Chris JohnsonInverse ProblemsComputational Electrophysiology |
Rob MacLeodInverse ProblemsComputational Electrophysiology |
Jeff WeissComputational Biomechanics |
Orly AlterComputational Biology |
Chris ButsonNeuromodulation |
SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism N.M. Bertagnolli, J.A. Drake, J.M. Tennessen, O. Alter. In Public Library of Science (PLoS) One, Vol. 8, No. 11, pp. article e78913. November, 2013. DOI: 10.1371/journal.pone.0078913 To search for evolutionary forces that might act upon transcript length, we use the singular value decomposition (SVD) to identify the length distribution functions of sets and subsets of human and yeast transcripts from profiles of mRNA abundance levels across gel electrophoresis migration distances that were previously measured by DNA microarrays. We show that the SVD identifies the transcript length distribution functions as “asymmetric generalized coherent states” from the DNA microarray data and with no a-priori assumptions. Comparing subsets of human and yeast transcripts of the same gene ontology annotations, we find that in both disparate eukaryotes, transcripts involved in protein synthesis or mitochondrial metabolism are significantly shorter than typical, and in particular, significantly shorter than those involved in glucose metabolism. Comparing the subsets of human transcripts that are overexpressed in glioblastoma multiforme (GBM) or normal brain tissue samples from The Cancer Genome Atlas, we find that GBM maintains normal brain overexpression of significantly short transcripts, enriched in transcripts that are involved in protein synthesis or mitochondrial metabolism, but suppresses normal overexpression of significantly longer transcripts, enriched in transcripts that are involved in glucose metabolism and brain activity. These global relations among transcript length, cellular metabolism and tumor development suggest a previously unrecognized physical mode for tumor and normal cells to differentially regulate metabolism in a transcript length-dependent manner. The identified distribution functions support a previous hypothesis from mathematical modeling of evolutionary forces that act upon transcript length in the manner of the restoring force of the harmonic oscillator. |
Graph Diffusion Distance: A Difference Measure for Weighted Graphs Based on the Graph Laplacian Exponential Kernel D.K. Hammond, Y. Gur, C.R. Johnson. In Proceedings of the IEEE global conference on information and signal processing (GlobalSIP'13), Austin, Texas, pp. 419--422. 2013. DOI: 10.1109/GlobalSIP.2013.6736904 We propose a novel difference metric, called the graph diffusion distance (GDD), for quantifying the difference between two weighted graphs with the same number of vertices. Our approach is based on measuring the average similarity of heat diffusion on each graph. We compute the graph Laplacian exponential kernel matrices, corresponding to repeatedly solving the heat diffusion problem with initial conditions localized to single vertices. The GDD is then given by the Frobenius norm of the difference of the kernels, at the diffusion time yielding the maximum difference. We study properties of the proposed distance on both synthetic examples, and on real-data graphs representing human anatomical brain connectivity. |
Inverse Electrocardiographic Source Localization of Ischemia: An Optimization Framework and Finite Element Solution D. Wang, R.M. Kirby, R.S. MacLeod, C.R. Johnson. In Journal of Computational Physics, Vol. 250, Academic Press, pp. 403--424. 2013. ISSN: 0021-9991 DOI: 10.1016/j.jcp.2013.05.027 With the goal of non-invasively localizing cardiac ischemic disease using bodysurface potential recordings, we attempted to reconstruct the transmembrane potential (TMP) throughout the myocardium with the bidomain heart model. The task is an inverse source problem governed by partial differential equations (PDE). Our main contribution is solving the inverse problem within a PDE-constrained optimization framework that enables various physically-based constraints in both equality and inequality forms. We formulated the optimality conditions rigorously in the continuum before deriving finite element discretization, thereby making the optimization independent of discretization choice. Such a formulation was derived for the L2-norm Tikhonov regularization and the total variation minimization. The subsequent numerical optimization was fulfilled by a primal-dual interior-point method tailored to our problem's specific structure. Our simulations used realistic, fiberincluded heart models consisting of up to 18,000 nodes, much finer than any inverse models previously reported. With synthetic ischemia data we localized ischemic regions with roughly a 10% false-negative rate or a 20% false-positive rate under conditions up to 5% input noise. With ischemia data measured from animal experiments, we reconstructed TMPs with roughly 0.9 correlation with the ground truth. While precisely estimating the TMP in general cases remains an open problem, our study shows the feasibility of reconstructing TMP during the ST interval as a means of ischemia localization. Keywords: cvrti, 2P41 GM103545-14 |
A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms S.P. Ponnapalli, M.A. Saunders, C.F. Van Loan, O. Alter. In PLoS One, Vol. 6, No. 12, pp. e28072. 2012. DOI: 10.1371/journal.pone.0028072 |
GSVD Comparison of Patient-Matched Normal and Tumor aCGH Profiles Reveals Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival C.H. Lee, B.O. Alpert, P. Sankaranarayanan, O. Alter. In PLoS ONE, Vol. 7, No. 1, Public Library of Science, pp. e30098. 2012. DOI: 10.1371/journal.pone.0030098 Despite recent large-scale profiling efforts, the best prognostic predictor of glioblastoma multiforme (GBM) remains the patient's age at diagnosis. We describe a global pattern of tumor-exclusive co-occurring copy-number alterations (CNAs) that is correlated, possibly coordinated with GBM patients' survival and response to chemotherapy. The pattern is revealed by GSVD comparison of patient-matched but probe-independent GBM and normal aCGH datasets from The Cancer Genome Atlas (TCGA). We find that, first, the GSVD, formulated as a framework for comparatively modeling two composite datasets, removes from the pattern copy-number variations (CNVs) that occur in the normal human genome (e.g., female-specific X chromosome amplification) and experimental variations (e.g., in tissue batch, genomic center, hybridization date and scanner), without a-priori knowledge of these variations. Second, the pattern includes most known GBM-associated changes in chromosome numbers and focal CNAs, as well as several previously unreported CNAs in greater than 3\% of the patients. These include the biochemically putative drug target, cell cycle-regulated serine/threonine kinase-encoding TLK2, the cyclin E1-encoding CCNE1, and the Rb-binding histone demethylase-encoding KDM5A. Third, the pattern provides a better prognostic predictor than the chromosome numbers or any one focal CNA that it identifies, suggesting that the GBM survival phenotype is an outcome of its global genotype. The pattern is independent of age, and combined with age, makes a better predictor than age alone. GSVD comparison of matched profiles of a larger set of TCGA patients, inclusive of the initial set, confirms the global pattern. GSVD classification of the GBM profiles of an independent set of patients validates the prognostic contribution of the pattern. |
An optimization framework for inversely estimating myocardial transmembrane potentials and localizing ischemia D. Wang, R.M. Kirby, R.S. Macleod, C.R. Johnson. In Proceedings of the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), pp. 1680--1683. 2011. DOI: 10.1109/IEMBS.2011.6090483 PubMed ID: 22254648 PubMed Central ID: PMC3336368 By combining a static bidomain heart model with a torso conduction model, we studied the inverse electrocardiographic problem of computing the transmembrane potentials (TMPs) throughout the myocardium from a body-surface potential map, and then used the recovered potentials to localize myocardial ischemia. Our main contribution is solving the inverse problem within a constrained optimization framework, which is a generalization of previous methods for calculating transmembrane potentials. The framework offers ample flexibility for users to apply various physiologically-based constraints, and is well supported by mature algorithms and solvers developed by the optimization community. By avoiding the traditional inverse ECG approach of building the lead-field matrix, the framework greatly reduces computation cost and, by setting the associated forward problem as a constraint, the framework enables one to flexibly set individualized resolutions for each physical variable, a desirable feature for balancing model accuracy, ill-conditioning and computation tractability. Although the task of computing myocardial TMPs at an arbitrary time instance remains an open problem, we showed that it is possible to obtain TMPs with moderate accuracy during the ST segment by assuming all cardiac cells are at the plateau phase. Moreover, the calculated TMPs yielded a good estimate of ischemic regions, which was of more clinical interest than the voltage values themselves. We conducted finite element simulations of a phantom experiment over a 2D torso model with synthetic ischemic data. Preliminary results indicated that our approach is feasible and suitably accurate for the common case of transmural myocardial ischemia. |
Cardiac Position Sensitivity Study in the Electrocardiographic Forward Problem Using Stochastic Collocation and Boundary Element Methods D.J. Swenson, S.E. Geneser, J.G. Stinstra, R.M. Kirby, R.S. MacLeod. In Annals of Biomedical Engineering, Vol. 39, No. 12, pp. 2900--2910. 2011. DOI: 10.1007/s10439-011-0391-5 PubMed ID: 21909818 PubMed Central ID: PMC336204 The electrocardiogram (ECG) is ubiquitously employed as a diagnostic and monitoring tool for patients experiencing cardiac distress and/or disease. It is widely known that changes in heart position resulting from, for example, posture of the patient (sitting, standing, lying) and respiration significantly affect the body-surface potentials; however, few studies have quantitatively and systematically evaluated the effects of heart displacement on the ECG. The goal of this study was to evaluate the impact of positional changes of the heart on the ECG in the specific clinical setting of myocardial ischemia. To carry out the necessary comprehensive sensitivity analysis, we applied a relatively novel and highly efficient statistical approach, the generalized polynomial chaos-stochastic collocation method, to a boundary element formulation of the electrocardiographic forward problem, and we drove these simulations with measured epicardial potentials from whole-heart experiments. Results of the analysis identified regions on the body-surface where the potentials were especially sensitive to realistic heart motion. The standard deviation (STD) of ST-segment voltage changes caused by the apex of a normal heart, swinging forward and backward or side-to-side was approximately 0.2 mV. Variations were even larger, 0.3 mV, for a heart exhibiting elevated ischemic potentials. These variations could be large enough to mask or to mimic signs of ischemia in the ECG. Our results suggest possible modifications to ECG protocols that could reduce the diagnostic error related to postural changes in patients possibly suffering from myocardial ischemia. |
Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing T.A. Quinn, S. Granite, M.A. Allessie, C. Antzelevitch, C. Bollensdorff, G. Bub, R.A.B. Burton, E. Cerbai, P.S. Chen, M. Delmar, D. DiFrancesco, Y.E. Earm, I.R. Efimov, M. Egger, E. Entcheva, M. Fink, R. Fischmeister, M.R. Franz, A. Garny, W.R. Giles, T. Hannes, S.E. Harding, P.J. Hunter, s, G. Iribe, J. Jalife, C.R. Johnson, R.S. Kass, I. Kodama, G. Koren, P. Lord, V.S. Markhasin, S. Matsuoka, A.D. McCulloch, G.R. Mirams, G.E. Morley, S. Nattel, D. Noble, S.P. Olesen, A.V. Panfilov, N.A. Trayanova, U. Ravens, S. Richard, D.S. Rosenbaum, Y. Rudy, F. Sachs, F.B. Sachse, D.A. Saint, U. Schotten, O. Solovyova, P. Taggart, L. Tung, A. Varrò, P.G. Volders, K. Wang, J.N. Weiss, E. Wettwer, E. White, R. Wilders, R.L. Winslow, P. Kohl. In Progress in Biophysics and Molecular Biology, Vol. 107, No. 1, Elsevier, pp. 4--10. October, 2011. DOI: 10.1016/j.pbiomolbio.2011.07.001 PubMed Central ID: PMC3190048 Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step toward establishing this, we present a draft standard, called Minimum Information about a Cardiac Electrophysiology Experiment (MICEE). The ultimate goal is to develop a useful tool for cardiac electrophysiologists which facilitates and improves dissemination of the minimum information necessary for reproduction of cardiac electrophysiology research, allowing for easier comparison and utilisation of findings by others. It is hoped that this will enhance the integration of individual results into experimental, computational, and conceptual models. In its present form, this draft is intended for assessment and development by the research community. We invite the reader to join this effort, and, if deemed productive, implement the Minimum Information about a Cardiac Electrophysiology Experiment standard in their own work. Keywords: Minimum Information Standard; Cardiac electrophysiology; Data sharing; Reproducibility; Integration; Computational modelling |
Quantifying variability in radiation dose due to respiratory-induced tumor motion S.E. Geneser, J.D. Hinkle, R.M. Kirby, Bo Wang, B. Salter, S. Joshi. In Medical Image Analysis, Vol. 15, No. 4, pp. 640--649. 2011. DOI: 10.1016/j.media.2010.07.003 |
Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA C. Muralidhara, A.M. Gross, R.R. Gutell, O. Alter. In PLoS ONE, Vol. 6, No. 4, Public Library of Science, pp. e18768. April, 2011. DOI: 10.1371/journal.pone.0018768 Evolutionary relationships among organisms are commonly described by using a hierarchy derived from comparisons of ribosomal RNA (rRNA) sequences. We propose that even on the level of a single rRNA molecule, an organism's evolution is composed of multiple pathways due to concurrent forces that act independently upon different rRNA degrees of freedom. Relationships among organisms are then compositions of coexisting pathway-dependent similarities and dissimilarities, which cannot be described by a single hierarchy. We computationally test this hypothesis in comparative analyses of 16S and 23S rRNA sequence alignments by using a tensor decomposition, i.e., a framework for modeling composite data. Each alignment is encoded in a cuboid, i.e., a third-order tensor, where nucleotides, positions and organisms, each represent a degree of freedom. A tensor mode-1 higher-order singular value decomposition (HOSVD) is formulated such that it separates each cuboid into combinations of patterns of nucleotide frequency variation across organisms and positions, i.e., \"eigenpositions\" and corresponding nucleotide-specific segments of \"eigenorganisms,\" respectively, independent of a-priori knowledge of the taxonomic groups or rRNA structures. We find, in support of our hypothesis that, first, the significant eigenpositions reveal multiple similarities and dissimilarities among the taxonomic groups. Second, the corresponding eigenorganisms identify insertions or deletions of nucleotides exclusively conserved within the corresponding groups, that map out entire substructures and are enriched in adenosines, unpaired in the rRNA secondary structure, that participate in tertiary structure interactions. This demonstrates that structural motifs involved in rRNA folding and function are evolutionary degrees of freedom. Third, two previously unknown coexisting subgenic relationships between Microsporidia and Archaea are revealed in both the 16S and 23S rRNA alignments, a convergence and a divergence, conferred by insertions and deletions of these motifs, which cannot be described by a single hierarchy. This shows that mode-1 HOSVD modeling of rRNA alignments might be used to computationally predict evolutionary mechanisms. |
Finite Element Based Discretization and Regularization Strategies for 3D Inverse Electrocardiography D. Wang, R.M. Kirby, C.R. Johnson. In IEEE Transactions for Biomedical Engineering, Vol. 58, No. 6, pp. 1827--1838. 2011. PubMed ID: 21382763 PubMed Central ID: PMC3109267 We consider the inverse electrocardiographic problem of computing epicardial potentials from a body-surface potential map. We study how to improve numerical approximation of the inverse problem when the finite-element method is used. Being ill-posed, the inverse problem requires different discretization strategies from its corresponding forward problem. We propose refinement guidelines that specifically address the ill-posedness of the problem. The resulting guidelines necessitate the use of hybrid finite elements composed of tetrahedra and prism elements. Also, in order to maintain consistent numerical quality when the inverse problem is discretized into different scales, we propose a new family of regularizers using the variational principle underlying finite-element methods. These variational-formed regularizers serve as an alternative to the traditional Tikhonov regularizers, but preserves the L_{2} norm and thereby achieves consistent regularization in multiscale simulations. The variational formulation also enables a simple construction of the discrete gradient operator over irregular meshes, which is difficult to define in traditional discretization schemes. We validated our hybrid element technique and the variational regularizers by simulations on a realistic 3-D torso/heart model with empirical heart data. Results show that discretization based on our proposed strategies mitigates the ill-conditioning and improves the inverse solution, and that the variational formulation may benefit a broader range of potential-based bioelectric problems. |
Using the stochastic collocation method for the uncertainty quantification of drug concentration due to depot shape variability J.S. Preston, T. Tasdizen, C.M. Terry, A.K. Cheung, R.M. Kirby. In IEEE Transactions on Biomedical Engineering, Vol. 56, No. 3, Note: Epub 2008 Dec 2, pp. 609--620. 2009. PubMed ID: 19272865 |
Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression, L. Omberg, J.R. Meyerson, K. Kobayashi, L.S. Drury, J.F.X. Diffley, O. Alter. In Nature Molecular Systems Biology, Vol. 5, No. 312, pp. (published online). October, 2009. DOI: 10.1038/msb.2009.70 |
Incorporating patient breathing variability into a stochastic model of dose deposition for stereotactic body radiation therapy S.E. Geneser, R.M. Kirby, Brian Wang, B. Salter, S. Joshi. In Information Processing in Medical Imaging, Lecture Notes in Computer Science LNCS, Vol. 5636, pp. 688--700. 2009. PubMed ID: 19694304 |