Sequencing studies are increasingly being conducted to identify rare variants associated with complex traits. The limited power of classical single-marker association analysis for rare variants poses ...a central challenge in such studies. We propose the sequence kernel association test (SKAT), a supervised, flexible, computationally efficient regression method to test for association between genetic variants (common and rare) in a region and a continuous or dichotomous trait while easily adjusting for covariates. As a score-based variance-component test, SKAT can quickly calculate p values analytically by fitting the null model containing only the covariates, and so can easily be applied to genome-wide data. Using SKAT to analyze a genome-wide sequencing study of 1000 individuals, by segmenting the whole genome into 30 kb regions, requires only 7 hr on a laptop. Through analysis of simulated data across a wide range of practical scenarios and triglyceride data from the Dallas Heart Study, we show that SKAT can substantially outperform several alternative rare-variant association tests. We also provide analytic power and sample-size calculations to help design candidate-gene, whole-exome, and whole-genome sequence association studies.
This paper builds on a recently developed immersogeometric fluid–structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed ...framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart.
High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Distance-based analysis is a popular strategy ...for evaluating the overall association between microbiome diversity and outcome, wherein the phylogenetic distance between individuals’ microbiome profiles is computed and tested for association via permutation. Despite their practical popularity, distance-based approaches suffer from important challenges, especially in selecting the best distance and extending the methods to alternative outcomes, such as survival outcomes. We propose the microbiome regression-based kernel association test (MiRKAT), which directly regresses the outcome on the microbiome profiles via the semi-parametric kernel machine regression framework. MiRKAT allows for easy covariate adjustment and extension to alternative outcomes while non-parametrically modeling the microbiome through a kernel that incorporates phylogenetic distance. It uses a variance-component score statistic to test for the association with analytical p value calculation. The model also allows simultaneous examination of multiple distances, alleviating the problem of choosing the best distance. Our simulations demonstrated that MiRKAT provides correctly controlled type I error and adequate power in detecting overall association. “Optimal” MiRKAT, which considers multiple candidate distances, is robust in that it suffers from little power loss in comparison to when the best distance is used and can achieve tremendous power gain in comparison to when a poor distance is chosen. Finally, we applied MiRKAT to real microbiome datasets to show that microbial communities are associated with smoking and with fecal protease levels after confounders are controlled for.
The transcatheter aortic valve replacement (TAVR) has emerged as a minimally invasive alternative to surgical treatments of valvular heart disease. TAVR offers many advantages, however, the safe ...anchoring of the transcatheter heart valve (THV) in the patient’s anatomy is key to a successful procedure. In this paper, we develop and apply a novel immersogeometric fluid–structure interaction (FSI) framework for the modeling and simulation of the TAVR procedure to study the anchoring ability of the THV. To account for physiological realism, methods are proposed to model and couple the main components of the system, including the arterial wall, blood flow, valve leaflets, skirt, and frame. The THV is first crimped and deployed into an idealized ascending aorta. During the FSI simulation, the radial outward force and friction force between the aortic wall and the THV frame are examined over the entire cardiac cycle. The ratio between these two forces is computed and compared with the experimentally estimated coefficient of friction to study the likelihood of valve migration.
•An immersogeometric analysis framework for transcatheter heart valves is proposed.•Components of the transcatheter heart valves are modeled and coupled.•Validation of the proposed structural and fluid mechanics methods is presented.•The framework is applied to the simulation of transcatheter aortic valve replacement.•Static friction is considered to study the risk of migration.
This paper considers an anisotropic hyperelastic soft tissue model, originally proposed for native valve tissue and referred to herein as the Lee–Sacks model, in an isogeometric thin shell analysis ...framework that can be readily combined with immersogeometric fluid–structure interaction (FSI) analysis for high-fidelity simulations of bioprosthetic heart valves (BHVs) interacting with blood flow. We find that the Lee–Sacks model is well-suited to reproduce the anisotropic stress–strain behavior of the cross-linked bovine pericardial tissues that are commonly used in BHVs. An automated procedure for parameter selection leads to an instance of the Lee–Sacks model that matches biaxial stress–strain data from the literature more closely, over a wider range of strains, than other soft tissue models. The relative simplicity of the Lee–Sacks model is attractive for computationally-demanding applications such as FSI analysis and we use the model to demonstrate how the presence and direction of material anisotropy affect the FSI dynamics of BHV leaflets.
With development of massively parallel sequencing technologies, there is a substantial need for developing powerful rare variant association tests. Common approaches include burden and non-burden ...tests. Burden tests assume all rare variants in the target region have effects on the phenotype in the same direction and of similar magnitude. The recently proposed sequence kernel association test (SKAT) (Wu, M. C., and others, 2011. Rare-variant association testing for sequencing data with the SKAT. The American Journal of Human Genetics 89, 82-93, an extension of the C-alpha test (Neale, B. M., and others, 2011. Testing for an unusual distribution of rare variants. PLoS Genetics 7, 161-165, provides a robust test that is particularly powerful in the presence of protective and deleterious variants and null variants, but is less powerful than burden tests when a large number of variants in a region are causal and in the same direction. As the underlying biological mechanisms are unknown in practice and vary from one gene to another across the genome, it is of substantial practical interest to develop a test that is optimal for both scenarios. In this paper, we propose a class of tests that include burden tests and SKAT as special cases, and derive an optimal test within this class that maximizes power. We show that this optimal test outperforms burden tests and SKAT in a wide range of scenarios. The results are illustrated using simulation studies and triglyceride data from the Dallas Heart Study. In addition, we have derived sample size/power calculation formula for SKAT with a new family of kernels to facilitate designing new sequence association studies.
System identification is a growing approach to sensory neurophysiology that facilitates the development of quantitative functional models of sensory processing. This approach provides a clear set of ...guidelines for combining experimental data with other knowledge about sensory function to obtain a description that optimally predicts the way that neurons process sensory information. This prediction paradigm provides an objective method for evaluating and comparing computational models. In this chapter we review many of the system identification algorithms that have been used in sensory neurophysiology, and we show how they can be viewed as variants of a single statistical inference problem. We then review many of the practical issues that arise when applying these methods to neurophysiological experiments: stimulus selection, behavioral control, model visualization, and validation. Finally we discuss several problems to which system identification has been applied recently, including one important long-term goal of sensory neuroscience: developing models of sensory systems that accurately predict neuronal responses under completely natural conditions.
A recently introduced NURBS mesh generation method for complex-geometry Isogeometric Analysis (IGA) is applied to building a high-quality mesh for a gas turbine. The compressible flow in the turbine ...is computed using the IGA and a stabilized method with improved discontinuity-capturing, weakly-enforced no-slip boundary-condition, and sliding-interface operators. The IGA results are compared with the results from the stabilized finite element simulation to reveal superior performance of the NURBS-based approach. Free-vibration analysis of the turbine rotor using the structural mechanics NURBS mesh is also carried out and shows that the NURBS mesh generation method can be used also in structural mechanics analysis. With the flow field from the NURBS-based turbine flow simulation, the Courant number is computed based on the NURBS mesh local length scale in the flow direction to show some of the other positive features of the mesh generation framework. The work presented further advances the IGA as a fully-integrated and robust design-to-analysis framework, and the IGA-based complex-geometry flow computation with moving boundaries and interfaces represents the first of its kind for compressible flows.
Valvular heart disease has recently become an increasing public health concern due to the high prevalence of valve degeneration in aging populations. For patients with severely impacted aortic valves ...that require replacement, catheter-based bioprosthetic valve deployment offers a minimally invasive treatment option that eliminates many of the risks associated with surgical valve replacement. Although recent percutaneous device advancements have incorporated thinner, more flexible biological tissues to streamline safer deployment through catheters, the impact of such tissues in the complex, mechanically demanding, and highly dynamic valvular system remains poorly understood. The present work utilized a validated computational fluid–structure interaction approach to isolate the behavior of thinner, more compliant aortic valve tissues in a physiologically realistic system. This computational study identified and quantified significant leaflet flutter induced by the use of thinner tissues that initiated blood flow disturbances and oscillatory leaflet strains. The aortic flow and valvular dynamics associated with these thinner valvular tissues have not been previously identified and provide essential information that can significantly advance fundamental knowledge about the cardiac system and support future medical device innovation. Considering the risks associated with such observed flutter phenomena, including blood damage and accelerated leaflet deterioration, this study demonstrates the potentially serious impact of introducing thinner, more flexible tissues into the cardiac system.
Surgical care episodes place opioid-naïve patients at risk for transitioning to new persistent postoperative opioid use. With one of the central principles being the application of multimodal pain ...interventions to reduce the reliance on opioid-based medications, enhanced recovery pathways provide a framework that decreases perioperative opioid use. The fourth Perioperative Quality Initiative brought together a group of international experts representing anesthesiology, surgery, and nursing with the objective of providing consensus recommendations on this important topic. Fourth Perioperative Quality Initiative was a consensus-building conference designed around a modified Delphi process in which the group alternately convened for plenary discussion sessions in between small group discussions. The process included several iterative steps including a literature review of the topics, building consensus around the important questions related to the topic, and sequential steps of content building and refinement until agreement was achieved and a consensus document was produced. During the fourth Perioperative Quality Initiative conference and thereafter as a writing group, reference applicability to the topic was discussed in any area where there was disagreement. For this manuscript, the questions answered included (1) What are the potential strategies for preventing persistent postoperative opioid use? (2) Is opioid-free anesthesia and analgesia feasible and appropriate for routine operations? and (3) Is opioid-free (intraoperative) anesthesia associated with equivalent or superior outcomes compared to an opioid minimization in the perioperative period? We will discuss the relevant literature for each questions, emphasize what we do not know, and prioritize the areas for future research.
PDF
