Martin BerzinsParallel ComputingGPUs |
Mike KirbyFinite Element MethodsUncertainty Quantification GPUs |
Valerio PascucciScientific Data Management |
Chris JohnsonProblem Solving Environments |
Ross WhitakerGPUs |
Chuck HansenGPUs |
Modeling 4D changes in pathological anatomy using domain adaptation: analysis of TBI imaging using a tumor database Bo Wang, M. Prastawa, A. Saha, S.P. Awate, A. Irimia, M.C. Chambers, P.M. Vespa, J.D. Van Horn, V. Pascucci, G. Gerig. In Proceedings of the 2013 MICCAI-MBIA Workshop, Lecture Notes in Computer Science (LNCS), Vol. 8159, Note: Awarded Best Paper!, pp. 31--39. 2013. DOI: 10.1007/978-3-319-02126-3_4 Analysis of 4D medical images presenting pathology (i.e., lesions) is signi cantly challenging due to the presence of complex changes over time. Image analysis methods for 4D images with lesions need to account for changes in brain structures due to deformation, as well as the formation and deletion of new structures (e.g., edema, bleeding) due to the physiological processes associated with damage, intervention, and recovery. We propose a novel framework that models 4D changes in pathological anatomy across time, and provides explicit mapping from a healthy template to subjects with pathology. Moreover, our framework uses transfer learning to leverage rich information from a known source domain, where we have a collection of completely segmented images, to yield effective appearance models for the input target domain. The automatic 4D segmentation method uses a novel domain adaptation technique for generative kernel density models to transfer information between different domains, resulting in a fully automatic method that requires no user interaction. We demonstrate the effectiveness of our novel approach with the analysis of 4D images of traumatic brain injury (TBI), using a synthetic tumor database as the source domain. |
A new discrete element analysis method for predicting hip joint contact stresses C.L. Abraham, S.A. Maas, J.A. Weiss, B.J. Ellis, C.L. Peters, A.E. Anderson. In Journal of Biomechanics, Vol. 46, No. 6, pp. 1121--1127. 2013. DOI: 10.1016/j.jbiomech.2013.01.012 Quantifying cartilage contact stress is paramount to understanding hip osteoarthritis. Discrete element analysis (DEA) is a computationally efficient method to estimate cartilage contact stresses. Previous applications of DEA have underestimated cartilage stresses and yielded unrealistic contact patterns because they assumed constant cartilage thickness and/or concentric joint geometry. The study objectives were to: (1) develop a DEA model of the hip joint with subject-specific bone and cartilage geometry, (2) validate the DEA model by comparing DEA predictions to those of a validated finite element analysis (FEA) model, and (3) verify both the DEA and FEA models with a linear-elastic boundary value problem. Springs representing cartilage in the DEA model were given lengths equivalent to the sum of acetabular and femoral cartilage thickness and gap distance in the FEA model. Material properties and boundary/loading conditions were equivalent. Walking, descending, and ascending stairs were simulated. Solution times for DEA and FEA models were ∼7 s and ∼65 min, respectively. Irregular, complex contact patterns predicted by DEA were in excellent agreement with FEA. DEA contact areas were 7.5%, 9.7% and 3.7% less than FEA for walking, descending stairs, and ascending stairs, respectively. DEA models predicted higher peak contact stresses (9.8–13.6 MPa) and average contact stresses (3.0–3.7 MPa) than FEA (6.2–9.8 and 2.0–2.5 MPa, respectively). DEA overestimated stresses due to the absence of the Poisson's effect and a direct contact interface between cartilage layers. Nevertheless, DEA predicted realistic contact patterns when subject-specific bone geometry and cartilage thickness were used. This DEA method may have application as an alternative to FEA for pre-operative planning of joint-preserving surgery such as acetabular reorientation during peri-acetabular osteotomy. |
Three-dimensional Quantification of Femoral Head Shape in Controls and Patients with Cam-type Femoroacetabular Impingement M.D. Harris, S.P. Reese, C.L. Peters, J.A. Weiss, A.E. Anderson. In Annals of Biomedical Engineering, Vol. 41, No. 6, pp. 1162--1171. 2013. DOI: 10.1007/s10439-013-0762-1 An objective measurement technique to quantify 3D femoral head shape was developed and applied to normal subjects and patients with cam-type femoroacetabular impingement (FAI). 3D reconstructions were made from high-resolution CT images of 15 cam and 15 control femurs. Femoral heads were fit to ideal geometries consisting of rotational conchoids and spheres. Geometric similarity between native femoral heads and ideal shapes was quantified. The maximum distance native femoral heads protruded above ideal shapes and the protrusion area were measured. Conchoids provided a significantly better fit to native femoral head geometry than spheres for both groups. Cam-type FAI femurs had significantly greater maximum deviations (4.99 ± 0.39 mm and 4.08 ± 0.37 mm) than controls (2.41 ± 0.31 mm and 1.75 ± 0.30 mm) when fit to spheres or conchoids, respectively. The area of native femoral heads protruding above ideal shapes was significantly larger in controls when a lower threshold of 0.1 mm (for spheres) and 0.01 mm (for conchoids) was used to define a protrusion. The 3D measurement technique described herein could supplement measurements of radiographs in the diagnosis of cam-type FAI. Deviations up to 2.5 mm from ideal shapes can be expected in normal femurs while deviations of 4–5 mm are characteristic of cam-type FAI. |
Data and Range-Bounded Polynomials in ENO Methods M. Berzins. In Journal of Computational Science, Vol. 4, No. 1-2, pp. 62--70. 2013. DOI: 10.1016/j.jocs.2012.04.006 Essentially Non-Oscillatory (ENO) methods and Weighted Essentially Non-Oscillatory (WENO) methods are of fundamental importance in the numerical solution of hyperbolic equations. A key property of such equations is that the solution must remain positive or lie between bounds. A modification of the polynomials used in ENO methods to ensure that the modified polynomials are either bounded by adjacent values (data-bounded) or lie within a specified range (range-bounded) is considered. It is shown that this approach helps both in the range boundedness in the preservation of extrema in the ENO polynomial solution. |
Effect of deltoid tension and humeral version in reverse total shoulder arthroplasty: a biomechanical study H.B. Henninger, Barg A, A.E. Anderson, K.N. Bachus, R.Z. Tashjian, R.T. Burks. In Journal of Shoulder and Elbow Surgery, Vol. 21, No. 4, pp. 483–-490. 2012. DOI: 10.1016/j.jse.2011.01.040 Background Materials and methods Results Conclusion Keywords: Shoulder, reverse arthroplasty, deltoid tension, humeral version, biomechanical simulator |
Extreme-Scale Visual Analytics P.C. Wong, H. Shen, V. Pascucci. In IEEE Computer Graphics and Applications, Vol. 32, No. 4, pp. 23--25. 2012. DOI: 10.1109/MCG.2012.73 Extreme-scale visual analytics (VA) is about applying VA to extreme-scale data. The articles in this special issue examine advances related to extreme-scale VA problems, their analytical and computational challenges, and their real-world applications. |
Atrial Fibrosis Quantified Using Late Gadolinium Enhancement MRI is AssociatedWith Sinus Node Dysfunction Requiring Pacemaker Implant N.W. Akoum, C.J. McGann, G. Vergara, T. Badger, R. Ranjan, C. Mahnkopf, E.G. Kholmovski, R.S. Macleod, N.F. Marrouche. In Journal of Cardiovascular Electrophysiology, Vol. 23, No. 1, pp. 44--50. 2012. DOI: 10.1111/j.1540-8167.2011.02140.x Atrial Fibrosis and Sinus Node Dysfunction. Introduction: Sinus node dysfunction (SND) commonly manifests with atrial arrhythmias alternating with sinus pauses and sinus bradycardia. The underlying process is thought to be because of atrial fibrosis. We assessed the value of atrial fibrosis, quantified using Late Gadolinium Enhanced-MRI (LGE-MRI), in predicting significant SND requiring pacemaker implant. Methods: Three hundred forty-four patients with atrial fibrillation (AF) presenting for catheter ablation underwent LGE-MRI. Left atrial (LA) fibrosis was quantified in all patients and right atrial (RA) fibrosis in 134 patients. All patients underwent catheter ablation with pulmonary vein isolation with posterior wall and septal debulking. Patients were followed prospectively for 329 ± 245 days. Ambulatory monitoring was instituted every 3 months. Symptomatic pauses and bradycardia were treated with pacemaker implantation per published guidelines. Results: The average patient age was 65 ± 12 years. The average wall fibrosis was 16.7 ± 11.1% in the LA, and 5.3 ± 6.4% in the RA. RA fibrosis was correlated with LA fibrosis (R^{2}= 0.26; P < 0.01). Patients were divided into 4 stages of LA fibrosis (Utah I: 35%). Twenty-two patients (mean atrial fibrosis, 23.9%) required pacemaker implantation during follow-up. Univariate and multivariate analysis identified LA fibrosis stage (OR, 2.2) as a significant predictor for pacemaker implantation with an area under the curve of 0.704. Conclusions: In patients with AF presenting for catheter ablation, LGE-MRI quantification of atrial fibrosis demonstrates preferential LA involvement. Significant atrial fibrosis is associated with clinically significant SND requiring pacemaker implantation. (J Cardiovasc Electrophysiol, Vol. 23, pp. 44-50, January 2012) |
30 Generation of Cloned Transgenic Goats with Cardiac Specific Overexpression of Transforming Growth Factor β1 Q. Meng, J. Hall, H. Rutigliano, X. Zhou, B.R. Sessions, R. Stott, K. Panter, C.J. Davies, R. Ranjan, D. Dosdall, R.S. MacLeod, N. Marrouche, K.L. White, Z. Wang, I.A. Polejaeva. In Reproduction, Fertility and Development, Vol. 25, No. 1, pp. 162--163. 2012. DOI: 10.1071/RDv25n1Ab30 Transforming growth factor β1 (TGF-β1) has a potent profibrotic function and is central to signaling cascades involved in interstitial fibrosis, which plays a critical role in the pathobiology of cardiomyopathy and contributes to diastolic and systolic dysfunction. In addition, fibrotic remodeling is responsible for generation of re-entry circuits that promote arrhythmias (Bujak and Frangogiannis 2007 Cardiovasc. Res. 74, 184–195). Due to the small size of the heart, functional electrophysiology of transgenic mice is problematic. Large transgenic animal models have the potential to offer insights into conduction heterogeneity associated with fibrosis and the role of fibrosis in cardiovascular diseases. The goal of this study was to generate transgenic goats overexpressing an active form of TGFβ-1 under control of the cardiac-specific α-myosin heavy chain promoter (α-MHC). A pcDNA3.1DV5-MHC-TGF-β1cys^{33}ser vector was constructed by subcloning the MHC-TGF-β1 fragment from the plasmid pUC-BM20-MHC-TGF-β1 (Nakajima et al. 2000 Circ. Res. 86, 571–579) into the pcDNA3.1D V5 vector. The Neon transfection system was used to electroporate primary goat fetal fibroblasts. After G418 selection and PCR screening, transgenic cells were used for SCNT. Oocytes were collected by slicing ovaries from an abattoir and matured in vitro in an incubator with 5\% CO_{2} in air. Cumulus cells were removed at 21 to 23 h post-maturation. Oocytes were enucleated by aspirating the first polar body and nearby cytoplasm by micromanipulation in Hepes-buffered SOF medium with 10 µg of cytochalasin B mL^{–1}. Transgenic somatic cells were individually inserted into the perivitelline space and fused with enucleated oocytes using double electrical pulses of 1.8 kV cm^{–1} (40 µs each). Reconstructed embryos were activated by ionomycin (5 min) and DMAP and cycloheximide (CHX) treatments. Cloned embryos were cultured in G1 medium for 12 to 60 h in vitro and then transferred into synchronized recipient females. Pregnancy was examined by ultrasonography on day 30 post-transfer. A total of 246 cloned embryos were transferred into 14 recipients that resulted in production of 7 kids. The pregnancy rate was higher in the group cultured for 12 h compared with those cultured 36 to 60 h [44.4\% (n = 9) v. 20\% (n = 5)]. The kidding rates per embryo transferred of these 2 groups were 3.8\% (n = 156) and 1.1\% (n = 90), respectively. The PCR results confirmed that all the clones were transgenic. Phenotype characterization [e.g. gene expression, electrocardiogram (ECG), and magnetic resonance imaging (MRI)] is underway. We demonstrated successful production of transgenic goat via SCNT. To our knowledge, this is the first transgenic goat model produced for cardiovascular research. |
Stochastic Collocation for Optimal Control Problems with Stochastic PDE Constraints H. Tiesler, R.M. Kirby, D. Xiu, T. Preusser. In SIAM Journal on Control and Optimization, Vol. 50, No. 5, pp. 2659--2682. 2012. DOI: 10.1137/110835438 We discuss the use of stochastic collocation for the solution of optimal control problems which are constrained by stochastic partial differential equations (SPDE). Thereby the constraining, SPDE depends on data which is not deterministic but random. Assuming a deterministic control, randomness within the states of the input data will propagate to the states of the system. For the solution of SPDEs there has recently been an increasing effort in the development of efficient numerical schemes based upon the mathematical concept of generalized polynomial chaos. Modal-based stochastic Galerkin and nodal-based stochastic collocation versions of this methodology exist, both of which rely on a certain level of smoothness of the solution in the random space to yield accelerated convergence rates. In this paper we apply the stochastic collocation method to develop a gradient descent as well as a sequential quadratic program (SQP) for the minimization of objective functions constrained by an SPDE. The stochastic function involves several higher-order moments of the random states of the system as well as classical regularization of the control. In particular we discuss several objective functions of tracking type. Numerical examples are presented to demonstrate the performance of our new stochastic collocation minimization approach. Keywords: stochastic collocation, optimal control, stochastic partial differential equations |
Efficient data restructuring and aggregation for I/O acceleration in PIDX S. Kumar, V. Vishwanath, P. Carns, J.A. Levine, R. Latham, G. Scorzelli, H. Kolla, R. Grout, R. Ross, M.E. Papka, J. Chen, V. Pascucci. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, IEEE Computer Society Press, pp. 50:1--50:11. 2012. ISBN: 978-1-4673-0804-5 Hierarchical, multiresolution data representations enable interactive analysis and visualization of large-scale simulations. One promising application of these techniques is to store high performance computing simulation output in a hierarchical Z (HZ) ordering that translates data from a Cartesian coordinate scheme to a one-dimensional array ordered by locality at different resolution levels. However, when the dimensions of the simulation data are not an even power of 2, parallel HZ ordering produces sparse memory and network access patterns that inhibit I/O performance. This work presents a new technique for parallel HZ ordering of simulation datasets that restructures simulation data into large (power of 2) blocks to facilitate efficient I/O aggregation. We perform both weak and strong scaling experiments using the S3D combustion application on both Cray-XE6 (65,536 cores) and IBM Blue Gene/P (131,072 cores) platforms. We demonstrate that data can be written in hierarchical, multiresolution format with performance competitive to that of native data-ordering methods. |
Smoothness-Increasing Accuracy-Conserving (SIAC) Filtering for discontinuous Galerkin Solutions: Improved Errors Versus Higher-Order Accuracy J. King, H. Mirzaee, J.K. Ryan, R.M. Kirby. In Journal of Scientific Computing, Vol. 53, pp. 129--149. 2012. DOI: 10.1007/s10915-012-9593-8 Smoothness-increasing accuracy-conserving (SIAC) filtering has demonstrated its effectiveness in raising the convergence rate of discontinuous Galerkin solutions from order k + 1/2 to order 2k + 1 for specific types of translation invariant meshes (Cockburn et al. in Math. Comput. 72:577–606, 2003; Curtis et al. in SIAM J. Sci. Comput. 30(1):272– 289, 2007; Mirzaee et al. in SIAM J. Numer. Anal. 49:1899–1920, 2011). Additionally, it improves the weak continuity in the discontinuous Galerkin method to k - 1 continuity. Typically this improvement has a positive impact on the error quantity in the sense that it also reduces the absolute errors. However, not enough emphasis has been placed on the difference between superconvergent accuracy and improved errors. This distinction is particularly important when it comes to understanding the interplay introduced through meshing, between geometry and filtering. The underlying mesh over which the DG solution is built is important because the tool used in SIAC filtering—convolution—is scaled by the geometric mesh size. This heavily contributes to the effectiveness of the post-processor. In this paper, we present a study of this mesh scaling and how it factors into the theoretical errors. To accomplish the large volume of post-processing necessary for this study, commodity streaming multiprocessors were used; we demonstrate for structured meshes up to a 50× speed up in the computational time over traditional CPU implementations of the SIAC filter. |
Multiscale Modeling of High Explosives for Transportation Accidents J.R. Peterson, J.C. Beckvermit, T. Harman, M. Berzins, C.A. Wight. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond, 2012. DOI: 10.1145/2335755.2335828 The development of a reaction model to simulate the accidental detonation of a large array of seismic boosters in a semi-truck subject to fire is considered. To test this model large scale simulations of explosions and detonations were performed by leveraging the massively parallel capabilities of the Uintah Computational Framework and the XSEDE computational resources. Computed stress profiles in bulk-scale explosive materials were validated using compaction simulations of hundred micron scale particles and found to compare favorably with experimental data. A validation study of reaction models for deflagration and detonation showed that computational grid cell sizes up to 10 mm could be used without loss of fidelity. The Uintah Computational Framework shows linear scaling up to 180K cores which combined with coarse resolution and validated models will now enable simulations of semi-truck scale transportation accidents for the first time. |