--- _id: '3984' abstract: - lang: eng text: 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: - first_name: Peer full_name: Bremer, Peer-Timo last_name: Bremer - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernd full_name: Hamann, Bernd last_name: Hamann - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics. 2004;10(4):385-396. doi:10.1109/TVCG.2004.3 apa: Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2004). A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.3 chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci. “A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.3. ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A topological hierarchy for functions on triangulated surfaces,” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 4. IEEE, pp. 385–396, 2004. ista: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2004. A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics. 10(4), 385–396. mla: Bremer, Peer, et al. “A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 4, IEEE, 2004, pp. 385–96, doi:10.1109/TVCG.2004.3. short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, IEEE Transactions on Visualization and Computer Graphics 10 (2004) 385–396. date_created: 2018-12-11T12:06:16Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T07:53:39Z day: '01' doi: 10.1109/TVCG.2004.3 extern: 1 intvolume: ' 10' issue: '4' month: '07' page: 385 - 396 publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '2139' quality_controlled: 0 status: public title: A topological hierarchy for functions on triangulated surfaces type: journal_article volume: 10 year: '2004' ... --- _id: '3987' abstract: - lang: eng text: '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: - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Natarajan V, Edelsbrunner H. Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics. 2004;10(5):587-597. doi:10.1109/TVCG.2004.32 apa: Natarajan, V., & Edelsbrunner, H. (2004). Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.32 chicago: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional Density Maps.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.32. ieee: V. Natarajan and H. Edelsbrunner, “Simplification of three-dimensional density maps,” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 5. IEEE, pp. 587–597, 2004. ista: Natarajan V, Edelsbrunner H. 2004. Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics. 10(5), 587–597. mla: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional Density Maps.” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 5, IEEE, 2004, pp. 587–97, doi:10.1109/TVCG.2004.32. short: V. Natarajan, H. Edelsbrunner, IEEE Transactions on Visualization and Computer Graphics 10 (2004) 587–597. date_created: 2018-12-11T12:06:17Z date_published: 2004-07-12T00:00:00Z date_updated: 2021-01-12T07:53:40Z day: '12' doi: 10.1109/TVCG.2004.32 extern: 1 intvolume: ' 10' issue: '5' month: '07' page: 587 - 597 publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '2142' quality_controlled: 0 status: public title: Simplification of three-dimensional density maps type: journal_article volume: 10 year: '2004' ... --- _id: '3985' abstract: - lang: eng text: 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. acknowledgement: Partially supported by NSF under Grants EIA-99-72879 and CCR-00-86013. author: - first_name: Kree full_name: Cole-McLaughlin, Kree last_name: Cole Mclaughlin - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 2004;32(2):231-244. doi:10.1007/s00454-004-1122-6 apa: Cole Mclaughlin, K., Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-004-1122-6 chicago: Cole Mclaughlin, Kree, Herbert Edelsbrunner, John Harer, Vijay Natarajan, and Valerio Pascucci. “Loops in Reeb Graphs of 2-Manifolds.” Discrete & Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1122-6. ieee: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Loops in Reeb graphs of 2-manifolds,” Discrete & Computational Geometry, vol. 32, no. 2. Springer, pp. 231–244, 2004. ista: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 32(2), 231–244. mla: Cole Mclaughlin, Kree, et al. “Loops in Reeb Graphs of 2-Manifolds.” Discrete & Computational Geometry, vol. 32, no. 2, Springer, 2004, pp. 231–44, doi:10.1007/s00454-004-1122-6. short: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, Discrete & Computational Geometry 32 (2004) 231–244. date_created: 2018-12-11T12:06:16Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T07:53:39Z day: '01' doi: 10.1007/s00454-004-1122-6 extern: 1 intvolume: ' 32' issue: '2' month: '07' page: 231 - 244 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2140' quality_controlled: 0 status: public title: Loops in Reeb graphs of 2-manifolds type: journal_article volume: 32 year: '2004' ... --- _id: '3989' abstract: - lang: eng text: 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: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Local and global comparison of continuous functions. In: IEEE; 2004:275-280. doi:10.1109/VISUAL.2004.68' apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Local and global comparison of continuous functions (pp. 275–280). Presented at the VIS: IEEE Visualization, IEEE. https://doi.org/10.1109/VISUAL.2004.68' chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci. “Local and Global Comparison of Continuous Functions,” 275–80. IEEE, 2004. https://doi.org/10.1109/VISUAL.2004.68. ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Local and global comparison of continuous functions,” presented at the VIS: IEEE Visualization, 2004, pp. 275–280.' ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Local and global comparison of continuous functions. VIS: IEEE Visualization, 275–280.' mla: Edelsbrunner, Herbert, et al. Local and Global Comparison of Continuous Functions. IEEE, 2004, pp. 275–80, doi:10.1109/VISUAL.2004.68. short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, IEEE, 2004, pp. 275–280. conference: name: 'VIS: IEEE Visualization' date_created: 2018-12-11T12:06:18Z date_published: 2004-10-01T00:00:00Z date_updated: 2021-01-12T07:53:41Z day: '01' doi: 10.1109/VISUAL.2004.68 extern: 1 month: '10' page: 275 - 280 publication_status: published publisher: IEEE publist_id: '2137' quality_controlled: 0 status: public title: Local and global comparison of continuous functions type: conference year: '2004' ... --- _id: '4172' abstract: - lang: eng text: '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.' article_processing_charge: No author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Montero J, Heisenberg C-PJ. Gastrulation dynamics: cells move into focus. Trends in Cell Biology. 2004;14(11):620-627. doi:10.1016/j.tcb.2004.09.008' apa: 'Montero, J., & Heisenberg, C.-P. J. (2004). Gastrulation dynamics: cells move into focus. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2004.09.008' chicago: 'Montero, Juan, and Carl-Philipp J Heisenberg. “Gastrulation Dynamics: Cells Move into Focus.” Trends in Cell Biology. Cell Press, 2004. https://doi.org/10.1016/j.tcb.2004.09.008.' ieee: 'J. Montero and C.-P. J. Heisenberg, “Gastrulation dynamics: cells move into focus,” Trends in Cell Biology, vol. 14, no. 11. Cell Press, pp. 620–627, 2004.' ista: 'Montero J, Heisenberg C-PJ. 2004. Gastrulation dynamics: cells move into focus. Trends in Cell Biology. 14(11), 620–627.' mla: 'Montero, Juan, and Carl-Philipp J. Heisenberg. “Gastrulation Dynamics: Cells Move into Focus.” Trends in Cell Biology, vol. 14, no. 11, Cell Press, 2004, pp. 620–27, doi:10.1016/j.tcb.2004.09.008.' short: J. Montero, C.-P.J. Heisenberg, Trends in Cell Biology 14 (2004) 620–627. date_created: 2018-12-11T12:07:23Z date_published: 2004-11-01T00:00:00Z date_updated: 2021-01-12T07:55:02Z day: '01' doi: 10.1016/j.tcb.2004.09.008 extern: '1' intvolume: ' 14' issue: '11' language: - iso: eng month: '11' oa_version: None page: 620 - 627 publication: Trends in Cell Biology publication_status: published publisher: Cell Press publist_id: '1948' status: public title: 'Gastrulation dynamics: cells move into focus' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2004' ... --- _id: '4238' abstract: - lang: eng text: 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. article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: J. full_name: González, J. last_name: González citation: ama: de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 2004;227(3):335-348. doi:3801 apa: de Vladar, H., & González, J. (2004). Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. Elsevier. https://doi.org/3801 chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology. Elsevier, 2004. https://doi.org/3801. ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” Journal of Theoretical Biology, vol. 227, no. 3. Elsevier, pp. 335–348, 2004. ista: de Vladar H, González J. 2004. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 227(3), 335–348. mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology, vol. 227, no. 3, Elsevier, 2004, pp. 335–48, doi:3801. short: H. de Vladar, J. González, Journal of Theoretical Biology 227 (2004) 335–348. date_created: 2018-12-11T12:07:46Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:55:31Z day: '01' doi: '3801' extern: '1' intvolume: ' 227' issue: '3' language: - iso: eng month: '01' oa_version: None page: 335 - 348 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1876' status: public title: Dynamic response of cancer under the influence of immunological activity and therapy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 227 year: '2004' ... --- _id: '4230' alternative_title: - Cellular Origin and Life in Extreme Habitats and Astrobiology author: - first_name: Harold full_name: Harold Vladar id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: Roberto full_name: Cipriani, Roberto last_name: Cipriani - first_name: Benjamin full_name: Scharifker, Benjamin last_name: Scharifker - first_name: Jose full_name: Bubis, Jose last_name: Bubis citation: ama: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. A mechanism for the prebiotic emergence of proteins. In: Hanslmeier A, Kempe S, Seckbach J, eds. Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds. Springer; 2004:83-87.' apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A mechanism for the prebiotic emergence of proteins. In A. Hanslmeier, S. Kempe, & J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds (pp. 83–87). Springer. chicago: Vladar, Harold de, Roberto Cipriani, Benjamin Scharifker, and Jose Bubis. “A Mechanism for the Prebiotic Emergence of Proteins.” In Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, edited by A. Hanslmeier, S. Kempe, and J. Seckbach, 83–87. Springer, 2004. ieee: H. de Vladar, R. Cipriani, B. Scharifker, and J. Bubis, “A mechanism for the prebiotic emergence of proteins,” in Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, A. Hanslmeier, S. Kempe, and J. Seckbach, Eds. Springer, 2004, pp. 83–87. ista: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. 2004.A mechanism for the prebiotic emergence of proteins. In: Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds. Cellular Origin and Life in Extreme Habitats and Astrobiology, , 83–87.' mla: de Vladar, Harold, et al. “A Mechanism for the Prebiotic Emergence of Proteins.” Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, edited by A. Hanslmeier et al., Springer, 2004, pp. 83–87. short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, A. Hanslmeier, S. Kempe, J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, Springer, 2004, pp. 83–87. date_created: 2018-12-11T12:07:44Z date_published: 2004-12-31T00:00:00Z date_updated: 2021-01-12T07:55:28Z day: '31' editor: - first_name: A. full_name: Hanslmeier,A. last_name: Hanslmeier - first_name: S. full_name: Kempe,S. last_name: Kempe - first_name: J. full_name: Seckbach,J. last_name: Seckbach extern: 1 month: '12' page: 83 - 87 publication: Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds publication_status: published publisher: Springer publist_id: '1884' quality_controlled: 0 status: public title: A mechanism for the prebiotic emergence of proteins type: book_chapter year: '2004' ... --- _id: '4236' article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares. 2004. doi:3810 apa: de Vladar, H. (2004). Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. https://doi.org/3810 chicago: Vladar, Harold de. “Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias de Poblaciones Celulares.” Centro de estudios avazados, IVIC, 2004. https://doi.org/3810. ieee: H. de Vladar, “Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares,” Centro de estudios avazados, IVIC, 2004. ista: de Vladar H. 2004. Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. mla: de Vladar, Harold. Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias de Poblaciones Celulares. Centro de estudios avazados, IVIC, 2004, doi:3810. short: H. de Vladar, Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias de Poblaciones Celulares, Centro de estudios avazados, IVIC, 2004. date_created: 2018-12-11T12:07:46Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:55:30Z day: '01' doi: '3810' extern: '1' language: - iso: eng month: '01' oa_version: None publication_status: published publisher: Centro de estudios avazados, IVIC publist_id: '1877' status: public title: Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2004' ... --- _id: '4372' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic citation: ama: 'Maler O, Nickovic D. Monitoring Temporal Properties of Continuous Signals. In: Springer; 2004:152-166. doi:1572' apa: 'Maler, O., & Nickovic, D. (2004). Monitoring Temporal Properties of Continuous Signals (pp. 152–166). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1572' chicago: Maler, Oded, and Dejan Nickovic. “Monitoring Temporal Properties of Continuous Signals,” 152–66. Springer, 2004. https://doi.org/1572. ieee: 'O. Maler and D. Nickovic, “Monitoring Temporal Properties of Continuous Signals,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2004, pp. 152–166.' ista: 'Maler O, Nickovic D. 2004. Monitoring Temporal Properties of Continuous Signals. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 152–166.' mla: Maler, Oded, and Dejan Nickovic. Monitoring Temporal Properties of Continuous Signals. Springer, 2004, pp. 152–66, doi:1572. short: O. Maler, D. Nickovic, in:, Springer, 2004, pp. 152–166. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2004-12-14T00:00:00Z date_updated: 2021-01-12T07:56:29Z day: '14' doi: '1572' extern: 1 month: '12' page: 152 - 166 publication_status: published publisher: Springer publist_id: '1088' quality_controlled: 0 status: public title: Monitoring Temporal Properties of Continuous Signals type: conference year: '2004' ... --- _id: '4424' abstract: - lang: eng text: "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.\r\n\r\nWe 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.\r\n\r\nLA 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." article_processing_charge: No author: - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala citation: ama: Jhala R. Program verification by lazy abstraction. 2004:1-165. apa: Jhala, R. (2004). Program verification by lazy abstraction. University of California, Berkeley. chicago: Jhala, Ranjit. “Program Verification by Lazy Abstraction.” University of California, Berkeley, 2004. ieee: R. Jhala, “Program verification by lazy abstraction,” University of California, Berkeley, 2004. ista: Jhala R. 2004. Program verification by lazy abstraction. University of California, Berkeley. mla: Jhala, Ranjit. Program Verification by Lazy Abstraction. University of California, Berkeley, 2004, pp. 1–165. short: R. Jhala, Program Verification by Lazy Abstraction, University of California, Berkeley, 2004. date_created: 2018-12-11T12:08:47Z date_published: 2004-12-01T00:00:00Z date_updated: 2021-01-12T07:56:52Z day: '01' extern: '1' language: - iso: eng month: '12' oa_version: None page: 1 - 165 publication_status: published publisher: University of California, Berkeley publist_id: '307' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: Program verification by lazy abstraction type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2004' ... --- _id: '4445' abstract: - lang: eng text: We present a type system for E code, which is an assembly language that manages the release, interaction, and termination of real-time tasks. E code specifies a deadline for each task, and the type system ensures that the deadlines are path-insensitive. We show that typed E programs allow, for given worst-case execution times of tasks, a simple schedulability analysis. Moreover, the real-time programming language Giotto can be compiled into typed E~code. This shows that typed E~code identifies an easily schedulable yet expressive class of real-time programs. We have extended the Giotto compiler to generate typed E code, and enabled the run-time system for E code to perform a type and schedulability check before executing the code. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and by the NSF grants CCR- 0208875 and CCR-0225610. author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch citation: ama: 'Henzinger TA, Kirsch C. A typed assembly language for real-time programs. In: ACM; 2004:104-113. doi:10.1145/1017753.1017774' apa: 'Henzinger, T. A., & Kirsch, C. (2004). A typed assembly language for real-time programs (pp. 104–113). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1017753.1017774' chicago: Henzinger, Thomas A, and Christoph Kirsch. “A Typed Assembly Language for Real-Time Programs,” 104–13. ACM, 2004. https://doi.org/10.1145/1017753.1017774. ieee: 'T. A. Henzinger and C. Kirsch, “A typed assembly language for real-time programs,” presented at the EMSOFT: Embedded Software , 2004, pp. 104–113.' ista: 'Henzinger TA, Kirsch C. 2004. A typed assembly language for real-time programs. EMSOFT: Embedded Software , 104–113.' mla: Henzinger, Thomas A., and Christoph Kirsch. A Typed Assembly Language for Real-Time Programs. ACM, 2004, pp. 104–13, doi:10.1145/1017753.1017774. short: T.A. Henzinger, C. Kirsch, in:, ACM, 2004, pp. 104–113. conference: name: 'EMSOFT: Embedded Software ' date_created: 2018-12-11T12:08:53Z date_published: 2004-09-01T00:00:00Z date_updated: 2021-01-12T07:57:01Z day: '01' doi: 10.1145/1017753.1017774 extern: 1 month: '09' page: 104 - 113 publication_status: published publisher: ACM publist_id: '285' quality_controlled: 0 status: public title: A typed assembly language for real-time programs type: conference year: '2004' ... --- _id: '4458' abstract: - lang: eng text: 'The success of model checking for large programs depends crucially on the ability to efficiently construct parsimonious abstractions. A predicate abstraction is parsimonious if at each control location, it specifies only relationships between current values of variables, and only those which are required for proving correctness. Previous methods for automatically refining predicate abstractions until sufficient precision is obtained do not systematically construct parsimonious abstractions: predicates usually contain symbolic variables, and are added heuristically and often uniformly to many or all control locations at once. We use Craig interpolation to efficiently construct, from a given abstract error trace which cannot be concretized, a parsominous abstraction that removes the trace. At each location of the trace, we infer the relevant predicates as an interpolant between the two formulas that define the past and the future segment of the trace. Each interpolant is a relationship between current values of program variables, and is relevant only at that particular program location. It can be found by a linear scan of the proof of infeasibility of the trace.We develop our method for programs with arithmetic and pointer expressions, and call-by-value function calls. For function calls, Craig interpolation offers a systematic way of generating relevant predicates that contain only the local variables of the function and the values of the formal parameters when the function was called. We have extended our model checker Blast with predicate discovery by Craig interpolation, and applied it successfully to C programs with more than 130,000 lines of code, which was not possible with approaches that build less parsimonious abstractions.' author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Kenneth full_name: McMillan, Kenneth L last_name: Mcmillan citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. Abstractions from proofs. In: ACM; 2004:232-244. doi:10.1145/964001.964021' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Mcmillan, K. (2004). Abstractions from proofs (pp. 232–244). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/964001.964021' chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Kenneth Mcmillan. “Abstractions from Proofs,” 232–44. ACM, 2004. https://doi.org/10.1145/964001.964021. ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and K. Mcmillan, “Abstractions from proofs,” presented at the POPL: Principles of Programming Languages, 2004, pp. 232–244.' ista: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. 2004. Abstractions from proofs. POPL: Principles of Programming Languages, 232–244.' mla: Henzinger, Thomas A., et al. Abstractions from Proofs. ACM, 2004, pp. 232–44, doi:10.1145/964001.964021. short: T.A. Henzinger, R. Jhala, R. Majumdar, K. Mcmillan, in:, ACM, 2004, pp. 232–244. conference: name: 'POPL: Principles of Programming Languages' date_created: 2018-12-11T12:08:57Z date_published: 2004-04-01T00:00:00Z date_updated: 2021-01-12T07:57:06Z day: '01' doi: 10.1145/964001.964021 extern: 1 month: '04' page: 232 - 244 publication_status: published publisher: ACM publist_id: '270' quality_controlled: 0 status: public title: Abstractions from proofs type: conference year: '2004' ... --- _id: '4461' abstract: - lang: eng text: One of the central axioms of extreme programming is the disciplined use of regression testing during stepwise software development. Due to recent progress in software model checking, it has become possible to supplement this process with automatic checks for behavioral safety properties of programs, such as conformance with locking idioms and other programming protocols and patterns. For efficiency reasons, all checks must be incremental, i.e., they must reuse partial results from previous checks in order to avoid all unnecessary repetition of expensive verification tasks. We show that the lazy-abstraction algorithm, and its implementation in Blast, can be extended to support the fully automatic and incremental checking of temporal safety properties during software development. acknowledgement: 'This work was supported in part by the NSF grants CCR-9988172, CCR-0085949, and CCR-0234690, the ONR grant N00014-02-1-0671, the DARPA grant F33615-00-C-1693, and the MARCO grant 98-DT-660. ' alternative_title: - LNCS author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Marco full_name: Sanvido, Marco A last_name: Sanvido citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. Extreme model checking. In: Verification: Theory and Practice. Vol 2772. Springer; 2004:332-358. doi:10.1007/978-3-540-39910-0_16' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sanvido, M. (2004). Extreme model checking. In Verification: Theory and Practice (Vol. 2772, pp. 332–358). Springer. https://doi.org/10.1007/978-3-540-39910-0_16' chicago: 'Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Marco Sanvido. “Extreme Model Checking.” In Verification: Theory and Practice, 2772:332–58. Springer, 2004. https://doi.org/10.1007/978-3-540-39910-0_16.' ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and M. Sanvido, “Extreme model checking,” in Verification: Theory and Practice, vol. 2772, Springer, 2004, pp. 332–358.' ista: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. 2004.Extreme model checking. In: Verification: Theory and Practice. LNCS, vol. 2772, 332–358.' mla: 'Henzinger, Thomas A., et al. “Extreme Model Checking.” Verification: Theory and Practice, vol. 2772, Springer, 2004, pp. 332–58, doi:10.1007/978-3-540-39910-0_16.' short: 'T.A. Henzinger, R. Jhala, R. Majumdar, M. Sanvido, in:, Verification: Theory and Practice, Springer, 2004, pp. 332–358.' date_created: 2018-12-11T12:08:58Z date_published: 2004-02-24T00:00:00Z date_updated: 2021-01-12T07:57:08Z day: '24' doi: 10.1007/978-3-540-39910-0_16 extern: 1 intvolume: ' 2772' month: '02' page: 332 - 358 publication: 'Verification: Theory and Practice' publication_status: published publisher: Springer publist_id: '269' quality_controlled: 0 status: public title: Extreme model checking type: book_chapter volume: 2772 year: '2004' ... --- _id: '4459' abstract: - lang: eng text: Software model checking has been successful for sequential programs, where predicate abstraction offers suitable models, and counterexample-guided abstraction refinement permits the automatic inference of models. When checking concurrent programs, we need to abstract threads as well as the contexts in which they execute. Stateless context models, such as predicates on global variables, prove insufficient for showing the absence of race conditions in many examples. We therefore use richer context models, which combine (1) predicates for abstracting data state, (2) control flow quotients for abstracting control state, and (3) counters for abstracting an unbounded number of threads. We infer suitable context models automatically by a combination of counterexample-guided abstraction refinement, bisimulation minimization, circular assume-guarantee reasoning, and parametric reasoning about an unbounded number of threads. This algorithm, called CIRC, has been implemented in BLAST and succeeds in checking many examples of NESC code for data races. In particular, BLAST proves the absence of races in several cases where previous race checkers give false positives. author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Henzinger TA, Jhala R, Majumdar R. Race checking by context inference. In: ACM; 2004:1-13. doi:10.1145/996841.996844' apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Race checking by context inference (pp. 1–13). Presented at the PLDI: Programming Languages Design and Implementation, ACM. https://doi.org/10.1145/996841.996844' chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Race Checking by Context Inference,” 1–13. ACM, 2004. https://doi.org/10.1145/996841.996844. ieee: 'T. A. Henzinger, R. Jhala, and R. Majumdar, “Race checking by context inference,” presented at the PLDI: Programming Languages Design and Implementation, 2004, pp. 1–13.' ista: 'Henzinger TA, Jhala R, Majumdar R. 2004. Race checking by context inference. PLDI: Programming Languages Design and Implementation, 1–13.' mla: Henzinger, Thomas A., et al. Race Checking by Context Inference. ACM, 2004, pp. 1–13, doi:10.1145/996841.996844. short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, ACM, 2004, pp. 1–13. conference: name: 'PLDI: Programming Languages Design and Implementation' date_created: 2018-12-11T12:08:57Z date_published: 2004-06-01T00:00:00Z date_updated: 2021-01-12T07:57:07Z day: '01' doi: 10.1145/996841.996844 extern: 1 month: '06' page: 1 - 13 publication_status: published publisher: ACM publist_id: '271' quality_controlled: 0 status: public title: Race checking by context inference type: conference year: '2004' ... --- _id: '4525' abstract: - lang: eng text: 'We present a new high-level programming language, called xGiotto, for programming applications with hard real-time constraints. Like its predecessor, xGiotto is based on the LET (logical execution time) assumption: the programmer specifies when the outputs of a task become available, and the compiler checks if the specification can be implemented on a given platform. However, while the predecessor language xGiotto was purely time-triggered, xGiotto accommodates also asynchronous events. Indeed, through a mechanism called event scoping, events are the main structuring principle of the new language. The xGiotto compiler and run-time system implement event scoping through a tree-based event filter. The compiler also checks programs for determinism (absence of race conditions).' acknowledgement: This research is supported by the AFOSR MURI grant F49620-00-1-0327, the DARPA SEC grant F33615-C-98-3614, the MARCO GSRC grant 98-DT-660, and the NSF grants CCR-0208875 and CCR-0225610. alternative_title: - LNCS author: - first_name: Arkadeb full_name: Ghosal, Arkadeb last_name: Ghosal - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch - first_name: Marco full_name: Sanvido, Marco A last_name: Sanvido citation: ama: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. Event-driven programming with logical execution times. In: Vol 2993. Springer; 2004:167-170. doi:10.1007/978-3-540-24743-2_24' apa: 'Ghosal, A., Henzinger, T. A., Kirsch, C., & Sanvido, M. (2004). Event-driven programming with logical execution times (Vol. 2993, pp. 167–170). Presented at the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/10.1007/978-3-540-24743-2_24' chicago: Ghosal, Arkadeb, Thomas A Henzinger, Christoph Kirsch, and Marco Sanvido. “Event-Driven Programming with Logical Execution Times,” 2993:167–70. Springer, 2004. https://doi.org/10.1007/978-3-540-24743-2_24. ieee: 'A. Ghosal, T. A. Henzinger, C. Kirsch, and M. Sanvido, “Event-driven programming with logical execution times,” presented at the HSCC: Hybrid Systems - Computation and Control, 2004, vol. 2993, pp. 167–170.' ista: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. 2004. Event-driven programming with logical execution times. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 2993, 167–170.' mla: Ghosal, Arkadeb, et al. Event-Driven Programming with Logical Execution Times. Vol. 2993, Springer, 2004, pp. 167–70, doi:10.1007/978-3-540-24743-2_24. short: A. Ghosal, T.A. Henzinger, C. Kirsch, M. Sanvido, in:, Springer, 2004, pp. 167–170. conference: name: 'HSCC: Hybrid Systems - Computation and Control' date_created: 2018-12-11T12:09:18Z date_published: 2004-03-12T00:00:00Z date_updated: 2021-01-12T07:59:26Z day: '12' doi: 10.1007/978-3-540-24743-2_24 extern: 1 intvolume: ' 2993' month: '03' page: 167 - 170 publication_status: published publisher: Springer publist_id: '200' quality_controlled: 0 status: public title: Event-driven programming with logical execution times type: conference volume: 2993 year: '2004' ... --- _id: '4555' abstract: - lang: eng text: Strategies in repeated games can be classified as to whether or not they use memory and/or randomization. We consider Markov decision processes and 2-player graph games, both of the deterministic and probabilistic varieties. We characterize when memory and/or randomization are required for winning with respect to various classes of w-regular objectives, noting particularly when the use of memory can be traded for the use of randomization. In particular, we show that Markov decision processes allow randomized memoryless optimal strategies for all M?ller objectives. Furthermore, we show that 2-player probabilistic graph games allow randomized memoryless strategies for winning with probability 1 those M?ller objectives which are upward-closed. Upward-closure means that if a set α of infinitely repeating vertices is winning, then all supersets of α are also winning. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, De Alfaro L, Henzinger TA. Trading memory for randomness. In: IEEE; 2004:206-217. doi:10.1109/QEST.2004.10051' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2004). Trading memory for randomness (pp. 206–217). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2004.10051' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Trading Memory for Randomness,” 206–17. IEEE, 2004. https://doi.org/10.1109/QEST.2004.10051. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Trading memory for randomness,” presented at the QEST: Quantitative Evaluation of Systems, 2004, pp. 206–217.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2004. Trading memory for randomness. QEST: Quantitative Evaluation of Systems, 206–217.' mla: Chatterjee, Krishnendu, et al. Trading Memory for Randomness. IEEE, 2004, pp. 206–17, doi:10.1109/QEST.2004.10051. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2004, pp. 206–217. conference: name: 'QEST: Quantitative Evaluation of Systems' date_created: 2018-12-11T12:09:27Z date_published: 2004-09-30T00:00:00Z date_updated: 2021-01-12T07:59:40Z day: '30' doi: 10.1109/QEST.2004.10051 extern: 1 month: '09' page: 206 - 217 publication_status: published publisher: IEEE publist_id: '155' quality_controlled: 0 status: public title: Trading memory for randomness type: conference year: '2004' ... --- _id: '4558' abstract: - lang: eng text: We study perfect-information stochastic parity games. These are two-player nonterminating games which are played on a graph with turn-based probabilistic transitions. A play results in an infinite path and the conflicting goals of the two players are ω-regular path properties, formalized as parity winning conditions. The qualitative solution of such a game amounts to computing the set of vertices from which a player has a strategy to win with probability 1 (or with positive probability). The quantitative solution amounts to computing the value of the game in every vertex, i.e., the highest probability with which a player can guarantee satisfaction of his own objective in a play that starts from the vertex.For the important special case of one-player stochastic parity games (parity Markov decision processes) we give polynomial-time algorithms both for the qualitative and the quantitative solution. The running time of the qualitative solution is O(d · m3/2) for graphs with m edges and d priorities. The quantitative solution is based on a linear-programming formulation.For the two-player case, we establish the existence of optimal pure memoryless strategies. This has several important ramifications. First, it implies that the values of the games are rational. This is in contrast to the concurrent stochastic parity games of de Alfaro et al.; there, values are in general algebraic numbers, optimal strategies do not exist, and ε-optimal strategies have to be mixed and with infinite memory. Second, the existence of optimal pure memoryless strategies together with the polynomial-time solution forone-player case implies that the quantitative two-player stochastic parity game problem is in NP ∩ co-NP. This generalizes a result of Condon for stochastic games with reachability objectives. It also constitutes an exponential improvement over the best previous algorithm, which is based on a doubly exponential procedure of de Alfaro and Majumdar for concurrent stochastic parity games and provides only ε-approximations of the values. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Jurdziński M, Henzinger TA. Quantitative stochastic parity games. In: SIAM; 2004:121-130.' apa: 'Chatterjee, K., Jurdziński, M., & Henzinger, T. A. (2004). Quantitative stochastic parity games (pp. 121–130). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.' chicago: Chatterjee, Krishnendu, Marcin Jurdziński, and Thomas A Henzinger. “Quantitative Stochastic Parity Games,” 121–30. SIAM, 2004. ieee: 'K. Chatterjee, M. Jurdziński, and T. A. Henzinger, “Quantitative stochastic parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2004, pp. 121–130.' ista: 'Chatterjee K, Jurdziński M, Henzinger TA. 2004. Quantitative stochastic parity games. SODA: Symposium on Discrete Algorithms, 121–130.' mla: Chatterjee, Krishnendu, et al. Quantitative Stochastic Parity Games. SIAM, 2004, pp. 121–30. short: K. Chatterjee, M. Jurdziński, T.A. Henzinger, in:, SIAM, 2004, pp. 121–130. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:09:28Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:59:41Z day: '01' extern: 1 month: '01' page: 121 - 130 publication_status: published publisher: SIAM publist_id: '153' quality_controlled: 0 status: public title: Quantitative stochastic parity games type: conference year: '2004' ... --- _id: '4556' abstract: - lang: eng text: We study the problem of determining stack boundedness and the exact maximum stack size for three classes of interrupt-driven programs. Interrupt-driven programs are used in many real-time applications that require responsive interrupt handling. In order to ensure responsiveness, programmers often enable interrupt processing in the body of lower-priority interrupt handlers. In such programs a programming error can allow interrupt handlers to be interrupted in a cyclic fashion to lead to an unbounded stack, causing the system to crash. For a restricted class of interrupt-driven programs, we show that there is a polynomial-time procedure to check stack boundedness, while determining the exact maximum stack size is PSPACE-complete. For a larger class of programs, the two problems are both PSPACE-complete, and for the largest class of programs we consider, the two problems are PSPACE-hard and can be solved in exponential time. While the complexities are high, our algorithms are exponential only in the number of handlers, and polynomial in the size of the program. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Di full_name: Ma, Di last_name: Ma - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Tian full_name: Zhao, Tian last_name: Zhao - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jens full_name: Palsberg, Jens last_name: Palsberg citation: ama: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. Stack size analysis for interrupt-driven programs. Information and Computation. 2004;194(2):144-174. doi:10.1016/j.ic.2004.06.001 apa: Chatterjee, K., Ma, D., Majumdar, R., Zhao, T., Henzinger, T. A., & Palsberg, J. (2004). Stack size analysis for interrupt-driven programs. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2004.06.001 chicago: Chatterjee, Krishnendu, Di Ma, Ritankar Majumdar, Tian Zhao, Thomas A Henzinger, and Jens Palsberg. “Stack Size Analysis for Interrupt-Driven Programs.” Information and Computation. Elsevier, 2004. https://doi.org/10.1016/j.ic.2004.06.001. ieee: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T. A. Henzinger, and J. Palsberg, “Stack size analysis for interrupt-driven programs,” Information and Computation, vol. 194, no. 2. Elsevier, pp. 144–174, 2004. ista: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. 2004. Stack size analysis for interrupt-driven programs. Information and Computation. 194(2), 144–174. mla: Chatterjee, Krishnendu, et al. “Stack Size Analysis for Interrupt-Driven Programs.” Information and Computation, vol. 194, no. 2, Elsevier, 2004, pp. 144–74, doi:10.1016/j.ic.2004.06.001. short: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T.A. Henzinger, J. Palsberg, Information and Computation 194 (2004) 144–174. date_created: 2018-12-11T12:09:28Z date_published: 2004-08-11T00:00:00Z date_updated: 2021-01-12T07:59:40Z day: '11' doi: 10.1016/j.ic.2004.06.001 extern: 1 intvolume: ' 194' issue: '2' month: '08' page: 144 - 174 publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '156' quality_controlled: 0 status: public title: Stack size analysis for interrupt-driven programs type: journal_article volume: 194 year: '2004' ... --- _id: '4578' abstract: - lang: eng text: 'BLAST is an automatic verification tool for checking temporal safety properties of C programs. Blast is based on lazy predicate abstraction driven by interpolation-based predicate discovery. In this paper, we present the Blast specification language. The language specifies program properties at two levels of precision. At the lower level, monitor automata are used to specify temporal safety properties of program executions (traces). At the higher level, relational reachability queries over program locations are used to combine lower-level trace properties. The two-level specification language can be used to break down a verification task into several independent calls of the model-checking engine. In this way, each call to the model checker may have to analyze only part of the program, or part of the specification, and may thus succeed in a reduction of the number of predicates needed for the analysis. In addition, the two-level specification language provides a means for structuring and maintaining specifications. ' acknowledgement: This research was supported in part by the NSF grants CCR-0085949, CCR-0234690, and ITR-0326577. alternative_title: - LNCS author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Adam full_name: Chlipala, Adam J last_name: Chlipala - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. The BLAST query language for software verification. In: Vol 3148. Springer; 2004:2-18. doi:10.1007/978-3-540-27864-1_2' apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). The BLAST query language for software verification (Vol. 3148, pp. 2–18). Presented at the SAS: Static Analysis Symposium, Springer. https://doi.org/10.1007/978-3-540-27864-1_2' chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “The BLAST Query Language for Software Verification,” 3148:2–18. Springer, 2004. https://doi.org/10.1007/978-3-540-27864-1_2. ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “The BLAST query language for software verification,” presented at the SAS: Static Analysis Symposium, 2004, vol. 3148, pp. 2–18.' ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. The BLAST query language for software verification. SAS: Static Analysis Symposium, LNCS, vol. 3148, 2–18.' mla: Beyer, Dirk, et al. The BLAST Query Language for Software Verification. Vol. 3148, Springer, 2004, pp. 2–18, doi:10.1007/978-3-540-27864-1_2. short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer, 2004, pp. 2–18. conference: name: 'SAS: Static Analysis Symposium' date_created: 2018-12-11T12:09:34Z date_published: 2004-08-17T00:00:00Z date_updated: 2021-01-12T07:59:50Z day: '17' doi: 10.1007/978-3-540-27864-1_2 extern: 1 intvolume: ' 3148' month: '08' page: 2 - 18 publication_status: published publisher: Springer publist_id: '130' quality_controlled: 0 status: public title: The BLAST query language for software verification type: conference volume: 3148 year: '2004' ... --- _id: '4577' abstract: - lang: eng text: While model checking has been successful in uncovering subtle bugs in code, its adoption in software engineering practice has been hampered by the absence of a simple interface to the programmer in an integrated development environment. We describe an integration of the software model checker BLAST into the Eclipse development environment. We provide a verification interface for practical solutions for some typical program analysis problems - assertion checking, reachability analysis, dead code analysis, and test generation - directly on the source code. The analysis is completely automatic, and assumes no knowledge of model checking or formal notation. Moreover, the interface supports incremental program verification to support incremental design and evolution of code. acknowledgement: This research was supported in part by the NSF grants CCR-0085949, CCR-0234690, and ITR-0326577. author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. An eclipse plug-in for model checking. In: IEEE; 2004:251-255. doi:10.1109/WPC.2004.1311069  ' apa: 'Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). An eclipse plug-in for model checking (pp. 251–255). Presented at the IWPC: Program Comprehension, IEEE. https://doi.org/10.1109/WPC.2004.1311069  ' chicago: Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “An Eclipse Plug-in for Model Checking,” 251–55. IEEE, 2004. https://doi.org/10.1109/WPC.2004.1311069  . ieee: 'D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “An eclipse plug-in for model checking,” presented at the IWPC: Program Comprehension, 2004, pp. 251–255.' ista: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. 2004. An eclipse plug-in for model checking. IWPC: Program Comprehension, 251–255.' mla: Beyer, Dirk, et al. An Eclipse Plug-in for Model Checking. IEEE, 2004, pp. 251–55, doi:10.1109/WPC.2004.1311069  . short: D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 251–255. conference: name: 'IWPC: Program Comprehension' date_created: 2018-12-11T12:09:34Z date_published: 2004-07-12T00:00:00Z date_updated: 2021-01-12T07:59:50Z day: '12' doi: '10.1109/WPC.2004.1311069 ' extern: 1 month: '07' page: 251 - 255 publication_status: published publisher: IEEE publist_id: '129' quality_controlled: 0 status: public title: An eclipse plug-in for model checking type: conference year: '2004' ... --- _id: '4581' abstract: - lang: eng text: We have extended the software model checker BLAST to automatically generate test suites that guarantee full coverage with respect to a given predicate. More precisely, given a C program and a target predicate p, BLAST determines the set L of program locations which program execution can reach with p true, and automatically generates a set of test vectors that exhibit the truth of p at all locations in L. We have used BLAST to generate test suites and to detect dead code in C programs with up to 30 K lines of code. The analysis and test vector generation is fully automatic (no user intervention) and exact (no false positives). author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Adam full_name: Chlipala, Adam J last_name: Chlipala - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. Generating tests from counterexamples. In: IEEE; 2004:326-335. doi:10.1109/ICSE.2004.1317455' apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Generating tests from counterexamples (pp. 326–335). Presented at the ICSE: Software Engineering, IEEE. https://doi.org/10.1109/ICSE.2004.1317455' chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Generating Tests from Counterexamples,” 326–35. IEEE, 2004. https://doi.org/10.1109/ICSE.2004.1317455. ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “Generating tests from counterexamples,” presented at the ICSE: Software Engineering, 2004, pp. 326–335.' ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. Generating tests from counterexamples. ICSE: Software Engineering, 326–335.' mla: Beyer, Dirk, et al. Generating Tests from Counterexamples. IEEE, 2004, pp. 326–35, doi:10.1109/ICSE.2004.1317455. short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 326–335. conference: name: 'ICSE: Software Engineering' date_created: 2018-12-11T12:09:35Z date_published: 2004-07-26T00:00:00Z date_updated: 2021-01-12T07:59:52Z day: '26' doi: 10.1109/ICSE.2004.1317455 extern: 1 month: '07' page: 326 - 335 publication_status: published publisher: IEEE publist_id: '128' quality_controlled: 0 status: public title: Generating tests from counterexamples type: conference year: '2004' ... --- _id: '4629' abstract: - lang: eng text: 'Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a generalization of the branching-time logic Ctl which achieves robustness with respect to model perturbations by giving a quantitative interpretation to predicates and logical operators, and by discounting the importance of events according to how late they occur. In every state, the value of a formula is a real number in the interval [0,1], where 1 corresponds to truth and 0 to falsehood. The boolean operators and and or are replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over all paths from a given state, and the temporal operators and □ specify sup and inf over a given path; a new operator averages all values along a path. Furthermore, all path operators are discounted by a parameter that can be chosen to give more weight to states that are closer to the beginning of the path. We interpret the resulting logic Dctl over transition systems, Markov chains, and Markov decision processes. We present two semantics for Dctl: a path semantics, inspired by the standard interpretation of state and path formulas in CTL, and a fixpoint semantics, inspired by the μ-calculus evaluation of CTL formulas. We show that, while these semantics coincide for CTL, they differ for Dctl, and we provide model-checking algorithms for both semantics.' acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the ONR grant N00014-02-1-0671, and the NSF grants CCR-0132780, CCR-9988172, CCR-0225610, and CCR-0234690. alternative_title: - LNCS author: - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Marco full_name: Faella, Marco last_name: Faella - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Mariëlle full_name: Stoelinga, Mariëlle last_name: Stoelinga citation: ama: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking discounted temporal properties. In: Vol 2988. Springer; 2004:77-92. doi:10.1007/978-3-540-24730-2_6' apa: 'De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2004). Model checking discounted temporal properties (Vol. 2988, pp. 77–92). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/978-3-540-24730-2_6' chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties,” 2988:77–92. Springer, 2004. https://doi.org/10.1007/978-3-540-24730-2_6. ieee: 'L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2004, vol. 2988, pp. 77–92.' ista: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2004. Model checking discounted temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 2988, 77–92.' mla: De Alfaro, Luca, et al. Model Checking Discounted Temporal Properties. Vol. 2988, Springer, 2004, pp. 77–92, doi:10.1007/978-3-540-24730-2_6. short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, Springer, 2004, pp. 77–92. conference: name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' date_created: 2018-12-11T12:09:50Z date_published: 2004-03-18T00:00:00Z date_updated: 2021-01-12T08:00:38Z day: '18' doi: 10.1007/978-3-540-24730-2_6 extern: 1 intvolume: ' 2988' month: '03' page: 77 - 92 publication_status: published publisher: Springer publist_id: '79' quality_controlled: 0 status: public title: Model checking discounted temporal properties type: conference volume: 2988 year: '2004' ... --- _id: '6155' abstract: - lang: eng text: 'The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.' author: - first_name: Benny H.H full_name: Cheung, Benny H.H last_name: Cheung - first_name: Fausto full_name: Arellano-Carbajal, Fausto last_name: Arellano-Carbajal - first_name: Irene full_name: Rybicki, Irene last_name: Rybicki - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 2004;14(12):1105-1111. doi:10.1016/j.cub.2004.06.027 apa: Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., & de Bono, M. (2004). Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.027 chicago: Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.027. ieee: B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior,” Current Biology, vol. 14, no. 12. Elsevier, pp. 1105–1111, 2004. ista: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 14(12), 1105–1111. mla: Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology, vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:10.1016/j.cub.2004.06.027. short: B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology 14 (2004) 1105–1111. date_created: 2019-03-21T09:42:01Z date_published: 2004-06-22T00:00:00Z date_updated: 2021-01-12T08:06:25Z day: '22' doi: 10.1016/j.cub.2004.06.027 extern: '1' external_id: pmid: - '15203005' intvolume: ' 14' issue: '12' language: - iso: eng month: '06' oa_version: None page: 1105-1111 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2004' ... --- _id: '7334' abstract: - lang: eng text: 'Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. ' article_processing_charge: No article_type: original author: - first_name: John full_name: Mantzaras, John last_name: Mantzaras - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi - first_name: Markus full_name: Roos, Markus last_name: Roos - first_name: Wilhelm full_name: Brandstätter, Wilhelm last_name: Brandstätter - first_name: Michel full_name: Prestat, Michel last_name: Prestat - first_name: Ludwig J. full_name: Gauckler, Ludwig J. last_name: Gauckler - first_name: Bernhard full_name: Andreaus, Bernhard last_name: Andreaus - first_name: Faegheh full_name: Hajbolouri, Faegheh last_name: Hajbolouri - first_name: Stephan M. full_name: Senn, Stephan M. last_name: Senn - first_name: Dimos full_name: Poulikakos, Dimos last_name: Poulikakos - first_name: Andreas K. full_name: Chaniotis, Andreas K. last_name: Chaniotis - first_name: Diego full_name: Larrain, Diego last_name: Larrain - first_name: Nordahl full_name: Autissier, Nordahl last_name: Autissier - first_name: François full_name: Maréchal, François last_name: Maréchal citation: ama: Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 2004;58(12):857-868. doi:10.2533/000942904777677029 apa: Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W., Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. Swiss Chemical Society. https://doi.org/10.2533/000942904777677029 chicago: Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos, Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International Journal for Chemistry. Swiss Chemical Society, 2004. https://doi.org/10.2533/000942904777677029. ieee: J. Mantzaras et al., “Fuel cell modeling and simulations,” CHIMIA International Journal for Chemistry, vol. 58, no. 12. Swiss Chemical Society, pp. 857–868, 2004. ista: Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M, Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 58(12), 857–868. mla: Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International Journal for Chemistry, vol. 58, no. 12, Swiss Chemical Society, 2004, pp. 857–68, doi:10.2533/000942904777677029. short: J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M. Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos, A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal for Chemistry 58 (2004) 857–868. date_created: 2020-01-15T12:24:23Z date_published: 2004-12-01T00:00:00Z date_updated: 2021-01-12T08:13:09Z day: '01' doi: 10.2533/000942904777677029 extern: '1' intvolume: ' 58' issue: '12' language: - iso: eng month: '12' oa_version: None page: 857-868 publication: CHIMIA International Journal for Chemistry publication_identifier: issn: - 0009-4293 publication_status: published publisher: Swiss Chemical Society quality_controlled: '1' status: public title: Fuel cell modeling and simulations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2004' ... --- _id: '7333' abstract: - lang: eng text: The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system. article_processing_charge: No article_type: original author: - first_name: M. full_name: Santis, M. last_name: Santis - first_name: D. full_name: Schmid, D. last_name: Schmid - first_name: M. full_name: Ruge, M. last_name: Ruge - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: F.N. full_name: Büchi, F.N. last_name: Büchi citation: ama: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 2004;4(3):214-218. doi:10.1002/fuce.200400028 apa: Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., & Büchi, F. N. (2004). Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. Wiley. https://doi.org/10.1002/fuce.200400028 chicago: Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N. Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” Fuel Cells. Wiley, 2004. https://doi.org/10.1002/fuce.200400028. ieee: M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular stack-internal air humidification concept-verification in a 1 kW stack,” Fuel Cells, vol. 4, no. 3. Wiley, pp. 214–218, 2004. ista: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218. mla: Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” Fuel Cells, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:10.1002/fuce.200400028. short: M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4 (2004) 214–218. date_created: 2020-01-15T12:24:14Z date_published: 2004-08-01T00:00:00Z date_updated: 2021-01-12T08:13:08Z day: '01' doi: 10.1002/fuce.200400028 extern: '1' intvolume: ' 4' issue: '3' language: - iso: eng month: '08' oa_version: None page: 214-218 publication: Fuel Cells publication_identifier: issn: - 1615-6846 - 1615-6854 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Modular stack-internal air humidification concept-verification in a 1 kW stack type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2004' ... --- _id: '864' abstract: - lang: eng text: 'We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.' acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport. author: - first_name: Anna full_name: Panchenko, Anna R last_name: Panchenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephen full_name: Bryant, Stephen H last_name: Bryant citation: ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 2004;13(4):884-892. doi:10.1110/ps.03465504 apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. Wiley-Blackwell. https://doi.org/10.1110/ps.03465504 chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504. ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” Protein Science, vol. 13, no. 4. Wiley-Blackwell, pp. 884–892, 2004. ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892. mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:10.1110/ps.03465504. short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892. date_created: 2018-12-11T11:48:55Z date_published: 2004-04-01T00:00:00Z date_updated: 2021-01-12T08:20:22Z day: '01' doi: 10.1110/ps.03465504 extern: 1 intvolume: ' 13' issue: '4' month: '04' page: 884 - 892 publication: Protein Science publication_status: published publisher: Wiley-Blackwell publist_id: '6786' quality_controlled: 0 status: public title: Prediction of functional sites by analysis of sequence and structure conservation type: journal_article volume: 13 year: '2004' ... --- _id: '870' abstract: - lang: eng text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330 apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkh330 chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University Press, 2004. https://doi.org/10.1093/nar/gkh330. ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004. ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737. mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:10.1093/nar/gkh330. short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737. date_created: 2018-12-11T11:48:56Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T08:20:37Z day: '01' doi: 10.1093/nar/gkh330 extern: 1 intvolume: ' 32' issue: '5' month: '01' page: 1731 - 1737 publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press publist_id: '6780' quality_controlled: 0 status: public title: Bioinformatical assay of human gene morbidity type: journal_article volume: 32 year: '2004' ... --- _id: '875' abstract: - lang: eng text: The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001 apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001 chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001. ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” Trends in Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004. ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291. mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001. short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291. date_created: 2018-12-11T11:48:58Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T08:20:54Z day: '01' doi: 10.1016/j.tig.2004.05.001 extern: 1 intvolume: ' 20' issue: '7' month: '07' page: 287 - 291 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6775' quality_controlled: 0 status: public title: A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications type: journal_article volume: 20 year: '2004' ... --- _id: '889' abstract: - lang: eng text: 'The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges.' acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp, S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were supported by a grant from the US National Institutes of Health to S. Nuzhdin, and A.D.K. is a Howard Hughes author: - first_name: Andrew full_name: Kern, Andrew D last_name: Kern - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212. doi:10.1038/ng1451 apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng1451 chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing Group, 2004. https://doi.org/10.1038/ng1451. ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004. ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212. mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451. short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212. date_created: 2018-12-11T11:49:02Z date_published: 2004-11-01T00:00:00Z date_updated: 2021-01-12T08:21:17Z day: '01' doi: 10.1038/ng1451 extern: 1 intvolume: ' 36' issue: '11' month: '11' page: 1207 - 1212 publication: Nature Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6759' quality_controlled: 0 status: public title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs type: journal_article volume: 36 year: '2004' ... --- _id: '9493' abstract: - lang: eng text: In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production. article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Xiaofeng full_name: Cao, Xiaofeng last_name: Cao - first_name: Lisa K. full_name: Johansen, Lisa K. last_name: Johansen - first_name: Zhixin full_name: Xie, Zhixin last_name: Xie - first_name: James C. full_name: Carrington, James C. last_name: Carrington - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen citation: ama: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055 apa: Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., & Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055 chicago: Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.055. ieee: D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004. ista: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220. mla: Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055. short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220. date_created: 2021-06-07T10:33:00Z date_published: 2004-07-13T00:00:00Z date_updated: 2021-12-14T08:52:00Z day: '13' department: - _id: DaZi doi: 10.1016/j.cub.2004.06.055 extern: '1' external_id: pmid: - '15242620 ' intvolume: ' 14' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2004.06.055 month: '07' oa: 1 oa_version: Published Version page: 1214-1220 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 14 year: '2004' ... --- _id: '9517' abstract: - lang: eng text: Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense. article_processing_charge: No article_type: original author: - first_name: Zhixin full_name: Xie, Zhixin last_name: Xie - first_name: Lisa K. full_name: Johansen, Lisa K. last_name: Johansen - first_name: Adam M. full_name: Gustafson, Adam M. last_name: Gustafson - first_name: Kristin D. full_name: Kasschau, Kristin D. last_name: Kasschau - first_name: 'Andrew D. ' full_name: 'Lellis, Andrew D. ' last_name: Lellis - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen - first_name: James C. full_name: Carrington, James C. last_name: Carrington citation: ama: Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104 apa: Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0020104 chicago: Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104. ieee: Z. Xie et al., “Genetic and functional diversification of small RNA pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004. ista: Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2(5), 0642–0652. mla: Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS Biology, vol. 2, no. 5, Public Library of Science, 2004, pp. 0642–52, doi:10.1371/journal.pbio.0020104. short: Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652. date_created: 2021-06-07T14:12:08Z date_published: 2004-02-24T00:00:00Z date_updated: 2021-12-14T08:43:57Z day: '24' department: - _id: DaZi doi: 10.1371/journal.pbio.0020104 extern: '1' external_id: pmid: - '15024409' intvolume: ' 2' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pbio.0020104 month: '02' oa: 1 oa_version: Published Version page: 0642-0652 pmid: 1 publication: PLoS Biology publication_identifier: eissn: - 1545-7885 issn: - 1544-9173 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Genetic and functional diversification of small RNA pathways in plants type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2004' ... --- _id: '9511' abstract: - lang: eng text: Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it. article_number: '249' article_processing_charge: No article_type: review author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: 'Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 2004;5(12). doi:10.1186/gb-2004-5-12-249' apa: 'Zilberman, D., & Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. Springer Nature. https://doi.org/10.1186/gb-2004-5-12-249' chicago: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” Genome Biology. Springer Nature, 2004. https://doi.org/10.1186/gb-2004-5-12-249.' ieee: 'D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” Genome Biology, vol. 5, no. 12. Springer Nature, 2004.' ista: 'Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.' mla: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” Genome Biology, vol. 5, no. 12, 249, Springer Nature, 2004, doi:10.1186/gb-2004-5-12-249.' short: D. Zilberman, S. Henikoff, Genome Biology 5 (2004). date_created: 2021-06-07T12:58:06Z date_published: 2004-11-16T00:00:00Z date_updated: 2021-12-14T08:44:24Z day: '16' department: - _id: DaZi doi: 10.1186/gb-2004-5-12-249 extern: '1' external_id: pmid: - '15575975' intvolume: ' 5' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/gb-2004-5-12-249 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: eissn: - 1465-6906 issn: - 1474-760X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Silencing of transposons in plant genomes: kick them when they''re down' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 5 year: '2004' ... --- _id: '8517' abstract: - lang: eng text: We consider the evolution of a connected set on the plane carried by a space periodic incompressible stochastic flow. While for almost every realization of the stochastic flow at time t most of the particles are at a distance of order equation image away from the origin, there is a measure zero set of points that escape to infinity at the linear rate. We study the set of points visited by the original set by time t and show that such a set, when scaled down by the factor of t, has a limiting nonrandom shape. article_processing_charge: No article_type: original author: - first_name: Dmitry full_name: Dolgopyat, Dmitry last_name: Dolgopyat - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Leonid full_name: Koralov, Leonid last_name: Koralov citation: ama: Dolgopyat D, Kaloshin V, Koralov L. A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. 2004;57(9):1127-1158. doi:10.1002/cpa.20032 apa: Dolgopyat, D., Kaloshin, V., & Koralov, L. (2004). A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.20032 chicago: Dolgopyat, Dmitry, Vadim Kaloshin, and Leonid Koralov. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” Communications on Pure and Applied Mathematics. Wiley, 2004. https://doi.org/10.1002/cpa.20032. ieee: D. Dolgopyat, V. Kaloshin, and L. Koralov, “A limit shape theorem for periodic stochastic dispersion,” Communications on Pure and Applied Mathematics, vol. 57, no. 9. Wiley, pp. 1127–1158, 2004. ista: Dolgopyat D, Kaloshin V, Koralov L. 2004. A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. 57(9), 1127–1158. mla: Dolgopyat, Dmitry, et al. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” Communications on Pure and Applied Mathematics, vol. 57, no. 9, Wiley, 2004, pp. 1127–58, doi:10.1002/cpa.20032. short: D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied Mathematics 57 (2004) 1127–1158. date_created: 2020-09-18T10:49:12Z date_published: 2004-09-01T00:00:00Z date_updated: 2021-01-12T08:19:50Z day: '01' doi: 10.1002/cpa.20032 extern: '1' intvolume: ' 57' issue: '9' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '09' oa_version: None page: 1127-1158 publication: Communications on Pure and Applied Mathematics publication_identifier: issn: - 0010-3640 - 1097-0312 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: A limit shape theorem for periodic stochastic dispersion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2004' ... --- _id: '8518' article_processing_charge: No article_type: original author: - first_name: Leonid full_name: Koralov, Leonid last_name: Koralov - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Dmitry full_name: Dolgopyat, Dmitry last_name: Dolgopyat citation: ama: Koralov L, Kaloshin V, Dolgopyat D. Sample path properties of the stochastic flows. The Annals of Probability. 2004;32(1A):1-27. doi:10.1214/aop/1078415827 apa: Koralov, L., Kaloshin, V., & Dolgopyat, D. (2004). Sample path properties of the stochastic flows. The Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/aop/1078415827 chicago: Koralov, Leonid, Vadim Kaloshin, and Dmitry Dolgopyat. “Sample Path Properties of the Stochastic Flows.” The Annals of Probability. Institute of Mathematical Statistics, 2004. https://doi.org/10.1214/aop/1078415827. ieee: L. Koralov, V. Kaloshin, and D. Dolgopyat, “Sample path properties of the stochastic flows,” The Annals of Probability, vol. 32, no. 1A. Institute of Mathematical Statistics, pp. 1–27, 2004. ista: Koralov L, Kaloshin V, Dolgopyat D. 2004. Sample path properties of the stochastic flows. The Annals of Probability. 32(1A), 1–27. mla: Koralov, Leonid, et al. “Sample Path Properties of the Stochastic Flows.” The Annals of Probability, vol. 32, no. 1A, Institute of Mathematical Statistics, 2004, pp. 1–27, doi:10.1214/aop/1078415827. short: L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004) 1–27. date_created: 2020-09-18T10:49:19Z date_published: 2004-03-04T00:00:00Z date_updated: 2021-01-12T08:19:50Z day: '04' doi: 10.1214/aop/1078415827 extern: '1' intvolume: ' 32' issue: 1A language: - iso: eng month: '03' oa_version: None page: 1-27 publication: The Annals of Probability publication_identifier: issn: - 0091-1798 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' status: public title: Sample path properties of the stochastic flows type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2004' ... --- _id: '898' abstract: - lang: eng text: New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement. acknowledgement: We thank N. Bierne for a number of suggestions. G.A.B. was supported by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation. author: - first_name: Georgii full_name: Bazykin, Georgii A last_name: Bazykin - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 2004;429(6991):558-562. doi:10.1038/nature02601 apa: Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., & Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02601 chicago: Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02601. ieee: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” Nature, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004. ista: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562. mla: Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601. short: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562. date_created: 2018-12-11T11:49:05Z date_published: 2004-06-03T00:00:00Z date_updated: 2021-01-12T08:21:37Z day: '03' doi: 10.1038/nature02601 extern: 1 intvolume: ' 429' issue: '6991' month: '06' page: 558 - 562 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6746' quality_controlled: 0 status: public title: Positive selection at sites of multiple amino acid replacements since rat-mouse divergence type: journal_article volume: 429 year: '2004' ... --- _id: '902' abstract: - lang: eng text: 'We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.' acknowledgement: |- We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact. author: - first_name: Cristian full_name: Castillo-Davis, Cristian I last_name: Castillo Davis - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Daniel full_name: Hartl, Daniel L last_name: Hartl - first_name: Rob full_name: Kulathinal, Rob J last_name: Kulathinal citation: ama: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 2004;14(5):802-811. doi:10.1101/gr.2195604' apa: 'Castillo Davis, C., Kondrashov, F., Hartl, D., & Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.2195604' chicago: 'Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research. Cold Spring Harbor Laboratory Press, 2004. https://doi.org/10.1101/gr.2195604.' ieee: 'C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.' ista: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.' mla: 'Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004, pp. 802–11, doi:10.1101/gr.2195604.' short: C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811. date_created: 2018-12-11T11:49:06Z date_published: 2004-05-01T00:00:00Z date_updated: 2021-01-12T08:21:47Z day: '01' doi: 10.1101/gr.2195604 extern: 1 intvolume: ' 14' issue: '5' month: '05' page: 802 - 811 publication: Genome Research publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '6750' quality_controlled: 0 status: public title: 'The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint' type: journal_article volume: 14 year: '2004' ... --- _id: '9454' article_processing_charge: No article_type: original author: - first_name: Simon W.-L. full_name: Chan, Simon W.-L. last_name: Chan - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: ' Zhixin' full_name: Xie, Zhixin last_name: Xie - first_name: ' Lisa K.' full_name: Johansen, Lisa K. last_name: Johansen - first_name: James C. full_name: Carrington, James C. last_name: Carrington - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen citation: ama: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336. doi:10.1126/science.1095989 apa: Chan, S. W.-L., Zilberman, D., Xie, Zhixin, Johansen, Lisa K., Carrington, J. C., & Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1095989 chicago: Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” Science. American Association for the Advancement of Science, 2004. https://doi.org/10.1126/science.1095989. ieee: S. W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004. ista: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336. mla: Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.” Science, vol. 303, no. 5662, American Association for the Advancement of Science, 2004, p. 1336, doi:10.1126/science.1095989. short: S.W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336. date_created: 2021-06-04T11:12:35Z date_published: 2004-02-27T00:00:00Z date_updated: 2021-12-14T09:13:53Z day: '27' department: - _id: DaZi doi: 10.1126/science.1095989 extern: '1' external_id: pmid: - '14988555' intvolume: ' 303' issue: '5662' keyword: - Multidisciplinary language: - iso: eng month: '02' oa_version: None page: '1336' pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: RNA silencing genes control de novo DNA methylation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 303 year: '2004' ... --- _id: '12203' abstract: - lang: eng text: 'Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.' acknowledgement: This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree. article_processing_charge: No article_type: original author: - first_name: Zhihua full_name: Liao, Zhihua last_name: Liao - first_name: Min full_name: Chen, Min last_name: Chen - first_name: Yifu full_name: Gong, Yifu last_name: Gong - first_name: Liang full_name: Guo, Liang last_name: Guo - first_name: Qiumin full_name: Tan, Qiumin last_name: Tan - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Xiaofen full_name: Sun, Xiaofen last_name: Sun - first_name: Feng full_name: Tan, Feng last_name: Tan - first_name: Kexuan full_name: Tang, Kexuan last_name: Tang citation: ama: Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 2004;15(2):153-158. doi:10.1080/10425170410001667348 apa: Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. Informa UK Limited. https://doi.org/10.1080/10425170410001667348 chicago: Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” DNA Sequence. Informa UK Limited, 2004. https://doi.org/10.1080/10425170410001667348. ieee: Z. Liao et al., “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” DNA Sequence, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004. ista: Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158. mla: Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” DNA Sequence, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:10.1080/10425170410001667348. short: Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158. date_created: 2023-01-16T09:24:50Z date_published: 2004-01-01T00:00:00Z date_updated: 2023-05-08T10:58:29Z department: - _id: XiFe doi: 10.1080/10425170410001667348 extern: '1' external_id: pmid: - '15352294' intvolume: ' 15' issue: '2' keyword: - Endocrinology - Genetics - Molecular Biology - Biochemistry language: - iso: eng oa_version: None page: 153-158 pmid: 1 publication: DNA Sequence publication_identifier: issn: - 1042-5179 publication_status: published publisher: Informa UK Limited quality_controlled: '1' scopus_import: '1' status: public title: A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2004' ... --- _id: '13435' abstract: - lang: eng text: Micropatterning of surfaces with several chemicals at different spatial locations usually requires multiple stamping and registration steps. Here, we describe an experimental method based on reaction–diffusion phenomena that allows for simultaneous micropatterning of a substrate with several coloured chemicals. In this method, called wet stamping (WETS), aqueous solutions of two or more inorganic salts are delivered onto a film of dry, ionically doped gelatin from an agarose stamp patterned in bas relief. Once in conformal contact, these salts diffuse into the gelatin, where they react to give deeply coloured precipitates. Separation of colours in the plane of the surface is the consequence of the differences in the diffusion coefficients, the solubility products, and the amounts of different salts delivered from the stamp, and is faithfully reproduced by a theoretical model based on a system of reaction–diffusion partial differential equations. The multicolour micropatterns are useful as non-binary optical elements, and could potentially form the basis of new applications in microseparations and in controlled delivery. article_processing_charge: No article_type: original author: - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Marcin full_name: Fialkowski, Marcin last_name: Fialkowski - first_name: Igor T. full_name: Bensemann, Igor T. last_name: Bensemann - first_name: Agnieszka full_name: Bitner, Agnieszka last_name: Bitner - first_name: C. J. full_name: Campbell, C. J. last_name: Campbell - first_name: Kyle full_name: Bishop, Kyle last_name: Bishop - first_name: Stoyan full_name: Smoukov, Stoyan last_name: Smoukov - first_name: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Klajn R, Fialkowski M, Bensemann IT, et al. Multicolour micropatterning of thin films of dry gels. Nature Materials. 2004;3:729-735. doi:10.1038/nmat1231 apa: Klajn, R., Fialkowski, M., Bensemann, I. T., Bitner, A., Campbell, C. J., Bishop, K., … Grzybowski, B. A. (2004). Multicolour micropatterning of thin films of dry gels. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat1231 chicago: Klajn, Rafal, Marcin Fialkowski, Igor T. Bensemann, Agnieszka Bitner, C. J. Campbell, Kyle Bishop, Stoyan Smoukov, and Bartosz A. Grzybowski. “Multicolour Micropatterning of Thin Films of Dry Gels.” Nature Materials. Springer Nature, 2004. https://doi.org/10.1038/nmat1231. ieee: R. Klajn et al., “Multicolour micropatterning of thin films of dry gels,” Nature Materials, vol. 3. Springer Nature, pp. 729–735, 2004. ista: Klajn R, Fialkowski M, Bensemann IT, Bitner A, Campbell CJ, Bishop K, Smoukov S, Grzybowski BA. 2004. Multicolour micropatterning of thin films of dry gels. Nature Materials. 3, 729–735. mla: Klajn, Rafal, et al. “Multicolour Micropatterning of Thin Films of Dry Gels.” Nature Materials, vol. 3, Springer Nature, 2004, pp. 729–35, doi:10.1038/nmat1231. short: R. Klajn, M. Fialkowski, I.T. Bensemann, A. Bitner, C.J. Campbell, K. Bishop, S. Smoukov, B.A. Grzybowski, Nature Materials 3 (2004) 729–735. date_created: 2023-08-01T10:39:23Z date_published: 2004-09-19T00:00:00Z date_updated: 2023-08-08T12:42:51Z day: '19' doi: 10.1038/nmat1231 extern: '1' external_id: pmid: - '15378052' intvolume: ' 3' keyword: - Mechanical Engineering - Mechanics of Materials - Condensed Matter Physics - General Materials Science - General Chemistry language: - iso: eng month: '09' oa_version: None page: 729-735 pmid: 1 publication: Nature Materials publication_identifier: eissn: - 1476-4660 issn: - 1476-1122 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Multicolour micropatterning of thin films of dry gels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2004' ... --- _id: '13434' abstract: - lang: eng text: Thin films of ionically doped gelatin have been color-patterned with submicrometer precision using the wet-stamping technique. Inorganic salts are delivered onto the gelatin surface from an agarose stamp, and diffuse into the gelatine layer, producting deeply colored precipitates. Reaction fronts originating from different features of the stamp cease within < 1 μm of each other, leaving sharp, transparent regions in between. article_processing_charge: No article_type: original author: - first_name: C. J. full_name: Campbell, C. J. last_name: Campbell - first_name: M. full_name: Fialkowski, M. last_name: Fialkowski - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: I. T. full_name: Bensemann, I. T. last_name: Bensemann - first_name: B. A. full_name: Grzybowski, B. A. last_name: Grzybowski citation: ama: Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. 2004;16(21):1912-1917. doi:10.1002/adma.200400383 apa: Campbell, C. J., Fialkowski, M., Klajn, R., Bensemann, I. T., & Grzybowski, B. A. (2004). Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. Wiley. https://doi.org/10.1002/adma.200400383 chicago: Campbell, C. J., M. Fialkowski, Rafal Klajn, I. T. Bensemann, and B. A. Grzybowski. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” Advanced Materials. Wiley, 2004. https://doi.org/10.1002/adma.200400383. ieee: C. J. Campbell, M. Fialkowski, R. Klajn, I. T. Bensemann, and B. A. Grzybowski, “Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts,” Advanced Materials, vol. 16, no. 21. Wiley, pp. 1912–1917, 2004. ista: Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. 2004. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. 16(21), 1912–1917. mla: Campbell, C. J., et al. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” Advanced Materials, vol. 16, no. 21, Wiley, 2004, pp. 1912–17, doi:10.1002/adma.200400383. short: C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski, Advanced Materials 16 (2004) 1912–1917. date_created: 2023-08-01T10:39:09Z date_published: 2004-11-14T00:00:00Z date_updated: 2023-08-08T12:41:23Z day: '14' doi: 10.1002/adma.200400383 extern: '1' intvolume: ' 16' issue: '21' keyword: - Mechanical Engineering - Mechanics of Materials - General Materials Science language: - iso: eng month: '11' oa_version: None page: 1912-1917 publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2004' ... --- _id: '7706' abstract: - lang: eng text: 'The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3''s ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3''s ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.' article_processing_charge: No article_type: original author: - first_name: Anne full_name: Brunet, Anne last_name: Brunet - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 - first_name: 'J Fitzhugh ' full_name: 'Sturgill, J Fitzhugh ' last_name: Sturgill - first_name: Katrin full_name: Chua, Katrin last_name: Chua - first_name: Paul full_name: Greer, Paul last_name: Greer - first_name: Yingxi full_name: Lin, Yingxi last_name: Lin - first_name: Hien full_name: Tran, Hien last_name: Tran - first_name: Sarah full_name: Ross, Sarah last_name: Ross - first_name: Raul full_name: Mostoslavsky, Raul last_name: Mostoslavsky - first_name: Haim full_name: Cohen, Haim last_name: Cohen - first_name: Linda full_name: Hu, Linda last_name: Hu - first_name: Hwei-Ling full_name: Chen, Hwei-Ling last_name: Chen - first_name: Mark full_name: Jedrychowski, Mark last_name: Jedrychowski - first_name: Steven full_name: Gygi, Steven last_name: Gygi - first_name: David full_name: Sinclair, David last_name: Sinclair - first_name: Frederick full_name: Alt, Frederick last_name: Alt - first_name: Michael full_name: Greenberg, Michael last_name: Greenberg citation: ama: Brunet A, Sweeney LB, Sturgill JF, et al. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science. 2004;303(5666):2011-2015. doi:10.1126/science.1094637 apa: Brunet, A., Sweeney, L. B., Sturgill, J. F., Chua, K., Greer, P., Lin, Y., … Greenberg, M. (2004). Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1094637 chicago: Brunet, Anne, Lora B. Sweeney, J Fitzhugh Sturgill, Katrin Chua, Paul Greer, Yingxi Lin, Hien Tran, et al. “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase.” Science. American Association for the Advancement of Science, 2004. https://doi.org/10.1126/science.1094637. ieee: A. Brunet et al., “Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase,” Science, vol. 303, no. 5666. American Association for the Advancement of Science, pp. 2011–2015, 2004. ista: Brunet A, Sweeney LB, Sturgill JF, Chua K, Greer P, Lin Y, Tran H, Ross S, Mostoslavsky R, Cohen H, Hu L, Chen H-L, Jedrychowski M, Gygi S, Sinclair D, Alt F, Greenberg M. 2004. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science. 303(5666), 2011–2015. mla: Brunet, Anne, et al. “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase.” Science, vol. 303, no. 5666, American Association for the Advancement of Science, 2004, pp. 2011–15, doi:10.1126/science.1094637. short: A. Brunet, L.B. Sweeney, J.F. Sturgill, K. Chua, P. Greer, Y. Lin, H. Tran, S. Ross, R. Mostoslavsky, H. Cohen, L. Hu, H.-L. Chen, M. Jedrychowski, S. Gygi, D. Sinclair, F. Alt, M. Greenberg, Science 303 (2004) 2011–2015. date_created: 2020-04-30T10:37:41Z date_published: 2004-03-26T00:00:00Z date_updated: 2024-01-31T10:14:17Z day: '26' doi: 10.1126/science.1094637 extern: '1' intvolume: ' 303' issue: '5666' language: - iso: eng month: '03' oa_version: None page: 2011-2015 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 303 year: '2004' ...