trajectories reside, while still preserving their salient features. PCA has often been used for dimension reduction and while it is computationally inexpensive, being a linear method, it does not achieve good data compression. In this thesis, I propose a different method, a nonmetric multidimensional scaling (nMDS) technique, which achieves superior data compression by virtue of being nonlinear, and also provides a clear insight into the structural processes underlying MD trajectories. I illustrate the capabilities of nMDS by analyzing three complete villin headpiece folding and six norleucine mutant (NLE) folding trajectories simulated by Freddolino and Schulten [1]. Using these trajectories, I make comparisons between nMDS, PCA and clustering to demonstrate the superiority of nMDS. The three villin headpiece trajectories showed great structural heterogeneity. Apart from a few trivial features like early formation of secondary structure, no commonalities between trajectories were found. There were no units of residues or atoms found moving in concert across the trajectories. A flipping transition, corresponding to the flipping of helix 1 relative to the plane formed by helices 2 and 3 was observed towards the end of the folding process in all trajectories, when nearly all native contacts had been formed. However, the transition occurred through a different series of steps in all trajectories, indicating that it may not be a common transition in villin folding. The trajectories showed competition between local structure formation/hydrophobic collapse and global structure formation in all trajectories. Our analysis on the NLE trajectories confirms the notion that a tight hydrophobic core inhibits correct 3-D rearrangement. Only one of the six NLE trajectories folded, and it showed no flipping transition. All the other trajectories get trapped in hydrophobically collapsed states. The NLE residues were found to be buried deeply into the core, compared to the corresponding lysines in the villin headpiece, thereby making the core tighter and harder to undo for 3-D rearrangement. Our results suggest that the NLE may not be a fast folder as experiments suggest. The tightness of the hydrophobic core may be a very important factor in the folding of larger proteins. It is likely that chaperones like GroEL act to undo the tight hydrophobic core of proteins, after most secondary structure elements have been formed, so that global rearrangement is easier. I conclude by presenting facts about chaperone-protein complexes and propose further directions for the study of protein folding.

Adhesion molecules and chemokines: relation to anthropometric, body composition, biochemical and dietary variables

Introduction: Among the inflammatory mediators involved in the pathogenesis of obesity, the cell adhesion molecules P-selectin, E-selectin, VCAM-1, ICAM-1 and the chemokine MCP-1 stand out. They play a crucial role in adherence of cells to endothelial surfaces, in the integrity of the vascular wall and can be modulated by body composition and dietary pattern. Objectives: To describe and discuss the relation of these cell adhesion molecules and chemokines to anthropometric, body composition, dietary and biochemical markers. Methods: Papers were located using scientific databases by topic searches with no restriction on year of publication. Results: All molecules were associated positively with anthropometric markers, but controversial results were found for ICAM-1 and VCAM-1. Not only obesity, but visceral fat is more strongly correlated with E-selectin and MCP-1 levels. Weight loss influences the reduction in the levels of these molecules, except VCAM-1. The distribution of macronutrients, excessive consumption of saturated and trans fat and a Western dietary pattern are associated with increased levels. The opposite could be observed with supplementation of w-3 fatty acid, healthy dietary pattern, high calcium diet and high dairy intake. Regarding the biochemical parameters, they have inverse relation to HDLC and positive relation to total cholesterol, triglycerides, blood glucose, fasting insulin and insulin resistance. Conclusion: Normal anthropometric indicators, body composition, biochemical parameters and eating pattern positively modulate the subclinical inflammation that results from obesity by reducing the cell adhesion molecules and chemokines.

Assessments of body composition and bone parameters of lactating rats treated with diet containing flaxseed meal (Linum usitatissinum) during post-weaning period

Introduction: There are few studies on body composition and the effects of diet on weight postpartum women. The aim was to evaluate the body composition and bone parameters in lactating rats treated with diet containing flaxseed flour during postweaning period. Methods: After weaning, the lactating rat were divided in control (n = 6) and experimental (F, n = 6) group, treated with 25% flaxseed flour diet. After 30 days, body composition by dual-energy X-ray absorptiometry, serum analysis, organs and intra-abdominal fat mass, femur and lumbar vertebra parameters were determined. Results: The groups showed similar food intake, body mass and bone parameters. While F group showed the following: lower body (-5%), gonadal (-17%), mesenteric (-23%) and intra-abdominal (-6%) fat mass. Increase of HDL-cholesterol (+10%) and lower glucose (-15%), triglycerides (P < 0.05, -37%) and cholesterol (P < 0.05, -21%). Conclusions: The findings highlight the effects of flaxseed for control of adiposity and to maintain a healthy biochemical profile during the postnatal period.