@article{3984, abstract = {We combine topological and geometric methods to construct a multiresolution representation for a function over a two-dimensional domain. In a preprocessing stage, we create the Morse-Smale complex of the function and progressively simplify its topology by cancelling pairs of critical points. Based on a simple notion of dependency among these cancellations, we construct a hierarchical data structure supporting traversal and reconstruction operations similarly to traditional geometry-based representations. We use this data structure to extract topologically valid approximations that satisfy error bounds provided at runtime.}, author = {Bremer, Peer-Timo and Herbert Edelsbrunner and Hamann, Bernd and Pascucci, Valerio}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {4}, pages = {385 -- 396}, publisher = {IEEE}, title = {{A topological hierarchy for functions on triangulated surfaces}}, doi = {10.1109/TVCG.2004.3}, volume = {10}, year = {2004}, } @article{3987, abstract = {We consider scientific data sets that describe density functions over three-dimensional geometric domains. Such data sets are often large and coarsened representations are needed for visualization and analysis. Assuming a tetrahedral mesh representation, we construct such representations with a simplification algorithm that combines three goals: the approximation of the function, the preservation of the mesh topology, and the improvement of the mesh quality. The third goal is achieved with a novel extension of the well-known quadric error metric. We perform a number of computational experiments to understand the effect of mesh quality improvement on the density map approximation. In addition, we study the effect of geometric simplification on the topological features of the function by monitoring its critical points.}, author = {Natarajan, Vijay and Herbert Edelsbrunner}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {5}, pages = {587 -- 597}, publisher = {IEEE}, title = {{Simplification of three-dimensional density maps}}, doi = {10.1109/TVCG.2004.32}, volume = {10}, year = {2004}, } @article{3985, abstract = {Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.}, author = {Cole-McLaughlin, Kree and Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio}, journal = {Discrete & Computational Geometry}, number = {2}, pages = {231 -- 244}, publisher = {Springer}, title = {{Loops in Reeb graphs of 2-manifolds}}, doi = {10.1007/s00454-004-1122-6}, volume = {32}, year = {2004}, } @inproceedings{3989, abstract = {We introduce local and global comparison measures for a collection of k less than or equal to d real-valued smooth functions on a common d-dimensional Riemannian manifold. For k = d = 2 we relate the measures to the set of critical points of one function restricted to the level sets of the other. The definition of the measures extends to piecewise linear functions for which they ace easy to compute. The computation of the measures forms the centerpiece of a software tool which we use to study scientific datasets.}, author = {Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio}, pages = {275 -- 280}, publisher = {IEEE}, title = {{Local and global comparison of continuous functions}}, doi = {10.1109/VISUAL.2004.68}, year = {2004}, } @article{4172, abstract = {During vertebrate gastrulation, a relatively limited number of blastodermal cells undergoes a stereotypical set of cellular movements that leads to formation of the three germ layers: ectoderm, mesoderm and endoderm. Gastrulation, therefore, provides a unique developmental system in which to study cell movements in vivo in a fairly simple cellular context. Recent advances have been made in elucidating the cellular and molecular mechanisms that underlie cell movements during zebrafish gastrulation. These findings can be compared with observations made in other model systems to identify potential general mechanisms of cell migration during development.}, author = {Montero, Juan and Heisenberg, Carl-Philipp J}, journal = {Trends in Cell Biology}, number = {11}, pages = {620 -- 627}, publisher = {Cell Press}, title = {{Gastrulation dynamics: cells move into focus}}, doi = {10.1016/j.tcb.2004.09.008}, volume = {14}, year = {2004}, } @article{4238, abstract = {The dynamical basis of tumoral growth has been controversial. Many models have been proposed to explain cancer development. The descriptions employ exponential, potential, logistic or Gompertzian growth laws. Some of these models are concerned with the interaction between cancer and the immunological, system. Among other properties, these models are concerned with the microscopic behavior of tumors and the emergence of cancer. We propose a modification of a previous model by Stepanova, which describes the specific immunological response against cancer. The modification consists of the substitution of a Gompertian law for the exponential rate used for tumoral growth. This modification is motivated by the numerous works confirming that Gompertz's equation correctly describes solid tumor growth. The modified model predicts that near zero, tumors always tend to grow. Immunological contraposition never suffices to induce a complete regression of the tumor. Instead, a stable microscopic equilibrium between cancer and immunological activity can be attained. In other words, our model predicts that the theory of immune surveillance is plausible. A macroscopic equilibrium in which the system develops cancer is also possible. In this case, immunological activity is depleted. This is consistent with the phenomena of cancer tolerance. Both equilibrium points can coexist or can exist without the other. In all cases the fixed point at zero tumor size is unstable. Since immunity cannot induce a complete tumor regression, a therapy is required. We include constant-dose therapies and show that they are insufficient. Final levels of immunocompetent cells and tumoral cells are finite, thus post-treatment regrowth of the tumor is certain. We also evaluate late-intensification therapies which are successful. They induce an asymptotic regression to zero tumor size. Immune response is also suppressed by the therapy, and thus plays a negligible role in the remission. We conclude that treatment evaluation should be successful without taking into account immunological effects. (C) 2003 Elsevier Ltd. All rights reserved.}, author = {de Vladar, Harold and González, J.}, journal = {Journal of Theoretical Biology}, number = {3}, pages = {335 -- 348}, publisher = {Elsevier}, title = {{Dynamic response of cancer under the influence of immunological activity and therapy}}, doi = {3801}, volume = {227}, year = {2004}, } @inbook{4230, author = {Harold Vladar and Cipriani, Roberto and Scharifker, Benjamin and Bubis, Jose}, booktitle = {Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds}, editor = {Hanslmeier,A. and Kempe,S. and Seckbach,J.}, pages = {83 -- 87}, publisher = {Springer}, title = {{A mechanism for the prebiotic emergence of proteins}}, year = {2004}, } @phdthesis{4236, author = {de Vladar, Harold}, publisher = {Centro de estudios avazados, IVIC}, title = {{Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares}}, doi = {3810}, year = {2004}, } @inproceedings{4372, author = {Maler, Oded and Dejan Nickovic}, pages = {152 -- 166}, publisher = {Springer}, title = {{Monitoring Temporal Properties of Continuous Signals}}, doi = {1572}, year = {2004}, } @phdthesis{4424, abstract = {The enormous cost and ubiquity of software errors necessitates the need for techniques and tools that can precisely analyze large systems and prove that they meet given specifications, or if they don't, return counterexample behaviors showing how the system fails. Recent advances in model checking, decision procedures, program analysis and type systems, and a shift of focus to partial specifications common to several systems (e.g., memory safety and race freedom) have resulted in several practical verification methods. However, these methods are either precise or they are scalable, depending on whether they track the values of variables or only a fixed small set of dataflow facts (e.g., types), and are usually insufficient for precisely verifying large programs. We describe a new technique called Lazy Abstraction (LA) which achieves both precision and scalability by localizing the use of precise information. LA automatically builds, explores and refines a single abstract model of the program in a way that different parts of the model exhibit different degrees of precision, namely just enough to verify the desired property. The algorithm automatically mines the information required by partitioning mechanical proofs of unsatisfiability of spurious counterexamples into Craig Interpolants. For multithreaded systems, we give a new technique based on analyzing the behavior of a single thread executing in a context which is an abstraction of the other (arbitrarily many) threads. We define novel context models and show how to automatically infer them and analyze the full system (thread + context) using LA. LA is implemented in BLAST. We have run BLAST on Windows and Linux Device Drivers to verify API conformance properties, and have used it to find (or guarantee the absence of) data races in multithreaded Networked Embedded Systems (NESC) applications. BLAST is able to prove the absence of races in several cases where earlier methods, which depend on lock-based synchronization, fail.}, author = {Jhala, Ranjit}, pages = {1 -- 165}, publisher = {University of California, Berkeley}, title = {{Program verification by lazy abstraction}}, year = {2004}, }