--- _id: '3933' abstract: - lang: eng text: Resident dendritic cells (DC) within the T cell area of the lymph node take up soluble antigens that enter via the afferent lymphatics before antigen carrying DC arrive from the periphery. The reticular network within the lymph node is a conduit system forming the infrastructure for the fast delivery of soluble substances from the afferent lymph to the lumen of high endothelial venules (HEVs). Using high-resolution light microscopy and 3D reconstruction, we show here that these conduits are unique basement membrane-like structures ensheathed by fibroblastic reticular cells with occasional resident DC embedded within this cell layer. Conduit-associated DC are capable of taking up and processing soluble antigens transported within the conduits, whereas immigrated mature DC occur remote from the reticular fibers. The conduit system is, therefore, not a closed compartment that shuttles substances through the lymph node but represents the morphological equivalent to the filtering function of the lymph node. author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Nobuo full_name: Kanazawa, Nobuo last_name: Kanazawa - first_name: Manuel full_name: Selg, Manuel last_name: Selg - first_name: Thomas full_name: Samson, Thomas last_name: Samson - first_name: Gunnel full_name: Roos, Gunnel last_name: Roos - first_name: Dieter full_name: Reinhardt, Dieter last_name: Reinhardt - first_name: Reinhard full_name: Pabst, Reinhard last_name: Pabst - first_name: Manfred full_name: Lutz, Manfred last_name: Lutz - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin citation: ama: Sixt MK, Kanazawa N, Selg M, et al. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. 2005;22(1):19-29. doi:10.1016/j.immuni.2004.11.013 apa: Sixt, M. K., Kanazawa, N., Selg, M., Samson, T., Roos, G., Reinhardt, D., … Sorokin, L. (2005). The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2004.11.013 chicago: Sixt, Michael K, Nobuo Kanazawa, Manuel Selg, Thomas Samson, Gunnel Roos, Dieter Reinhardt, Reinhard Pabst, Manfred Lutz, and Lydia Sorokin. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” Immunity. Cell Press, 2005. https://doi.org/10.1016/j.immuni.2004.11.013. ieee: M. K. Sixt et al., “The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node,” Immunity, vol. 22, no. 1. Cell Press, pp. 19–29, 2005. ista: Sixt MK, Kanazawa N, Selg M, Samson T, Roos G, Reinhardt D, Pabst R, Lutz M, Sorokin L. 2005. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. 22(1), 19–29. mla: Sixt, Michael K., et al. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” Immunity, vol. 22, no. 1, Cell Press, 2005, pp. 19–29, doi:10.1016/j.immuni.2004.11.013. short: M.K. Sixt, N. Kanazawa, M. Selg, T. Samson, G. Roos, D. Reinhardt, R. Pabst, M. Lutz, L. Sorokin, Immunity 22 (2005) 19–29. date_created: 2018-12-11T12:05:58Z date_published: 2005-01-25T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '25' doi: 10.1016/j.immuni.2004.11.013 extern: '1' intvolume: ' 22' issue: '1' language: - iso: eng month: '01' oa_version: None page: 19 - 29 publication: Immunity publication_status: published publisher: Cell Press publist_id: '2195' status: public title: The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2005' ... --- _id: '3983' abstract: - lang: eng text: Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack of structural information about how Cdc25s interact with their native protein substrates, the cyclin-dependent kinases. Herein, we predict a docked orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body docking method and refine the docked models with full-scale molecular dynamics simulations and minimization. We validate the stable ensemble structure experimentally by a variety of in vitro and in vivo techniques. Specifically, we compare our model with a crystal structure of the substrate-trapping mutant of Cdc25B. We identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that plays a central role in protein substrate recognition. We identify a hot-spot residue on the Substrate Cdk2 (Asp206) and confirm its interaction with hot-spot residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction energies. Our experimentally validated model is consistent with previous studies of Cdk2 and its interaction partners and initiates the opportunity for drug discovery of inhibitors that target the remote binding sites of this protein-protein interaction. author: - first_name: Jungsan full_name: Sohn, Jungsan last_name: Sohn - first_name: Jerry full_name: Parks, Jerry M last_name: Parks - first_name: Gregory full_name: Buhrman, Gregory last_name: Buhrman - first_name: Paul full_name: Brown, Paul last_name: Brown - first_name: Kolbrun full_name: Kristjánsdóttir, Kolbrun last_name: Kristjánsdóttir - first_name: Alexias full_name: Safi, Alexias last_name: Safi - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Weitao full_name: Yang, Weitao T last_name: Yang - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: Sohn J, Parks J, Buhrman G, et al. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 2005;44(50):16563-16573. doi:10.1021/bi0516879 apa: Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A., … Rudolph, J. (2005). Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. ACS. https://doi.org/10.1021/bi0516879 chicago: Sohn, Jungsan, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjánsdóttir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang, and Johannes Rudolph. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” Biochemistry. ACS, 2005. https://doi.org/10.1021/bi0516879. ieee: J. Sohn et al., “Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate,” Biochemistry, vol. 44, no. 50. ACS, pp. 16563–16573, 2005. ista: Sohn J, Parks J, Buhrman G, Brown P, Kristjánsdóttir K, Safi A, Edelsbrunner H, Yang W, Rudolph J. 2005. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 44(50), 16563–16573. mla: Sohn, Jungsan, et al. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” Biochemistry, vol. 44, no. 50, ACS, 2005, pp. 16563–73, doi:10.1021/bi0516879. short: J. Sohn, J. Parks, G. Buhrman, P. Brown, K. Kristjánsdóttir, A. Safi, H. Edelsbrunner, W. Yang, J. Rudolph, Biochemistry 44 (2005) 16563–16573. date_created: 2018-12-11T12:06:16Z date_published: 2005-11-24T00:00:00Z date_updated: 2021-01-12T07:53:39Z day: '24' doi: 10.1021/bi0516879 extern: 1 intvolume: ' 44' issue: '50' month: '11' page: 16563 - 16573 publication: Biochemistry publication_status: published publisher: ACS publist_id: '2144' quality_controlled: 0 status: public title: Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate type: journal_article volume: 44 year: '2005' ... --- _id: '3982' abstract: - lang: eng text: We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems. author: - first_name: Yusu full_name: Wang, Yusu last_name: Wang - first_name: Pankaj full_name: Agarwal, Pankaj K last_name: Agarwal - first_name: Paul full_name: Brown, Paul last_name: Brown - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: 'Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. Coarse and reliable geometric alignment for protein docking. In: World Scientific Publishing; 2005:64-75. doi:10.1142/9789812702456_0007' apa: 'Wang, Y., Agarwal, P., Brown, P., Edelsbrunner, H., & Rudolph, J. (2005). Coarse and reliable geometric alignment for protein docking (pp. 64–75). Presented at the PSB: Pacific Symposium on Biocomputing, World Scientific Publishing. https://doi.org/10.1142/9789812702456_0007' chicago: Wang, Yusu, Pankaj Agarwal, Paul Brown, Herbert Edelsbrunner, and Johannes Rudolph. “Coarse and Reliable Geometric Alignment for Protein Docking,” 64–75. World Scientific Publishing, 2005. https://doi.org/10.1142/9789812702456_0007. ieee: 'Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph, “Coarse and reliable geometric alignment for protein docking,” presented at the PSB: Pacific Symposium on Biocomputing, 2005, pp. 64–75.' ista: 'Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. 2005. Coarse and reliable geometric alignment for protein docking. PSB: Pacific Symposium on Biocomputing, 64–75.' mla: Wang, Yusu, et al. Coarse and Reliable Geometric Alignment for Protein Docking. World Scientific Publishing, 2005, pp. 64–75, doi:10.1142/9789812702456_0007. short: Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, J. Rudolph, in:, World Scientific Publishing, 2005, pp. 64–75. conference: name: 'PSB: Pacific Symposium on Biocomputing' date_created: 2018-12-11T12:06:16Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:53:38Z day: '01' doi: 10.1142/9789812702456_0007 extern: 1 month: '01' page: 64 - 75 publication_status: published publisher: World Scientific Publishing publist_id: '2143' quality_controlled: 0 status: public title: Coarse and reliable geometric alignment for protein docking type: conference year: '2005' ... --- _id: '4144' abstract: - lang: eng text: Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation, but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain poorly understood. Here, we show that Wnt11 functions during zebrafish gastrulation by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation. article_processing_charge: No author: - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Michael full_name: Krieg, Michael last_name: Krieg - first_name: Eva full_name: Schötz, Eva last_name: Schötz - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Viktor full_name: Schnabel, Viktor last_name: Schnabel - first_name: Anna full_name: Taubenberger, Anna last_name: Taubenberger - first_name: Daniel full_name: Müller, Daniel last_name: Müller - first_name: Pierre full_name: Puech, Pierre last_name: Puech - 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: Ulrich F, Krieg M, Schötz E, et al. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 2005;9(4):555-564. doi:10.1016/j.devcel.2005.08.011 apa: Ulrich, F., Krieg, M., Schötz, E., Link, V., Castanon, I., Schnabel, V., … Heisenberg, C.-P. J. (2005). Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2005.08.011 chicago: Ulrich, Florian, Michael Krieg, Eva Schötz, Vinzenz Link, Irinka Castanon, Viktor Schnabel, Anna Taubenberger, Daniel Müller, Pierre Puech, and Carl-Philipp J Heisenberg. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” Developmental Cell. Cell Press, 2005. https://doi.org/10.1016/j.devcel.2005.08.011. ieee: F. Ulrich et al., “Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin,” Developmental Cell, vol. 9, no. 4. Cell Press, pp. 555–564, 2005. ista: Ulrich F, Krieg M, Schötz E, Link V, Castanon I, Schnabel V, Taubenberger A, Müller D, Puech P, Heisenberg C-PJ. 2005. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 9(4), 555–564. mla: Ulrich, Florian, et al. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” Developmental Cell, vol. 9, no. 4, Cell Press, 2005, pp. 555–64, doi:10.1016/j.devcel.2005.08.011. short: F. Ulrich, M. Krieg, E. Schötz, V. Link, I. Castanon, V. Schnabel, A. Taubenberger, D. Müller, P. Puech, C.-P.J. Heisenberg, Developmental Cell 9 (2005) 555–564. date_created: 2018-12-11T12:07:12Z date_published: 2005-10-01T00:00:00Z date_updated: 2021-01-12T07:54:50Z day: '01' doi: 10.1016/j.devcel.2005.08.011 extern: '1' intvolume: ' 9' issue: '4' language: - iso: eng month: '10' oa_version: None page: 555 - 564 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '1977' status: public title: Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2005' ... --- _id: '4138' abstract: - lang: eng text: |- Adaptive dynamics describes the evolution of an asexual population through the successive substitution of mutations of small effect. Waxman & Gavrilets (2005) give an excellent overview of the method and its applications. In this note, we focus on the plausibility of the key assumption that mutations have small effects, and the consequences of relaxing that assumption. We argue that: (i) successful mutations often have large effects; (ii) such mutations generate a qualitatively different evolutionary pattern, which is inherently stochastic; and (iii) in models of competition for a continuous resource, selection becomes very weak once several phenotypes are established. This makes the effects of introducing new mutations unpredictable using the methods of adaptive dynamics. We should make clear at the outset that our criticism is of methods that rely on local analysis of fitness gradients (eqn 2 of Waxman & Gavrilets, 2005), and not of the broader idea that evolution can be understood by examining the invasion of successive mutations. We use the term ‘adaptive dynamics’ to refer to the former technique, and contrast it with a more general population genetic analysis of probabilities of invasion. author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jitka full_name: Jitka Polechova id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: Barton NH, Polechova J. The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. 2005;18(5):1186-1190. doi:10.1111/j.1420-9101.2005.00943.x apa: Barton, N. H., & Polechova, J. (2005). The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/j.1420-9101.2005.00943.x chicago: Barton, Nicholas H, and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” Journal of Evolutionary Biology. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1420-9101.2005.00943.x. ieee: N. H. Barton and J. Polechova, “The limitations of adaptive dynamics as a model of evolution,” Journal of Evolutionary Biology, vol. 18, no. 5. Wiley-Blackwell, pp. 1186–1190, 2005. ista: Barton NH, Polechova J. 2005. The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. 18(5), 1186–1190. mla: Barton, Nicholas H., and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” Journal of Evolutionary Biology, vol. 18, no. 5, Wiley-Blackwell, 2005, pp. 1186–90, doi:10.1111/j.1420-9101.2005.00943.x. short: N.H. Barton, J. Polechova, Journal of Evolutionary Biology 18 (2005) 1186–1190. date_created: 2018-12-11T12:07:10Z date_published: 2005-09-01T00:00:00Z date_updated: 2021-01-12T07:54:47Z day: '01' doi: 10.1111/j.1420-9101.2005.00943.x extern: 1 intvolume: ' 18' issue: '5' month: '09' page: 1186 - 1190 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley-Blackwell publist_id: '1982' quality_controlled: 0 status: public title: The limitations of adaptive dynamics as a model of evolution type: journal_article volume: 18 year: '2005' ... --- _id: '4155' abstract: - lang: eng text: During vertebrate gastrulation, progenitor cells of different germ layers acquire specific adhesive properties that contribute to germ layer formation and separation. Wnt signals have been suggested to function in this process by modulating the different levels of adhesion between the germ layers, however, direct evidence for this is still lacking. Here we show that Wnt11, a key signal regulating gastrulation movements, is needed for the adhesion of zebrafish mesendodermal progenitor cells to fibronectin, an abundant extracellular matrix component during gastrulation. To measure this effect, we developed an assay to quantify the adhesion of single zebrafish primary mesendodermal progenitors using atomic-force microscopy (AFM). We observed significant differences in detachment force and work between cultured mesendodermal progenitors from wild-type embryos and from slb/wit11 mutant embryos, which carry a loss-of-function mutation in the wnt11 gene, when tested on fibronectin-coated substrates. These differences were probably due to reduced adhesion to the fibronectin substrate as neither the overall cell morphology nor the cell elasticity grossly differed between wild-type and mutant cells. Furthermore, in the presence of inhibitors of fibronectin-integrin binding, such as RGD peptides, the adhesion force and work were strongly decreased, indicating that integrins are involved in the binding of mesendodermal progenitors in our assay. These findings demonstrate that AFM can be used to quantitatively determine the substrate-adhesion of cultured primary gastrulating cells and provide insight into the role of Wnt11 signalling in modulating cell adhesion at the single cell scale. article_processing_charge: No author: - first_name: Pierre full_name: Puech, Pierre last_name: Puech - first_name: Anna full_name: Taubenberger, Anna last_name: Taubenberger - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Michael full_name: Krieg, Michael last_name: Krieg - first_name: Daniel full_name: Mueller, Daniel last_name: Mueller - 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: Puech P, Taubenberger A, Ulrich F, Krieg M, Mueller D, Heisenberg C-PJ. Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. Journal of Cell Science. 2005;118(18):4199-4206. doi:10.1242/​jcs.02547 apa: Puech, P., Taubenberger, A., Ulrich, F., Krieg, M., Mueller, D., & Heisenberg, C.-P. J. (2005). Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/​jcs.02547 chicago: Puech, Pierre, Anna Taubenberger, Florian Ulrich, Michael Krieg, Daniel Mueller, and Carl-Philipp J Heisenberg. “Measuring Cell Adhesion Forces of Primary Gastrulating Cells from Zebrafish Using Atomic Force Microscopy.” Journal of Cell Science. Company of Biologists, 2005. https://doi.org/10.1242/​jcs.02547. ieee: P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, and C.-P. J. Heisenberg, “Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy,” Journal of Cell Science, vol. 118, no. 18. Company of Biologists, pp. 4199–4206, 2005. ista: Puech P, Taubenberger A, Ulrich F, Krieg M, Mueller D, Heisenberg C-PJ. 2005. Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. Journal of Cell Science. 118(18), 4199–4206. mla: Puech, Pierre, et al. “Measuring Cell Adhesion Forces of Primary Gastrulating Cells from Zebrafish Using Atomic Force Microscopy.” Journal of Cell Science, vol. 118, no. 18, Company of Biologists, 2005, pp. 4199–206, doi:10.1242/​jcs.02547. short: P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, C.-P.J. Heisenberg, Journal of Cell Science 118 (2005) 4199–4206. date_created: 2018-12-11T12:07:16Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:54:54Z day: '01' doi: 10.1242/​jcs.02547 extern: '1' intvolume: ' 118' issue: '18' language: - iso: eng month: '01' oa_version: None page: 4199 - 4206 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '1964' status: public title: Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2005' ... --- _id: '4171' abstract: - lang: eng text: During vertebrate gastrulation, the three germ layers, ectoderm, mesoderm and endoderm are formed, and the resulting progenitor cells are brought into the positions from which they will later contribute more complex tissues and organs. A core element in this process is the internalization of mesodermal and endodermal progenitors at the onset of gastrulation. Although many of the molecules that induce mesendoderm have been identified, much less is known about the cellular mechanisms underlying mesendodermal cell internalization and germ layer formation. Here we show that at the onset of zebrafish gastrulation, mesendodermal progenitors in dorsal/axial regions of the germ ring internalize by single cell delamination. Once internalized, mesendodermal progenitors upregulate ECadherin (Cadherin 1) expression, become increasingly motile and eventually migrate along the overlying epiblast (ectodermal) cell layer towards the animal pole of the gastrula. When E-Cadherin function is compromised, mesendodermal progenitors still internalize, but, with gastrulation proceeding, fail to elongate and efficiently migrate along the epiblast, whereas epiblast cells themselves exhibit reduced radial cell intercalation movements. This indicates that cadherin-mediated cell-cell adhesion is needed within the forming shield for both epiblast cell intercalation, and mesendodermal progenitor cell elongation and migration during zebrafish gastrulation. Our data provide insight into the cellular mechanisms underlying mesendodermal progenitor cell internalization and subsequent migration during zebrafish gastrulation, and the role of cadherin-mediated cell-cell adhesion in these processes. article_processing_charge: No author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Michaela full_name: Wilsch Bräuninger, Michaela last_name: Wilsch Bräuninger - first_name: Beate full_name: Kilian, Beate last_name: Kilian - first_name: Chigdem full_name: Mustafa, Chigdem last_name: Mustafa - 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, Carvalho L, Wilsch Bräuninger M, Kilian B, Mustafa C, Heisenberg C-PJ. Shield formation at the onset of zebrafish gastrulation. Development. 2005;132(6):1187-1198. doi:10.1242/dev.01667 apa: Montero, J., Carvalho, L., Wilsch Bräuninger, M., Kilian, B., Mustafa, C., & Heisenberg, C.-P. J. (2005). Shield formation at the onset of zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.01667 chicago: Montero, Juan, Lara Carvalho, Michaela Wilsch Bräuninger, Beate Kilian, Chigdem Mustafa, and Carl-Philipp J Heisenberg. “Shield Formation at the Onset of Zebrafish Gastrulation.” Development. Company of Biologists, 2005. https://doi.org/10.1242/dev.01667. ieee: J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, and C.-P. J. Heisenberg, “Shield formation at the onset of zebrafish gastrulation,” Development, vol. 132, no. 6. Company of Biologists, pp. 1187–1198, 2005. ista: Montero J, Carvalho L, Wilsch Bräuninger M, Kilian B, Mustafa C, Heisenberg C-PJ. 2005. Shield formation at the onset of zebrafish gastrulation. Development. 132(6), 1187–1198. mla: Montero, Juan, et al. “Shield Formation at the Onset of Zebrafish Gastrulation.” Development, vol. 132, no. 6, Company of Biologists, 2005, pp. 1187–98, doi:10.1242/dev.01667. short: J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, C.-P.J. Heisenberg, Development 132 (2005) 1187–1198. date_created: 2018-12-11T12:07:22Z date_published: 2005-03-15T00:00:00Z date_updated: 2021-01-12T07:55:02Z day: '15' doi: 10.1242/dev.01667 extern: '1' intvolume: ' 132' issue: '6' language: - iso: eng month: '03' oa_version: None page: 1187 - 1198 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1947' status: public title: Shield formation at the onset of zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 132 year: '2005' ... --- _id: '4249' abstract: - lang: eng text: We examined causes of speciation in asexual populations in both sympatry and parapatry, providing an alternative explanation for the speciation patterns reported by Dieckmann and Doebeli (1999) and Doebeli and Dieckmann (2003). Both in sympatry and parapatry, they find that speciation occurs relatively easily. We reveal that in the sympatric clonal model, the equilibrium distribution is continuous and the disruptive selection driving evolution of discrete clusters is only transient. Hence, if discrete phenotypes are to remain stable in the sympatric sexual model, there should be some source of nontransient disruptive selection that will drive evolution of assortment. We analyze sexually reproducing populations using the Bulmer’s infinitesimal model and show that cost-free assortment alone leads to speciation and disruptive selection only arises when the optimal distribution cannot be matched—in this example, because the phenotypic range is limited. In addition, Doebeli and Dieckmann’s analyses assumed a high genetic variance and a high mutation rate. Thus, these theoretical models do not support the conclusion that sympatric speciation is a likely outcome of competition for resources. In their parapatric model (Doebeli and Dieckmann 2003), clustering into distinct phenotypes is driven by edge effects, rather than by frequency-dependent competition. author: - first_name: Jitka full_name: Jitka Polechova id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Polechova J, Barton NH. Speciation through competition: A critical review. Evolution; International Journal of Organic Evolution. 2005;59(6):1194-1210. doi:10.1111/j.0014-3820.2005.tb01771.x' apa: 'Polechova, J., & Barton, N. H. (2005). Speciation through competition: A critical review. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2005.tb01771.x' chicago: 'Polechova, Jitka, and Nicholas H Barton. “Speciation through Competition: A Critical Review.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.0014-3820.2005.tb01771.x.' ieee: 'J. Polechova and N. H. Barton, “Speciation through competition: A critical review,” Evolution; International Journal of Organic Evolution, vol. 59, no. 6. Wiley-Blackwell, pp. 1194–1210, 2005.' ista: 'Polechova J, Barton NH. 2005. Speciation through competition: A critical review. Evolution; International Journal of Organic Evolution. 59(6), 1194–1210.' mla: 'Polechova, Jitka, and Nicholas H. Barton. “Speciation through Competition: A Critical Review.” Evolution; International Journal of Organic Evolution, vol. 59, no. 6, Wiley-Blackwell, 2005, pp. 1194–210, doi:10.1111/j.0014-3820.2005.tb01771.x.' short: J. Polechova, N.H. Barton, Evolution; International Journal of Organic Evolution 59 (2005) 1194–1210. date_created: 2018-12-11T12:07:50Z date_published: 2005-06-01T00:00:00Z date_updated: 2021-01-12T07:55:36Z day: '01' doi: 10.1111/j.0014-3820.2005.tb01771.x extern: 1 intvolume: ' 59' issue: '6' month: '06' page: 1194 - 1210 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '1849' quality_controlled: 0 status: public title: 'Speciation through competition: A critical review' type: journal_article volume: 59 year: '2005' ... --- _id: '4251' abstract: - lang: eng text: In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e. multiplicatively) upon all loci. Negative disequilibrium reduces the variance in fitness and hence, by FISHER's Fundamental Theorem (1930), slows the rate of increase in mean fitness. Modifiers that increase recombination eliminate the negative disequilibria that impede selection and consequently increase in frequency by 'hitch-hiking'. In addition, recombinant progeny are more fit on average than non-recombinant progeny when there is negative linkage disequilibrium and loci interact multiplicatively. For both these reasons, stochastic fluctuations in linkage disequilibrium in finite populations favor the evolution of increased rates of recombination, even in the absence of epistatic interactions among loci and even when disequilibrium is initially absent. The method developed within this paper quantifies the strength of selection on a modifier allele that increases recombination due to stochastically generated linkage disequilibria. The analysis indicates that, in a population subject to multiplicative selection, genetic associations generated by drift do select for increased recombination, a result that is confirmed by Monte Carlo simulations. Selection for a modifier that increases recombination is highest when linkage among all loci is tight, when beneficial alleles rise from low to high frequency, and when the population size is small. author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Sarah full_name: Otto, Sarah P last_name: Otto citation: ama: Barton NH, Otto S. Evolution of recombination due to random drift. Genetics. 2005;169(4):2353-2370. doi:10.1534/genetics.104.032821 apa: Barton, N. H., & Otto, S. (2005). Evolution of recombination due to random drift. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.104.032821 chicago: Barton, Nicholas H, and Sarah Otto. “Evolution of Recombination Due to Random Drift.” Genetics. Genetics Society of America, 2005. https://doi.org/10.1534/genetics.104.032821. ieee: N. H. Barton and S. Otto, “Evolution of recombination due to random drift,” Genetics, vol. 169, no. 4. Genetics Society of America, pp. 2353–2370, 2005. ista: Barton NH, Otto S. 2005. Evolution of recombination due to random drift. Genetics. 169(4), 2353–2370. mla: Barton, Nicholas H., and Sarah Otto. “Evolution of Recombination Due to Random Drift.” Genetics, vol. 169, no. 4, Genetics Society of America, 2005, pp. 2353–70, doi:10.1534/genetics.104.032821. short: N.H. Barton, S. Otto, Genetics 169 (2005) 2353–2370. date_created: 2018-12-11T12:07:51Z date_published: 2005-03-01T00:00:00Z date_updated: 2021-01-12T07:55:37Z day: '01' doi: 10.1534/genetics.104.032821 extern: 1 intvolume: ' 169' issue: '4' month: '03' page: 2353 - 2370 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '1846' quality_controlled: 0 status: public title: Evolution of recombination due to random drift type: journal_article volume: 169 year: '2005' ... --- _id: '4252' abstract: - lang: eng text: Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some author: - first_name: Toby full_name: Johnson, Toby last_name: Johnson - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Johnson T, Barton NH. Theoretical models of selection and mutationon quantitative traits. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2005;360(1459):1411-1425. doi:10.1098/rstb.2005.1667 apa: Johnson, T., & Barton, N. H. (2005). Theoretical models of selection and mutationon quantitative traits. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2005.1667 chicago: Johnson, Toby, and Nicholas H Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2005. https://doi.org/10.1098/rstb.2005.1667. ieee: T. Johnson and N. H. Barton, “Theoretical models of selection and mutationon quantitative traits,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 360, no. 1459. Royal Society, The, pp. 1411–1425, 2005. ista: Johnson T, Barton NH. 2005. Theoretical models of selection and mutationon quantitative traits. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360(1459), 1411–1425. mla: Johnson, Toby, and Nicholas H. Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 360, no. 1459, Royal Society, The, 2005, pp. 1411–25, doi:10.1098/rstb.2005.1667. short: T. Johnson, N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360 (2005) 1411–1425. date_created: 2018-12-11T12:07:51Z date_published: 2005-07-29T00:00:00Z date_updated: 2021-01-12T07:55:38Z day: '29' doi: 10.1098/rstb.2005.1667 extern: 1 intvolume: ' 360' issue: '1459' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569515/ month: '07' oa: 1 page: 1411 - 1425 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '1847' quality_controlled: 0 status: public title: Theoretical models of selection and mutationon quantitative traits type: journal_article volume: 360 year: '2005' ... --- _id: '4404' author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Pavol full_name: Pavol Cerny id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: P. full_name: Madhusudan,P. last_name: Madhusudan - first_name: Wonhong full_name: Nam,Wonhong last_name: Nam citation: ama: 'Alur R, Cerny P, Madhusudan P, Nam W. Synthesis of interface specifications for Java classes. In: ACM; 2005:98-109. doi:1542' apa: 'Alur, R., Cerny, P., Madhusudan, P., & Nam, W. (2005). Synthesis of interface specifications for Java classes (pp. 98–109). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/1542' chicago: Alur, Rajeev, Pavol Cerny, P. Madhusudan, and Wonhong Nam. “Synthesis of Interface Specifications for Java Classes,” 98–109. ACM, 2005. https://doi.org/1542. ieee: 'R. Alur, P. Cerny, P. Madhusudan, and W. Nam, “Synthesis of interface specifications for Java classes,” presented at the POPL: Principles of Programming Languages, 2005, pp. 98–109.' ista: 'Alur R, Cerny P, Madhusudan P, Nam W. 2005. Synthesis of interface specifications for Java classes. POPL: Principles of Programming Languages, 98–109.' mla: Alur, Rajeev, et al. Synthesis of Interface Specifications for Java Classes. ACM, 2005, pp. 98–109, doi:1542. short: R. Alur, P. Cerny, P. Madhusudan, W. Nam, in:, ACM, 2005, pp. 98–109. conference: name: 'POPL: Principles of Programming Languages' date_created: 2018-12-11T12:08:41Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:56:44Z day: '01' doi: '1542' extern: 1 month: '01' page: 98 - 109 publication_status: published publisher: ACM publist_id: '1053' quality_controlled: 0 status: public title: Synthesis of interface specifications for Java classes type: conference year: '2005' ... --- _id: '4412' abstract: - lang: eng text: The periodic resource model for hierarchical, compositional scheduling abstracts task groups by resource requirements. We study this model in the presence of dataflow constraints between the tasks within a group (intragroup dependencies), and between tasks in different groups (inter-group dependencies). We consider two natural semantics for dataflow constraints, namely, RTW (real-time workshop) semantics and LET (logical execution time) semantics. We show that while RTW semantics offers better end-to-end latency on the task group level, LET semantics allows tighter resource bounds in the abstraction hierarchy and therefore provides better composability properties. This result holds both for intragroup and intergroup dependencies, as well as for shared and for distributed resources. author: - first_name: Slobodan full_name: Matic, Slobodan last_name: Matic - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Matic S, Henzinger TA. Trading end-to-end latency for composability. In: IEEE; 2005:99-110. doi:10.1109/RTSS.2005.43' apa: 'Matic, S., & Henzinger, T. A. (2005). Trading end-to-end latency for composability (pp. 99–110). Presented at the RTSS: Real-Time Systems Symposium, IEEE. https://doi.org/10.1109/RTSS.2005.43' chicago: Matic, Slobodan, and Thomas A Henzinger. “Trading End-to-End Latency for Composability,” 99–110. IEEE, 2005. https://doi.org/10.1109/RTSS.2005.43. ieee: 'S. Matic and T. A. Henzinger, “Trading end-to-end latency for composability,” presented at the RTSS: Real-Time Systems Symposium, 2005, pp. 99–110.' ista: 'Matic S, Henzinger TA. 2005. Trading end-to-end latency for composability. RTSS: Real-Time Systems Symposium, 99–110.' mla: Matic, Slobodan, and Thomas A. Henzinger. Trading End-to-End Latency for Composability. IEEE, 2005, pp. 99–110, doi:10.1109/RTSS.2005.43. short: S. Matic, T.A. Henzinger, in:, IEEE, 2005, pp. 99–110. conference: name: 'RTSS: Real-Time Systems Symposium' date_created: 2018-12-11T12:08:43Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:56:47Z day: '01' doi: 10.1109/RTSS.2005.43 extern: 1 month: '01' page: 99 - 110 publication_status: published publisher: IEEE publist_id: '317' quality_controlled: 0 status: public title: Trading end-to-end latency for composability type: conference year: '2005' ... --- _id: '4418' abstract: - lang: eng text: 'We present a new software system architecture for the implementation of hard real-time applications. The core of the system is a microkernel whose reactivity (interrupt handling as in synchronous reactive programs) and proactivity (task scheduling as in traditional RTOSs) are fully programmable. The microkernel, which we implemented on a StrongARM processor, consists of two interacting domain-specific virtual machines, a reactive E (Embedded) machine and a proactive S (Scheduling) machine. The microkernel code (or microcode) that runs on the microkernel is partitioned into E and S code. E code manages the interaction of the system with the physical environment: the execution of E code is triggered by environment interrupts, which signal external events such as the arrival of a message or sensor value, and it releases application tasks to the S machine. S code manages the interaction of the system with the processor: the execution of S code is triggered by hardware interrupts, which signal internal events such as the completion of a task or time slice, and it dispatches application tasks to the CPU, possibly preempting a running task. This partition of the system orthogonalizes the two main concerns of real-time implementations: E code refers to environment time and thus defines the reactivity of the system in a hardware- and scheduler-independent fashion; S code refers to CPU time and defines a system scheduler. If both time lines can be reconciled, then the code is called time safe; violations of time safety are handled again in a programmable way, by run-time exceptions. The separation of E from S code permits the independent programming, verification, optimization, composition, dynamic adaptation, and reuse of both reaction and scheduling mechanisms. Our measurements show that the system overhead is very acceptable even for large sets of task, generally in the 0.2--0.3% range.' author: - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch - first_name: Marco full_name: Sanvido, Marco A last_name: Sanvido - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Kirsch C, Sanvido M, Henzinger TA. A programmable microkernel for real-time systems. In: ACM; 2005:35-45. doi:10.1145/1064979.1064986' apa: 'Kirsch, C., Sanvido, M., & Henzinger, T. A. (2005). A programmable microkernel for real-time systems (pp. 35–45). Presented at the VEE: Virtual Execution Environments, ACM. https://doi.org/10.1145/1064979.1064986' chicago: Kirsch, Christoph, Marco Sanvido, and Thomas A Henzinger. “A Programmable Microkernel for Real-Time Systems,” 35–45. ACM, 2005. https://doi.org/10.1145/1064979.1064986. ieee: 'C. Kirsch, M. Sanvido, and T. A. Henzinger, “A programmable microkernel for real-time systems,” presented at the VEE: Virtual Execution Environments, 2005, pp. 35–45.' ista: 'Kirsch C, Sanvido M, Henzinger TA. 2005. A programmable microkernel for real-time systems. VEE: Virtual Execution Environments, 35–45.' mla: Kirsch, Christoph, et al. A Programmable Microkernel for Real-Time Systems. ACM, 2005, pp. 35–45, doi:10.1145/1064979.1064986. short: C. Kirsch, M. Sanvido, T.A. Henzinger, in:, ACM, 2005, pp. 35–45. conference: name: 'VEE: Virtual Execution Environments' date_created: 2018-12-11T12:08:45Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:56:49Z day: '01' doi: 10.1145/1064979.1064986 extern: 1 month: '01' page: 35 - 45 publication_status: published publisher: ACM publist_id: '311' quality_controlled: 0 status: public title: A programmable microkernel for real-time systems type: conference year: '2005' ... --- _id: '4454' abstract: - lang: eng text: We define five increasingly comprehensive classes of infinite-state systems, called STS1--STS5, whose state spaces have finitary structure. For four of these classes, we provide examples from hybrid systems.STS1 These are the systems with finite bisimilarity quotients. They can be analyzed symbolically by iteratively applying predecessor and Boolean operations on state sets, starting from a finite number of observable state sets. Any such iteration is guaranteed to terminate in that only a finite number of state sets can be generated. This enables model checking of the μ-calculus.STS2 These are the systems with finite similarity quotients. They can be analyzed symbolically by iterating the predecessor and positive Boolean operations. This enables model checking of the existential and universal fragments of the μ-calculus.STS3 These are the systems with finite trace-equivalence quotients. They can be analyzed symbolically by iterating the predecessor operation and a restricted form of positive Boolean operations (intersection is restricted to intersection with observables). This enables model checking of all ω-regular properties, including linear temporal logic.STS4 These are the systems with finite distance-equivalence quotients (two states are equivalent if for every distance d, the same observables can be reached in d transitions). The systems in this class can be analyzed symbolically by iterating the predecessor operation and terminating when no new state sets are generated. This enables model checking of the existential conjunction-free and universal disjunction-free fragments of the μ-calculus.STS5 These are the systems with finite bounded-reachability quotients (two states are equivalent if for every distance d, the same observables can be reached in d or fewer transitions). The systems in this class can be analyzed symbolically by iterating the predecessor operation and terminating when no new states are encountered (this is a weaker termination condition than above). This enables model checking of reachability properties. 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: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: Henzinger TA, Majumdar R, Raskin J. A classification of symbolic transition systems. ACM Transactions on Computational Logic (TOCL). 2005;6(1):1-32. doi:10.1145/1042038.1042039 apa: Henzinger, T. A., Majumdar, R., & Raskin, J. (2005). A classification of symbolic transition systems. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/1042038.1042039 chicago: Henzinger, Thomas A, Ritankar Majumdar, and Jean Raskin. “A Classification of Symbolic Transition Systems.” ACM Transactions on Computational Logic (TOCL). ACM, 2005. https://doi.org/10.1145/1042038.1042039. ieee: T. A. Henzinger, R. Majumdar, and J. Raskin, “A classification of symbolic transition systems,” ACM Transactions on Computational Logic (TOCL), vol. 6, no. 1. ACM, pp. 1–32, 2005. ista: Henzinger TA, Majumdar R, Raskin J. 2005. A classification of symbolic transition systems. ACM Transactions on Computational Logic (TOCL). 6(1), 1–32. mla: Henzinger, Thomas A., et al. “A Classification of Symbolic Transition Systems.” ACM Transactions on Computational Logic (TOCL), vol. 6, no. 1, ACM, 2005, pp. 1–32, doi:10.1145/1042038.1042039. short: T.A. Henzinger, R. Majumdar, J. Raskin, ACM Transactions on Computational Logic (TOCL) 6 (2005) 1–32. date_created: 2018-12-11T12:08:56Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:57:05Z day: '01' doi: 10.1145/1042038.1042039 extern: 1 intvolume: ' 6' issue: '1' month: '01' page: 1 - 32 publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '272' quality_controlled: 0 status: public title: A classification of symbolic transition systems type: journal_article volume: 6 year: '2005' ... --- _id: '4455' abstract: - lang: eng text: We define quantitative similarity functions between timed transition systems that measure the degree of closeness of two systems as a real, in contrast to the traditional boolean yes/no approach to timed simulation and language inclusion. Two systems are close if for each timed trace of one system, there exists a corresponding timed trace in the other system with the same sequence of events and closely corresponding event timings. We show that timed CTL is robust with respect to our quantitative version of bisimilarity, in particular, if a system satisfies a formula, then every close system satisfies a close formula. We also define a discounted version of CTL over timed systems, which assigns to every CTL formula a real value that is obtained by discounting real time. We prove the robustness of discounted CTL by establishing that close states in the bisimilarity metric have close values for all discounted CTL formulas. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF grants CCR-0208875, CCR-0225610, and CCR-0427202. 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: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Vinayak full_name: Prabhu, Vinayak S last_name: Prabhu citation: ama: 'Henzinger TA, Majumdar R, Prabhu V. Quantifying similarities between timed systems. In: Vol 3829. Springer; 2005:226-241. doi:10.1007/11603009_18' apa: 'Henzinger, T. A., Majumdar, R., & Prabhu, V. (2005). Quantifying similarities between timed systems (Vol. 3829, pp. 226–241). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/10.1007/11603009_18' chicago: Henzinger, Thomas A, Ritankar Majumdar, and Vinayak Prabhu. “Quantifying Similarities between Timed Systems,” 3829:226–41. Springer, 2005. https://doi.org/10.1007/11603009_18. ieee: 'T. A. Henzinger, R. Majumdar, and V. Prabhu, “Quantifying similarities between timed systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2005, vol. 3829, pp. 226–241.' ista: 'Henzinger TA, Majumdar R, Prabhu V. 2005. Quantifying similarities between timed systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 3829, 226–241.' mla: Henzinger, Thomas A., et al. Quantifying Similarities between Timed Systems. Vol. 3829, Springer, 2005, pp. 226–41, doi:10.1007/11603009_18. short: T.A. Henzinger, R. Majumdar, V. Prabhu, in:, Springer, 2005, pp. 226–241. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:56Z date_published: 2005-12-13T00:00:00Z date_updated: 2021-01-12T07:57:05Z day: '13' doi: 10.1007/11603009_18 extern: 1 intvolume: ' 3829' month: '12' page: 226 - 241 publication_status: published publisher: Springer publist_id: '273' quality_controlled: 0 status: public title: Quantifying similarities between timed systems type: conference volume: 3829 year: '2005' ... --- _id: '4456' abstract: - lang: eng text: 'A modular program analysis considers components independently and provides a succinct summary for each component, which is used when checking the rest of the system. Consider a system consisting of a library and a client. A temporal summary, or interface, of the library specifies legal sequences of library calls. The interface is safe if no call sequence violates the library''s internal invariants; the interface is permissive if it contains every such sequence. Modular program analysis requires full interfaces, which are both safe and permissive: the client does not cause errors in the library if and only if it makes only sequences of library calls that are allowed by the full interface of the library.Previous interface-based methods have focused on safe interfaces, which may be too restrictive and thus reject good clients. We present an algorithm for automatically synthesizing software interfaces that are both safe and permissive. The algorithm generates interfaces as graphs whose vertices are labeled with predicates over the library''s internal state, and whose edges are labeled with library calls. The interface state is refined incrementally until the full interface is constructed. In other words, the algorithm automatically synthesizes a typestate system for the library, against which any client can be checked for compatibility. We present an implementation of the algorithm which is based on the BLAST model checker, and we evaluate some case studies.' 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. Permissive interfaces. In: ACM; 2005:31-40. doi:10.1145/1081706.1081713' apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2005). Permissive interfaces (pp. 31–40). Presented at the FSE: Foundations of Software Engineering, ACM. https://doi.org/10.1145/1081706.1081713' chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Permissive Interfaces,” 31–40. ACM, 2005. https://doi.org/10.1145/1081706.1081713. ieee: 'T. A. Henzinger, R. Jhala, and R. Majumdar, “Permissive interfaces,” presented at the FSE: Foundations of Software Engineering, 2005, pp. 31–40.' ista: 'Henzinger TA, Jhala R, Majumdar R. 2005. Permissive interfaces. FSE: Foundations of Software Engineering, 31–40.' mla: Henzinger, Thomas A., et al. Permissive Interfaces. ACM, 2005, pp. 31–40, doi:10.1145/1081706.1081713. short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, ACM, 2005, pp. 31–40. conference: name: 'FSE: Foundations of Software Engineering' date_created: 2018-12-11T12:08:56Z date_published: 2005-09-01T00:00:00Z date_updated: 2021-01-12T07:57:06Z day: '01' doi: 10.1145/1081706.1081713 extern: 1 month: '09' page: 31 - 40 publication_status: published publisher: ACM publist_id: '274' quality_controlled: 0 status: public title: Permissive interfaces type: conference year: '2005' ... --- _id: '4457' abstract: - lang: eng text: We present a compositional approach to the implementation of hard real-time software running on a distributed platform. We explain how several code suppliers, coordinated by a system integrator, can independently generate different parts of the distributed software. The task structure, interaction, and timing is specified as a Giotto program. Each supplier is given a part of the Giotto program and a timing interface, from which the supplier generates task and scheduling code. The integrator then checks, individually for each supplier, in pseudo-polynomial time, if the supplied code meets its timing specification. If all checks succeed, then the supplied software parts are guaranteed to work together and implement the original Giotto program. The feasibility of the approach is demonstrated by a prototype implementation. 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 - first_name: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: 'Henzinger TA, Kirsch C, Matic S. Composable code generation for distributed Giotto. In: ACM; 2005:21-30. doi:10.1145/1065910.1065914' apa: 'Henzinger, T. A., Kirsch, C., & Matic, S. (2005). Composable code generation for distributed Giotto (pp. 21–30). Presented at the LCTES: Languages, Compilers, and Tools for Embedded Systems, ACM. https://doi.org/10.1145/1065910.1065914' chicago: Henzinger, Thomas A, Christoph Kirsch, and Slobodan Matic. “Composable Code Generation for Distributed Giotto,” 21–30. ACM, 2005. https://doi.org/10.1145/1065910.1065914. ieee: 'T. A. Henzinger, C. Kirsch, and S. Matic, “Composable code generation for distributed Giotto,” presented at the LCTES: Languages, Compilers, and Tools for Embedded Systems, 2005, pp. 21–30.' ista: 'Henzinger TA, Kirsch C, Matic S. 2005. Composable code generation for distributed Giotto. LCTES: Languages, Compilers, and Tools for Embedded Systems, 21–30.' mla: Henzinger, Thomas A., et al. Composable Code Generation for Distributed Giotto. ACM, 2005, pp. 21–30, doi:10.1145/1065910.1065914. short: T.A. Henzinger, C. Kirsch, S. Matic, in:, ACM, 2005, pp. 21–30. conference: name: 'LCTES: Languages, Compilers, and Tools for Embedded Systems' date_created: 2018-12-11T12:08:57Z date_published: 2005-06-01T00:00:00Z date_updated: 2021-01-12T07:57:06Z day: '01' doi: 10.1145/1065910.1065914 extern: 1 month: '06' page: 21 - 30 publication_status: published publisher: ACM publist_id: '275' quality_controlled: 0 status: public title: Composable code generation for distributed Giotto type: conference year: '2005' ... --- _id: '4536' abstract: - lang: eng text: 'We show how to automatically construct and refine rectangular abstractions of systems of linear differential equations. From a hybrid automaton whose dynamics are given by a system of linear differential equations, our method computes automatically a sequence of rectangular hybrid automata that are increasingly precise overapproximations of the original hybrid automaton. We prove an optimality criterion for successive refinements. We also show that this method can take into account a safety property to be verified, refining only relevant parts of the state space. The practicability of the method is illustrated on a benchmark case study. ' acknowledgement: Supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF grants CCR-0208875 and CCR-0225610. alternative_title: - LNCS author: - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: 'Doyen L, Henzinger TA, Raskin J. Automatic rectangular refinement of affine hybrid systems. In: Vol 3829. Springer; 2005:144-161. doi:DOI: 10.1007/11603009_13' apa: 'Doyen, L., Henzinger, T. A., & Raskin, J. (2005). Automatic rectangular refinement of affine hybrid systems (Vol. 3829, pp. 144–161). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/DOI: 10.1007/11603009_13' chicago: 'Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Automatic Rectangular Refinement of Affine Hybrid Systems,” 3829:144–61. Springer, 2005. https://doi.org/DOI: 10.1007/11603009_13.' ieee: 'L. Doyen, T. A. Henzinger, and J. Raskin, “Automatic rectangular refinement of affine hybrid systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2005, vol. 3829, pp. 144–161.' ista: 'Doyen L, Henzinger TA, Raskin J. 2005. Automatic rectangular refinement of affine hybrid systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 3829, 144–161.' mla: 'Doyen, Laurent, et al. Automatic Rectangular Refinement of Affine Hybrid Systems. Vol. 3829, Springer, 2005, pp. 144–61, doi:DOI: 10.1007/11603009_13.' short: L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2005, pp. 144–161. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:09:22Z date_published: 2005-12-13T00:00:00Z date_updated: 2021-01-12T07:59:31Z day: '13' doi: 'DOI: 10.1007/11603009_13' extern: 1 intvolume: ' 3829' month: '12' page: 144 - 161 publication_status: published publisher: Springer publist_id: '190' quality_controlled: 0 status: public title: Automatic rectangular refinement of affine hybrid systems type: conference volume: 3829 year: '2005' ... --- _id: '4541' abstract: - lang: eng text: | Much recent research has focused on the applications of games with ω-regular objectives in the control and verification of reactive systems. However, many of the game-based models are ill-suited for these applications, because they assume that each player has complete information about the state of the system (they are “perfect-information” games). This is because in many situations, a controller does not see the private state of the plant. Such scenarios are naturally modeled by “partial-information” games. On the other hand, these games are intractable; for example, partial-information games with simple reachability objectives are 2EXPTIME-complete. We study the intermediate case of “semiperfect-information” games, where one player has complete knowledge of the state, while the other player has only partial knowledge. This model is appropriate in control situations where a controller must cope with plant behavior that is as adversarial as possible, i.e., the controller has partial information while the plant has perfect information. As is customary, we assume that the controller and plant take turns to make moves. We show that these semiperfect-information turn-based games are equivalent to perfect-information concurrent games, where the two players choose their moves simultaneously and independently. Since the perfect-information concurrent games are well-understood, we obtain several results of how semiperfect-information turn-based games differ from perfect-information turn-based games on one hand, and from partial-information turn-based games on the other hand. In particular, semiperfect-information turn-based games can benefit from randomized strategies while the perfect-information variety cannot, and semiperfect-information turn-based games are in NP ∩ coNP for all parity objectives. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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, Henzinger TA. Semiperfect-information games. In: Vol 3821. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2005:1-18. doi:10.1007/11590156_1' apa: 'Chatterjee, K., & Henzinger, T. A. (2005). Semiperfect-information games (Vol. 3821, pp. 1–18). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11590156_1' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Semiperfect-Information Games,” 3821:1–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005. https://doi.org/10.1007/11590156_1. ieee: 'K. Chatterjee and T. A. Henzinger, “Semiperfect-information games,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, 2005, vol. 3821, pp. 1–18.' ista: 'Chatterjee K, Henzinger TA. 2005. Semiperfect-information games. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LNCS, vol. 3821, 1–18.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Semiperfect-Information Games. Vol. 3821, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 1–18, doi:10.1007/11590156_1. short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 1–18. conference: name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science' date_created: 2018-12-11T12:09:23Z date_published: 2005-12-07T00:00:00Z date_updated: 2021-01-12T07:59:34Z day: '07' doi: 10.1007/11590156_1 extern: 1 intvolume: ' 3821' month: '12' page: 1 - 18 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '182' quality_controlled: 0 status: public title: Semiperfect-information games type: conference volume: 3821 year: '2005' ... --- _id: '4553' abstract: - lang: eng text: 'The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We show that for Rabin winning conditions, both problems are in NP. As these problems were known to be NP-hard, it follows that they are NP-complete for Rabin conditions, and dually, coNP-complete for Streett conditions. The proof proceeds by showing that pure memoryless strategies suffice for qualitatively and quantitatively winning stochastic graph games with Rabin conditions. This insight is of interest in its own right, as it implies that controllers for Rabin objectives have simple implementations. We also prove that for every ω-regular condition, optimal winning strategies are no more complex than almost-sure winning strategies.' acknowledgement: This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610. alternative_title: - LNCS 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. The complexity of stochastic Rabin and Streett games. In: Vol 3580. Springer; 2005:878-890. doi:10.1007/11523468_71' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2005). The complexity of stochastic Rabin and Streett games (Vol. 3580, pp. 878–890). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11523468_71' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity of Stochastic Rabin and Streett Games,” 3580:878–90. Springer, 2005. https://doi.org/10.1007/11523468_71. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of stochastic Rabin and Streett games,” presented at the ICALP: Automata, Languages and Programming, 2005, vol. 3580, pp. 878–890.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2005. The complexity of stochastic Rabin and Streett games. ICALP: Automata, Languages and Programming, LNCS, vol. 3580, 878–890.' mla: Chatterjee, Krishnendu, et al. The Complexity of Stochastic Rabin and Streett Games. Vol. 3580, Springer, 2005, pp. 878–90, doi:10.1007/11523468_71. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, Springer, 2005, pp. 878–890. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:09:27Z date_published: 2005-06-24T00:00:00Z date_updated: 2021-01-12T07:59:39Z day: '24' doi: 10.1007/11523468_71 extern: 1 intvolume: ' 3580' month: '06' page: 878 - 890 publication_status: published publisher: Springer publist_id: '158' quality_controlled: 0 status: public title: The complexity of stochastic Rabin and Streett games type: conference volume: 3580 year: '2005' ... --- _id: '4554' abstract: - lang: eng text: Games played on graphs may have qualitative objectives, such as the satisfaction of an ω-regular property, or quantitative objectives, such as the optimization of a real-valued reward. When games are used to model reactive systems with both fairness assumptions and quantitative (e.g., resource) constraints, then the corresponding objective combines both a qualitative and a quantitative component. In a general case of interest, the qualitative component is a parity condition and the quantitative component is a mean-payoff reward. We study and solve such mean-payoff parity games. We also prove some interesting facts about mean-payoff parity games which distinguish them both from mean-payoff and from parity games. In particular, we show that optimal strategies exist in mean-payoff parity games, but they may require infinite memory. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński citation: ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Mean-payoff parity games. In: IEEE; 2005:178-187. doi:10.1109/LICS.2005.26' apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2005). Mean-payoff parity games (pp. 178–187). Presented at the LICS: Logic in Computer Science, IEEE. https://doi.org/10.1109/LICS.2005.26' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Mean-Payoff Parity Games,” 178–87. IEEE, 2005. https://doi.org/10.1109/LICS.2005.26. ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Mean-payoff parity games,” presented at the LICS: Logic in Computer Science, 2005, pp. 178–187.' ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2005. Mean-payoff parity games. LICS: Logic in Computer Science, 178–187.' mla: Chatterjee, Krishnendu, et al. Mean-Payoff Parity Games. IEEE, 2005, pp. 178–87, doi:10.1109/LICS.2005.26. short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, IEEE, 2005, pp. 178–187. conference: name: 'LICS: Logic in Computer Science' date_created: 2018-12-11T12:09:27Z date_published: 2005-09-19T00:00:00Z date_updated: 2021-01-12T07:59:39Z day: '19' doi: 10.1109/LICS.2005.26 extern: 1 month: '09' page: 178 - 187 publication_status: published publisher: IEEE publist_id: '159' quality_controlled: 0 status: public title: Mean-payoff parity games type: conference year: '2005' ... --- _id: '4560' abstract: - lang: eng text: | We define and study a quantitative generalization of the traditional boolean framework of model-based specification and verification. In our setting, propositions have integer values at states, and properties have integer values on traces. For example, the value of a quantitative proposition at a state may represent power consumed at the state, and the value of a quantitative property on a trace may represent energy used along the trace. The value of a quantitative property at a state, then, is the maximum (or minimum) value achievable over all possible traces from the state. In this framework, model checking can be used to compute, for example, the minimum battery capacity necessary for achieving a given objective, or the maximal achievable lifetime of a system with a given initial battery capacity. In the case of open systems, these problems require the solution of games with integer values. Quantitative model checking and game solving is undecidable, except if bounds on the computation can be found. Indeed, many interesting quantitative properties, like minimal necessary battery capacity and maximal achievable lifetime, can be naturally specified by quantitative-bound automata, which are finite automata with integer registers whose analysis is constrained by a bound function f that maps each system K to an integer f(K). Along with the linear-time, automaton-based view of quantitative verification, we present a corresponding branching-time view based on a quantitative-bound μ-calculus, and we study the relationship, expressive power, and complexity of both views. alternative_title: - LNCS author: - first_name: Arindam full_name: Chakrabarti, Arindam last_name: Chakrabarti - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Chakrabarti A, Chatterjee K, Henzinger TA, Kupferman O, Majumdar R. Verifying quantitative properties using bound functions. In: Vol 3725. Springer; 2005:50-64. doi:10.1007/11560548_7' apa: 'Chakrabarti, A., Chatterjee, K., Henzinger, T. A., Kupferman, O., & Majumdar, R. (2005). Verifying quantitative properties using bound functions (Vol. 3725, pp. 50–64). Presented at the CHARME: Correct Hardware Design and Verification Methods, Springer. https://doi.org/10.1007/11560548_7' chicago: Chakrabarti, Arindam, Krishnendu Chatterjee, Thomas A Henzinger, Orna Kupferman, and Ritankar Majumdar. “Verifying Quantitative Properties Using Bound Functions,” 3725:50–64. Springer, 2005. https://doi.org/10.1007/11560548_7. ieee: 'A. Chakrabarti, K. Chatterjee, T. A. Henzinger, O. Kupferman, and R. Majumdar, “Verifying quantitative properties using bound functions,” presented at the CHARME: Correct Hardware Design and Verification Methods, 2005, vol. 3725, pp. 50–64.' ista: 'Chakrabarti A, Chatterjee K, Henzinger TA, Kupferman O, Majumdar R. 2005. Verifying quantitative properties using bound functions. CHARME: Correct Hardware Design and Verification Methods, LNCS, vol. 3725, 50–64.' mla: Chakrabarti, Arindam, et al. Verifying Quantitative Properties Using Bound Functions. Vol. 3725, Springer, 2005, pp. 50–64, doi:10.1007/11560548_7. short: A. Chakrabarti, K. Chatterjee, T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Springer, 2005, pp. 50–64. conference: name: 'CHARME: Correct Hardware Design and Verification Methods' date_created: 2018-12-11T12:09:29Z date_published: 2005-09-19T00:00:00Z date_updated: 2021-01-12T07:59:42Z day: '19' doi: 10.1007/11560548_7 extern: 1 intvolume: ' 3725' month: '09' page: 50 - 64 publication_status: published publisher: Springer publist_id: '149' quality_controlled: 0 status: public title: Verifying quantitative properties using bound functions type: conference volume: 3725 year: '2005' ... --- _id: '4557' abstract: - lang: eng text: 'Planning in adversarial and uncertain environments can be modeled as the problem of devising strategies in stochastic perfect information games. These games are generalizations of Markov decision processes (MDPs): there are two (adversarial) players, and a source of randomness. The main practical obstacle to computing winning strategies in such games is the size of the state space. In practice therefore, one typically works with abstractions of the model. The diffculty is to come up with an abstraction that is neither too coarse to remove all winning strategies (plans), nor too fine to be intractable. In verification, the paradigm of counterexample-guided abstraction refinement has been successful to construct useful but parsimonious abstractions automatically. We extend this paradigm to probabilistic models (namely, perfect information games and, as a special case, MDPs). This allows us to apply the counterexample-guided abstraction paradigm to the AI planning problem. As special cases, we get planning algorithms for MDPs and deterministic systems that automatically construct system abstractions.' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: 'Chatterjee K, Henzinger TA, Jhala R, Majumdar R. Counterexample-guided planning. In: AUAI Press; 2005:104-111.' apa: 'Chatterjee, K., Henzinger, T. A., Jhala, R., & Majumdar, R. (2005). Counterexample-guided planning (pp. 104–111). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press.' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided Planning,” 104–11. AUAI Press, 2005. ieee: 'K. Chatterjee, T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided planning,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 104–111.' ista: 'Chatterjee K, Henzinger TA, Jhala R, Majumdar R. 2005. Counterexample-guided planning. UAI: Uncertainty in Artificial Intelligence, 104–111.' mla: Chatterjee, Krishnendu, et al. Counterexample-Guided Planning. AUAI Press, 2005, pp. 104–11. short: K. Chatterjee, T.A. Henzinger, R. Jhala, R. Majumdar, in:, AUAI Press, 2005, pp. 104–111. conference: name: 'UAI: Uncertainty in Artificial Intelligence' date_created: 2018-12-11T12:09:28Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:59:41Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://uai.sis.pitt.edu/papers/05/p104-chatterjee.pdf month: '01' page: 104 - 111 publication_status: published publisher: AUAI Press publist_id: '157' quality_controlled: 0 status: public title: Counterexample-guided planning type: conference year: '2005' ... --- _id: '4579' abstract: - lang: eng text: BLAST is an automatic verification tool for checking temporal safety properties of C programs. Given a C program and a temporal safety property, BLAST statically proves that either the program satisfies the safety property or the program has an execution trace that exhibits a violation of the property. BLAST constructs, explores, and refines abstractions of the program state space based on lazy predicate abstraction and interpolation-based predicate discovery. We show how BLAST can be used to statically prove memory safety for C programs. We take a two-step approach. First, we use Ccured, a type-based memory safety analyzer, to annotate with run-time checks all program points that cannot be proved memory safe by the type system. Second, we use BLAST to remove as many of the run-time checks as possible (by proving that these checks never fail), and to generate for the remaining run-time checks execution traces that witness them fail. Our experience shows that BLAST can remove many of the run-time checks added by Ccured and provide useful information to the programmer about many of the remaining checks. acknowledgement: This research was supported in part by the NSF grants CCR-0234690, CCR-0225610, and ITR-0326577. alternative_title: - LNCS 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. Checking memory safety with BLAST. In: Vol 3442. Springer; 2005:2-18. doi:10.1007/978-3-540-31984-9_2' apa: 'Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2005). Checking memory safety with BLAST (Vol. 3442, pp. 2–18). Presented at the FASE: Fundamental Approaches To Software Engineering, Springer. https://doi.org/10.1007/978-3-540-31984-9_2' chicago: Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Checking Memory Safety with BLAST,” 3442:2–18. Springer, 2005. https://doi.org/10.1007/978-3-540-31984-9_2. ieee: 'D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “Checking memory safety with BLAST,” presented at the FASE: Fundamental Approaches To Software Engineering, 2005, vol. 3442, pp. 2–18.' ista: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. 2005. Checking memory safety with BLAST. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 3442, 2–18.' mla: Beyer, Dirk, et al. Checking Memory Safety with BLAST. Vol. 3442, Springer, 2005, pp. 2–18, doi:10.1007/978-3-540-31984-9_2. short: D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer, 2005, pp. 2–18. conference: name: 'FASE: Fundamental Approaches To Software Engineering' date_created: 2018-12-11T12:09:34Z date_published: 2005-03-24T00:00:00Z date_updated: 2021-01-12T07:59:51Z day: '24' doi: 10.1007/978-3-540-31984-9_2 extern: 1 intvolume: ' 3442' month: '03' page: 2 - 18 publication_status: published publisher: Springer publist_id: '131' quality_controlled: 0 status: public title: Checking memory safety with BLAST type: conference volume: 3442 year: '2005' ... --- _id: '4576' abstract: - lang: eng text: We present a language for specifying web service interfaces. A web service interface puts three kinds of constraints on the users of the service. First, the interface specifies the methods that can be called by a client, together with types of input and output parameters; these are called signature constraints. Second, the interface may specify propositional constraints on method calls and output values that may oc- cur in a web service conversation; these are called consis- tency constraints. Third, the interface may specify temporal constraints on the ordering of method calls; these are called protocol constraints. The interfaces can be used to check, first, if two or more web services are compatible, and second, if a web service A can be safely substituted for a web ser- vice B. The algorithm for compatibility checking verifies that two or more interfaces fulfill each others’ constraints. The algorithm for substitutivity checking verifies that service A demands fewer and fulfills more constraints than service B. acknowledgement: This research was supported in part by the ONR grant N00014-02-1-0671 and by the NSF grants CCR-0234690 and CCR-0225610. author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Arindam full_name: Chakrabarti, Arindam last_name: Chakrabarti - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Beyer D, Chakrabarti A, Henzinger TA. Web service interfaces. In: ACM; 2005:148-159. doi:10.1145/1060745.1060770' apa: 'Beyer, D., Chakrabarti, A., & Henzinger, T. A. (2005). Web service interfaces (pp. 148–159). Presented at the WWW: World Wide Web Conference, ACM. https://doi.org/10.1145/1060745.1060770' chicago: Beyer, Dirk, Arindam Chakrabarti, and Thomas A Henzinger. “Web Service Interfaces,” 148–59. ACM, 2005. https://doi.org/10.1145/1060745.1060770. ieee: 'D. Beyer, A. Chakrabarti, and T. A. Henzinger, “Web service interfaces,” presented at the WWW: World Wide Web Conference, 2005, pp. 148–159.' ista: 'Beyer D, Chakrabarti A, Henzinger TA. 2005. Web service interfaces. WWW: World Wide Web Conference, 148–159.' mla: Beyer, Dirk, et al. Web Service Interfaces. ACM, 2005, pp. 148–59, doi:10.1145/1060745.1060770. short: D. Beyer, A. Chakrabarti, T.A. Henzinger, in:, ACM, 2005, pp. 148–159. conference: name: 'WWW: World Wide Web Conference' date_created: 2018-12-11T12:09:33Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:59:50Z day: '01' doi: 10.1145/1060745.1060770 extern: 1 month: '05' page: 148 - 159 publication_status: published publisher: ACM publist_id: '132' quality_controlled: 0 status: public title: Web service interfaces type: conference year: '2005' ... --- _id: '4625' abstract: - lang: eng text: |- Temporal logic is two-valued: formulas are interpreted as 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. 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. Theoretical Computer Science. 2005;345(1):139-170. doi:10.1016/j.tcs.2005.07.033 apa: De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2005). Model checking discounted temporal properties. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2005.07.033 chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties.” Theoretical Computer Science. Elsevier, 2005. https://doi.org/10.1016/j.tcs.2005.07.033. ieee: L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” Theoretical Computer Science, vol. 345, no. 1. Elsevier, pp. 139–170, 2005. ista: De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2005. Model checking discounted temporal properties. Theoretical Computer Science. 345(1), 139–170. mla: De Alfaro, Luca, et al. “Model Checking Discounted Temporal Properties.” Theoretical Computer Science, vol. 345, no. 1, Elsevier, 2005, pp. 139–70, doi:10.1016/j.tcs.2005.07.033. short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, Theoretical Computer Science 345 (2005) 139–170. date_created: 2018-12-11T12:09:49Z date_published: 2005-11-21T00:00:00Z date_updated: 2021-01-12T08:00:37Z day: '21' doi: 10.1016/j.tcs.2005.07.033 extern: 1 intvolume: ' 345' issue: '1' month: '11' page: 139 - 170 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '80' quality_controlled: 0 status: public title: Model checking discounted temporal properties type: journal_article volume: 345 year: '2005' ... --- _id: '4624' abstract: - lang: eng text: Surveying results from [5] and [6], we motivate and introduce the theory behind formalizing rich interfaces for software and hardware components. Rich interfaces specify the protocol aspects of component interaction. Their formalization, called interface automata, permits a compiler to check the compatibility of component interaction protocols. Interface automata support incremental design and independent implementability. Incremental design means that the compatibility checking of interfaces can proceed for partial system descriptions, without knowing the interfaces of all components. Independent implementability means that compatible interfaces can be refined separately, while still maintaining compatibility. alternative_title: - 'NATO Science Series: Mathematics, Physics, and Chemistry' author: - 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: 'De Alfaro L, Henzinger TA. Interface-based design. In: Vol 195. Springer; 2005:83-104. doi:10.1007/1-4020-3532-2_3' apa: De Alfaro, L., & Henzinger, T. A. (2005). Interface-based design (Vol. 195, pp. 83–104). Presented at the Engineering Theories of Software Intensive Systems, Springer. https://doi.org/10.1007/1-4020-3532-2_3 chicago: De Alfaro, Luca, and Thomas A Henzinger. “Interface-Based Design,” 195:83–104. Springer, 2005. https://doi.org/10.1007/1-4020-3532-2_3. ieee: L. De Alfaro and T. A. Henzinger, “Interface-based design,” presented at the Engineering Theories of Software Intensive Systems, 2005, vol. 195, pp. 83–104. ista: 'De Alfaro L, Henzinger TA. 2005. Interface-based design. Engineering Theories of Software Intensive Systems, NATO Science Series: Mathematics, Physics, and Chemistry, vol. 195, 83–104.' mla: De Alfaro, Luca, and Thomas A. Henzinger. Interface-Based Design. Vol. 195, Springer, 2005, pp. 83–104, doi:10.1007/1-4020-3532-2_3. short: L. De Alfaro, T.A. Henzinger, in:, Springer, 2005, pp. 83–104. conference: name: Engineering Theories of Software Intensive Systems date_created: 2018-12-11T12:09:49Z date_published: 2005-07-15T00:00:00Z date_updated: 2021-01-12T08:00:36Z day: '15' doi: 10.1007/1-4020-3532-2_3 extern: 1 intvolume: ' 195' month: '07' page: 83 - 104 publication_status: published publisher: Springer publist_id: '85' quality_controlled: 0 status: public title: Interface-based design type: conference volume: 195 year: '2005' ... --- _id: '575' abstract: - lang: eng text: We present the first demonstration of Jozsa's "counterfactual computation", using an optical Grover's search algorithm. We put the algorithm in a superposition of 'running' and 'not-running', obtaining information even though the algorithm does not run. alternative_title: - QELS author: - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Matthew full_name: Rakher, Matthew T last_name: Rakher - first_name: Julio full_name: Barreiro, Julio T last_name: Barreiro - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation. In: Vol 1. IEEE; 2005:365-367. doi: 10.1109/QELS.2005.1548783' apa: 'Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2005). Counterfactual quantum computation (Vol. 1, pp. 365–367). Presented at the QELS: Quantum Electronics and Laser Science, IEEE. https://doi.org/ 10.1109/QELS.2005.1548783' chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation,” 1:365–67. IEEE, 2005. https://doi.org/ 10.1109/QELS.2005.1548783. ieee: 'O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation,” presented at the QELS: Quantum Electronics and Laser Science, 2005, vol. 1, pp. 365–367.' ista: 'Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2005. Counterfactual quantum computation. QELS: Quantum Electronics and Laser Science, QELS, vol. 1, 365–367.' mla: Hosten, Onur, et al. Counterfactual Quantum Computation. Vol. 1, IEEE, 2005, pp. 365–67, doi: 10.1109/QELS.2005.1548783. short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, in:, IEEE, 2005, pp. 365–367. conference: name: 'QELS: Quantum Electronics and Laser Science' date_created: 2018-12-11T11:47:16Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T08:03:18Z day: '01' doi: ' 10.1109/QELS.2005.1548783' extern: 1 intvolume: ' 1' month: '01' page: 365 - 367 publication_status: published publisher: IEEE publist_id: '7237' quality_controlled: 0 status: public title: Counterfactual quantum computation type: conference volume: 1 year: '2005' ... --- _id: '6153' abstract: - lang: eng text: A current challenge in neuroscience is to bridge the gaps between genes, proteins, neurons, neural circuits, and behavior in a single animal model. The nematode Caenorhabditis elegans has unique features that facilitate this synthesis. Its nervous system includes exactly 302 neurons, and their pattern of synaptic connectivity is known. With only five olfactory neurons, C. elegans can dynamically respond to dozens of attractive and repellant odors. Thermosensory neurons enable the nematode to remember its cultivation temperature and to track narrow isotherms. Polymodal sensory neurons detect a wide range of nociceptive cues and signal robust escape responses. Pairing of sensory stimuli leads to long-lived changes in behavior consistent with associative learning. Worms exhibit social behaviors and complex ultradian rhythms driven by Ca2+ oscillators with clock-like properties. Genetic analysis has identified gene products required for nervous system function and elucidated the molecular and neural bases of behaviors. article_processing_charge: No article_type: original author: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Andres full_name: Villu Maricq, Andres last_name: Villu Maricq citation: ama: de Bono M, Villu Maricq A. Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. 2005;28:451-501. doi:10.1146/annurev.neuro.27.070203.144259 apa: de Bono, M., & Villu Maricq, A. (2005). Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev.neuro.27.070203.144259 chicago: Bono, Mario de, and Andres Villu Maricq. “Neuronal Substrates of Complex Behaviors in C. Elegans.” Annual Review of Neuroscience. Annual Reviews, 2005. https://doi.org/10.1146/annurev.neuro.27.070203.144259. ieee: M. de Bono and A. Villu Maricq, “Neuronal substrates of complex behaviors in C. elegans,” Annual Review of Neuroscience, vol. 28. Annual Reviews, pp. 451–501, 2005. ista: de Bono M, Villu Maricq A. 2005. Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. 28, 451–501. mla: de Bono, Mario, and Andres Villu Maricq. “Neuronal Substrates of Complex Behaviors in C. Elegans.” Annual Review of Neuroscience, vol. 28, Annual Reviews, 2005, pp. 451–501, doi:10.1146/annurev.neuro.27.070203.144259. short: M. de Bono, A. Villu Maricq, Annual Review of Neuroscience 28 (2005) 451–501. date_created: 2019-03-21T09:31:29Z date_published: 2005-07-21T00:00:00Z date_updated: 2021-01-12T08:06:24Z day: '21' doi: 10.1146/annurev.neuro.27.070203.144259 extern: '1' external_id: pmid: - '16022603' intvolume: ' 28' language: - iso: eng month: '07' oa_version: None page: 451-501 pmid: 1 publication: Annual Review of Neuroscience publication_identifier: issn: - 0147-006X - 1545-4126 publication_status: published publisher: Annual Reviews quality_controlled: '1' status: public title: Neuronal substrates of complex behaviors in C. elegans type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 28 year: '2005' ... --- _id: '6154' author: - first_name: Benny H.H. full_name: Cheung, Benny H.H. last_name: Cheung - first_name: Merav full_name: Cohen, Merav last_name: Cohen - first_name: Candida full_name: Rogers, Candida last_name: Rogers - first_name: Onder full_name: Albayram, Onder last_name: Albayram - 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 BHH, Cohen M, Rogers C, Albayram O, de Bono M. Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. 2005;15(10):905-917. doi:10.1016/j.cub.2005.04.017 apa: Cheung, B. H. H., Cohen, M., Rogers, C., Albayram, O., & de Bono, M. (2005). Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.04.017 chicago: Cheung, Benny H.H., Merav Cohen, Candida Rogers, Onder Albayram, and Mario de Bono. “Experience-Dependent Modulation of C. Elegans Behavior by Ambient Oxygen.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.04.017. ieee: B. H. H. Cheung, M. Cohen, C. Rogers, O. Albayram, and M. de Bono, “Experience-dependent modulation of C. elegans behavior by ambient oxygen,” Current Biology, vol. 15, no. 10. Elsevier, pp. 905–917, 2005. ista: Cheung BHH, Cohen M, Rogers C, Albayram O, de Bono M. 2005. Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. 15(10), 905–917. mla: Cheung, Benny H. H., et al. “Experience-Dependent Modulation of C. Elegans Behavior by Ambient Oxygen.” Current Biology, vol. 15, no. 10, Elsevier, 2005, pp. 905–17, doi:10.1016/j.cub.2005.04.017. short: B.H.H. Cheung, M. Cohen, C. Rogers, O. Albayram, M. de Bono, Current Biology 15 (2005) 905–917. date_created: 2019-03-21T09:37:48Z date_published: 2005-05-24T00:00:00Z date_updated: 2021-01-12T08:06:24Z day: '24' doi: 10.1016/j.cub.2005.04.017 extern: '1' external_id: pmid: - '15916947' intvolume: ' 15' issue: '10' language: - iso: eng month: '05' oa_version: None page: 905-917 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Experience-dependent modulation of C. elegans behavior by ambient oxygen type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2005' ... --- _id: '8028' abstract: - lang: eng text: 'Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.' article_processing_charge: No article_type: original author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: L. F. full_name: Abbott, L. F. last_name: Abbott citation: ama: Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 2005;25(46):10786-10795. doi:10.1523/jneurosci.3508-05.2005 apa: Vogels, T. P., & Abbott, L. F. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.3508-05.2005 chicago: Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience. Society for Neuroscience, 2005. https://doi.org/10.1523/jneurosci.3508-05.2005. ieee: T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” Journal of Neuroscience, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005. ista: Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795. mla: Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience, vol. 25, no. 46, Society for Neuroscience, 2005, pp. 10786–95, doi:10.1523/jneurosci.3508-05.2005. short: T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795. date_created: 2020-06-25T13:12:33Z date_published: 2005-11-16T00:00:00Z date_updated: 2021-01-12T08:16:37Z day: '16' doi: 10.1523/jneurosci.3508-05.2005 extern: '1' external_id: pmid: - '16291952' intvolume: ' 25' issue: '46' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/ month: '11' oa: 1 oa_version: Published Version page: 10786-10795 pmid: 1 publication: Journal of Neuroscience publication_identifier: issn: - 0270-6474 - 1529-2401 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' status: public title: Signal propagation and logic gating in networks of integrate-and-fire neurons type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 25 year: '2005' ... --- _id: '8029' abstract: - lang: eng text: 'Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function.' article_processing_charge: No article_type: review author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Kanaka full_name: Rajan, Kanaka last_name: Rajan - first_name: L.F. full_name: Abbott, L.F. last_name: Abbott citation: ama: Vogels TP, Rajan K, Abbott LF. Neural network dynamics. Annual Review of Neuroscience. 2005;28(1):357-376. doi:10.1146/annurev.neuro.28.061604.135637 apa: Vogels, T. P., Rajan, K., & Abbott, L. F. (2005). Neural network dynamics. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev.neuro.28.061604.135637 chicago: Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.” Annual Review of Neuroscience. Annual Reviews, 2005. https://doi.org/10.1146/annurev.neuro.28.061604.135637. ieee: T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” Annual Review of Neuroscience, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005. ista: Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review of Neuroscience. 28(1), 357–376. mla: Vogels, Tim P., et al. “Neural Network Dynamics.” Annual Review of Neuroscience, vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:10.1146/annurev.neuro.28.061604.135637. short: T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005) 357–376. date_created: 2020-06-25T13:13:11Z date_published: 2005-07-21T00:00:00Z date_updated: 2021-01-12T08:16:37Z day: '21' doi: 10.1146/annurev.neuro.28.061604.135637 extern: '1' external_id: pmid: - '16022600' intvolume: ' 28' issue: '1' language: - iso: eng month: '07' oa_version: None page: 357-376 pmid: 1 publication: Annual Review of Neuroscience publication_identifier: issn: - 0147-006X - 1545-4126 publication_status: published publisher: Annual Reviews quality_controlled: '1' status: public title: Neural network dynamics type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 28 year: '2005' ... --- _id: '9491' abstract: - lang: eng text: Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units. article_processing_charge: No article_type: original author: - first_name: Robert K. full_name: Tran, Robert K. last_name: Tran - first_name: Jorja G. full_name: Henikoff, Jorja G. last_name: Henikoff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Renata F. full_name: Ditt, Renata F. last_name: Ditt - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008 apa: Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., & Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.01.008 chicago: Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008. ieee: R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159, 2005. ista: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159. mla: Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology, vol. 15, no. 2, Elsevier, 2005, pp. 154–59, doi:10.1016/j.cub.2005.01.008. short: R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159. date_created: 2021-06-07T10:24:30Z date_published: 2005-01-26T00:00:00Z date_updated: 2021-12-14T09:12:26Z day: '26' department: - _id: DaZi doi: 10.1016/j.cub.2005.01.008 extern: '1' external_id: pmid: - '15668172 ' intvolume: ' 15' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2005.01.008 month: '01' oa: 1 oa_version: Published Version page: 154-159 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: DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 15 year: '2005' ... --- _id: '9514' abstract: - lang: eng text: "Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements." article_number: R90 article_processing_charge: No article_type: original author: - first_name: Robert K. full_name: Tran, Robert K. last_name: Tran - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Cecilia full_name: de Bustos, Cecilia last_name: de Bustos - first_name: Renata F. full_name: Ditt, Renata F. last_name: Ditt - first_name: Jorja G. full_name: Henikoff, Jorja G. last_name: Henikoff - first_name: Anders M. full_name: Lindroth, Anders M. last_name: Lindroth - first_name: Jeffrey full_name: Delrow, Jeffrey last_name: Delrow - first_name: Tom full_name: Boyle, Tom last_name: Boyle - first_name: Samson full_name: Kwong, Samson last_name: Kwong - first_name: Terri D. full_name: Bryson, Terri D. last_name: Bryson - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90 apa: Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. Springer Nature. https://doi.org/10.1186/gb-2005-6-11-r90 chicago: Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90. ieee: R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” Genome Biology, vol. 6, no. 11. Springer Nature, 2005. ista: Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), R90. mla: Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology, vol. 6, no. 11, R90, Springer Nature, 2005, doi:10.1186/gb-2005-6-11-r90. short: R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005). date_created: 2021-06-07T13:12:41Z date_published: 2005-10-19T00:00:00Z date_updated: 2021-12-14T09:09:41Z day: '19' department: - _id: DaZi doi: 10.1186/gb-2005-6-11-r90 extern: '1' external_id: pmid: - '16277745' intvolume: ' 6' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/gb-2005-6-11-r90 month: '10' 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: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2005' ... --- _id: '843' abstract: - lang: eng text: The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by >10-2, 10-2-10-4, 10-4-10-5 and <10-5 are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients. author: - first_name: Lev full_name: Yampolsky, Lev Y last_name: Yampolsky - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 2005;14(21):3191-3201. doi:10.1093/hmg/ddi350 apa: Yampolsky, L., Kondrashov, F., & Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi350 chicago: Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi350. ieee: L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005. ista: Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201. mla: Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350. short: L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201. date_created: 2018-12-11T11:48:48Z date_published: 2005-11-01T00:00:00Z date_updated: 2021-01-12T08:19:13Z day: '01' doi: 10.1093/hmg/ddi350 extern: 1 intvolume: ' 14' issue: '21' month: '11' page: 3191 - 3201 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6807' quality_controlled: 0 status: public title: Distribution of the strength of selection against amino acid replacements in human proteins type: journal_article volume: 14 year: '2005' ... --- _id: '8491' abstract: - lang: eng text: Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Ēriks full_name: Kupče, Ēriks last_name: Kupče - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Schanda P, Kupče Ē, Brutscher B. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. 2005;33(4):199-211. doi:10.1007/s10858-005-4425-x apa: Schanda, P., Kupče, Ē., & Brutscher, B. (2005). SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-005-4425-x chicago: Schanda, Paul, Ēriks Kupče, and Bernhard Brutscher. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” Journal of Biomolecular NMR. Springer Nature, 2005. https://doi.org/10.1007/s10858-005-4425-x. ieee: P. Schanda, Ē. Kupče, and B. Brutscher, “SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds,” Journal of Biomolecular NMR, vol. 33, no. 4. Springer Nature, pp. 199–211, 2005. ista: Schanda P, Kupče Ē, Brutscher B. 2005. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. 33(4), 199–211. mla: Schanda, Paul, et al. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” Journal of Biomolecular NMR, vol. 33, no. 4, Springer Nature, 2005, pp. 199–211, doi:10.1007/s10858-005-4425-x. short: P. Schanda, Ē. Kupče, B. Brutscher, Journal of Biomolecular NMR 33 (2005) 199–211. date_created: 2020-09-18T10:13:59Z date_published: 2005-12-01T00:00:00Z date_updated: 2021-01-12T08:19:38Z day: '01' doi: 10.1007/s10858-005-4425-x extern: '1' intvolume: ' 33' issue: '4' keyword: - Spectroscopy - Biochemistry language: - iso: eng month: '12' oa_version: None page: 199-211 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2005' ... --- _id: '8492' abstract: - lang: eng text: We demonstrate for different protein samples that 2D 1H−15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Schanda P, Brutscher B. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. 2005;127(22):8014-8015. doi:10.1021/ja051306e apa: Schanda, P., & Brutscher, B. (2005). Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja051306e chicago: Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” Journal of the American Chemical Society. American Chemical Society, 2005. https://doi.org/10.1021/ja051306e. ieee: P. Schanda and B. Brutscher, “Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds,” Journal of the American Chemical Society, vol. 127, no. 22. American Chemical Society, pp. 8014–8015, 2005. ista: Schanda P, Brutscher B. 2005. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. 127(22), 8014–8015. mla: Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” Journal of the American Chemical Society, vol. 127, no. 22, American Chemical Society, 2005, pp. 8014–15, doi:10.1021/ja051306e. short: P. Schanda, B. Brutscher, Journal of the American Chemical Society 127 (2005) 8014–8015. date_created: 2020-09-18T10:14:05Z date_published: 2005-05-14T00:00:00Z date_updated: 2021-01-12T08:19:39Z day: '14' doi: 10.1021/ja051306e extern: '1' intvolume: ' 127' issue: '22' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '05' oa_version: None page: 8014-8015 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 127 year: '2005' ... --- _id: '8516' abstract: - lang: eng text: "The purpose of this paper is to construct examples of diffusion for E-Hamiltonian perturbations\r\nof completely integrable Hamiltonian systems in 2d-dimensional phase space, with d large.\r\nIn the first part of the paper, simple and explicit examples are constructed illustrating absence\r\nof ‘long-time’ stability for size E Hamiltonian perturbations of quasi-convex integrable systems\r\nalready when the dimension 2d of phase space becomes as large as log 1/E . We first produce\r\nthe example in Gevrey class and then a real analytic one, with some additional work.\r\nIn the second part, we consider again E-Hamiltonian perturbations of completely integrable\r\nHamiltonian system in 2d-dimensional space with E-small but not too small, |E| > exp(−d), with\r\nd the number of degrees of freedom assumed large. It is shown that for a class of analytic\r\ntime-periodic perturbations, there exist linearly diffusing trajectories. The underlying idea for\r\nboth examples is similar and consists in coupling a fixed degree of freedom with a large\r\nnumber of them. The procedure and analytical details are however significantly different. As\r\nmentioned, the construction in Part I is totally elementary while Part II is more involved, relying\r\nin particular on the theory of normally hyperbolic invariant manifolds, methods of generating\r\nfunctions, Aubry–Mather theory, and Mather’s variational methods." article_processing_charge: No article_type: original author: - first_name: Jean full_name: Bourgain, Jean last_name: Bourgain - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Bourgain J, Kaloshin V. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 2005;229(1):1-61. doi:10.1016/j.jfa.2004.09.006 apa: Bourgain, J., & Kaloshin, V. (2005). On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2004.09.006 chicago: Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” Journal of Functional Analysis. Elsevier, 2005. https://doi.org/10.1016/j.jfa.2004.09.006. ieee: J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian systems,” Journal of Functional Analysis, vol. 229, no. 1. Elsevier, pp. 1–61, 2005. ista: Bourgain J, Kaloshin V. 2005. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 229(1), 1–61. mla: Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” Journal of Functional Analysis, vol. 229, no. 1, Elsevier, 2005, pp. 1–61, doi:10.1016/j.jfa.2004.09.006. short: J. Bourgain, V. Kaloshin, Journal of Functional Analysis 229 (2005) 1–61. date_created: 2020-09-18T10:49:06Z date_published: 2005-12-01T00:00:00Z date_updated: 2021-01-12T08:19:49Z day: '01' doi: 10.1016/j.jfa.2004.09.006 extern: '1' intvolume: ' 229' issue: '1' keyword: - Analysis language: - iso: eng month: '12' oa_version: None page: 1-61 publication: Journal of Functional Analysis publication_identifier: issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: On diffusion in high-dimensional Hamiltonian systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 229 year: '2005' ... --- _id: '877' abstract: - lang: eng text: "Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions\r\nproducing pathogenic effects in humans are often found in normal, healthy individuals from other species.\r\nAnalysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations can be neutralized by other, compensatory substitutions that restore the structural stability of the\r\nmolecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis-\r\neases that may be based on the correction of molecule stability as a whole instead of reversing an individual\r\npathogenic mutation." article_processing_charge: No article_type: original author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 2005;50(3):389-395. apa: Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. Pleiades Publishing. chicago: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” Biofizika. Pleiades Publishing, 2005. ieee: F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005. ista: Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395. mla: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95. short: F. Kondrashov, Biofizika 50 (2005) 389–395. date_created: 2018-12-11T11:48:58Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T08:21:01Z day: '01' extern: '1' external_id: pmid: - '15977826' intvolume: ' 50' issue: '3' language: - iso: eng main_file_link: - url: http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf month: '05' oa_version: None page: 389 - 395 pmid: 1 publication: Biofizika publication_status: published publisher: Pleiades Publishing publist_id: '6769' quality_controlled: '1' status: public title: The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2005' ... --- _id: '878' abstract: - lang: eng text: | Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. In search of the limits of evolution. Nature Genetics. 2005;37(1):9-10. doi:10.1038/ng0105-9 apa: Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng0105-9 chicago: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics. Nature Publishing Group, 2005. https://doi.org/10.1038/ng0105-9. ieee: F. Kondrashov, “In search of the limits of evolution,” Nature Genetics, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005. ista: Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10. mla: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9. short: F. Kondrashov, Nature Genetics 37 (2005) 9–10. date_created: 2018-12-11T11:48:59Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T08:21:02Z day: '01' doi: 10.1038/ng0105-9 extern: 1 intvolume: ' 37' issue: '1' month: '01' page: 9 - 10 publication: Nature Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6770' quality_controlled: 0 status: public title: In search of the limits of evolution type: journal_article volume: 37 year: '2005' ... --- _id: '882' abstract: - lang: eng text: Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively. acknowledgement: | The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 2005;14(16):2415-2419. doi:10.1093/hmg/ddi243 apa: Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi243 chicago: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi243. ieee: F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005. ista: Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419. mla: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243. short: F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419. date_created: 2018-12-11T11:49:00Z date_published: 2005-08-15T00:00:00Z date_updated: 2021-01-12T08:21:10Z day: '15' doi: 10.1093/hmg/ddi243 extern: 1 intvolume: ' 14' issue: '16' month: '08' page: 2415 - 2419 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6767' quality_controlled: 0 status: public title: Prediction of pathogenic mutations in mitochondrially encoded human tRNAs type: journal_article volume: 14 year: '2005' ... --- _id: '880' abstract: - lang: eng text: Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution. article_processing_charge: No author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 2005;50(3):396-403. apa: Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. Pleiades Publishing. chicago: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” Biofizika. Pleiades Publishing, 2005. ieee: F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005. ista: Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403. mla: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403. short: F. Kondrashov, Biofizika 50 (2005) 396–403. date_created: 2018-12-11T11:48:59Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T08:21:07Z day: '01' extern: '1' external_id: pmid: - '15977827' intvolume: ' 50' issue: '3' language: - iso: eng main_file_link: - url: http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf month: '05' oa_version: None page: 396 - 403 pmid: 1 publication: Biofizika publication_status: published publisher: Pleiades Publishing publist_id: '6768' quality_controlled: '1' status: public title: The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2005' ... --- _id: '893' abstract: - lang: eng text: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day. acknowledgement: S.S. and I.A.A. were supported by the Genome Canada Foundation. author: - first_name: Ingo full_name: Jordan, Ingo K last_name: Jordan - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ivan full_name: Adzhubeǐ, Ivan A last_name: Adzhubeǐ - first_name: Yuri full_name: Wolf, Yuri I last_name: Wolf - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev citation: ama: Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005;433(7026):633-638. doi:10.1038/nature03306 apa: Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov, A., & Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03306 chicago: Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03306. ieee: I. Jordan et al., “A universal trend of amino acid gain and loss in protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005. ista: Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638. mla: Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:10.1038/nature03306. short: I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638. date_created: 2018-12-11T11:49:03Z date_published: 2005-02-10T00:00:00Z date_updated: 2021-01-12T08:21:23Z day: '10' doi: 10.1038/nature03306 extern: 1 intvolume: ' 433' issue: '7026' month: '02' page: 633 - 638 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6757' quality_controlled: 0 status: public title: A universal trend of amino acid gain and loss in protein evolution type: journal_article volume: 433 year: '2005' ... --- _id: '9529' abstract: - lang: eng text: Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes. 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. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 2005;15(5):557-562. doi:10.1016/j.gde.2005.07.002' apa: 'Zilberman, D., & Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2005.07.002' chicago: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” Current Opinion in Genetics and Development. Elsevier, 2005. https://doi.org/10.1016/j.gde.2005.07.002.' ieee: 'D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” Current Opinion in Genetics and Development, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.' ista: 'Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.' mla: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” Current Opinion in Genetics and Development, vol. 15, no. 5, Elsevier, 2005, pp. 557–62, doi:10.1016/j.gde.2005.07.002.' short: D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562. date_created: 2021-06-08T09:05:56Z date_published: 2005-10-01T00:00:00Z date_updated: 2021-12-14T09:13:13Z department: - _id: DaZi doi: 10.1016/j.gde.2005.07.002 extern: '1' external_id: pmid: - '16085410' intvolume: ' 15' issue: '5' language: - iso: eng month: '10' oa_version: None page: 557-562 pmid: 1 publication: Current Opinion in Genetics and Development publication_identifier: issn: - 0959-437X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Epigenetic inheritance in Arabidopsis: Selective silence' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 15 year: '2005' ... --- _id: '13431' abstract: - lang: eng text: 'Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface topology of metals, glasses, and crystals. It is demonstrated that stamps soaked in an appropriate etchant can remove material with micrometer-scale precision. The Figure shows an array of concentric circles etched in glass using the immersion wet stamping process described (scale bar: 500 μm).' article_processing_charge: No article_type: original author: - first_name: S. K. full_name: Smoukov, S. K. last_name: Smoukov - first_name: K. J. M. full_name: Bishop, K. J. M. last_name: Bishop - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: C. J. full_name: Campbell, C. J. last_name: Campbell - first_name: B. A. full_name: Grzybowski, B. A. last_name: Grzybowski citation: ama: Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. Cutting into solids with micropatterned gels. Advanced Materials. 2005;17(11):1361-1365. doi:10.1002/adma.200402086 apa: Smoukov, S. K., Bishop, K. J. M., Klajn, R., Campbell, C. J., & Grzybowski, B. A. (2005). Cutting into solids with micropatterned gels. Advanced Materials. Wiley. https://doi.org/10.1002/adma.200402086 chicago: Smoukov, S. K., K. J. M. Bishop, Rafal Klajn, C. J. Campbell, and B. A. Grzybowski. “Cutting into Solids with Micropatterned Gels.” Advanced Materials. Wiley, 2005. https://doi.org/10.1002/adma.200402086. ieee: S. K. Smoukov, K. J. M. Bishop, R. Klajn, C. J. Campbell, and B. A. Grzybowski, “Cutting into solids with micropatterned gels,” Advanced Materials, vol. 17, no. 11. Wiley, pp. 1361–1365, 2005. ista: Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. 2005. Cutting into solids with micropatterned gels. Advanced Materials. 17(11), 1361–1365. mla: Smoukov, S. K., et al. “Cutting into Solids with Micropatterned Gels.” Advanced Materials, vol. 17, no. 11, Wiley, 2005, pp. 1361–65, doi:10.1002/adma.200402086. short: S.K. Smoukov, K.J.M. Bishop, R. Klajn, C.J. Campbell, B.A. Grzybowski, Advanced Materials 17 (2005) 1361–1365. date_created: 2023-08-01T10:38:01Z date_published: 2005-06-24T00:00:00Z date_updated: 2023-08-08T11:53:16Z day: '24' doi: 10.1002/adma.200402086 extern: '1' external_id: pmid: - '34412440' intvolume: ' 17' issue: '11' keyword: - Mechanical Engineering - Mechanics of Materials - General Materials Science language: - iso: eng month: '06' oa_version: None page: 1361-1365 pmid: 1 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: Cutting into solids with micropatterned gels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2005' ... --- _id: '13433' abstract: - lang: eng text: Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals are versatile constructs with which to study interfacial phenomena and reactions at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse environments, propensity to interact with or to resist adsorption of macromolecules -- depend on and can be controlled flexibly by the properties of the functional (head) groups in the w position of the alkyl chain. SAMs provide a basis for many important scientific and technological applications, ranging from micropatterning methods, through sensing, to biological recognition. Despite their importance, the literature on SAMs and the synthesis of molecules that constitute them remains scattered and often conflicting. The purpose of this Review is (i) to summarize the applications and physical properties of SAMs and (ii) to systematize the strategies of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme is developed that allows efficient synthetic planning. Issues related to the selection of appropriate protecting groups and the ways of introduction of the thiol functionality are discussed in detail, and illustrated with examples of syntheses of several complex alkane thiols. article_processing_charge: No article_type: original author: - first_name: Dariusz full_name: Witt, Dariusz last_name: Witt - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Piotr full_name: Barski, Piotr last_name: Barski - first_name: Bartosz full_name: Grzybowski, Bartosz last_name: Grzybowski citation: ama: Witt D, Klajn R, Barski P, Grzybowski B. Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers. Current Organic Chemistry. 2005;8(18):1763-1797. doi:10.2174/1385272043369421 apa: Witt, D., Klajn, R., Barski, P., & Grzybowski, B. (2005). Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers. Current Organic Chemistry. Bentham Science. https://doi.org/10.2174/1385272043369421 chicago: Witt, Dariusz, Rafal Klajn, Piotr Barski, and Bartosz Grzybowski. “Applications, Properties and Synthesis of w-Functionalized n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.” Current Organic Chemistry. Bentham Science, 2005. https://doi.org/10.2174/1385272043369421. ieee: D. Witt, R. Klajn, P. Barski, and B. Grzybowski, “Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers,” Current Organic Chemistry, vol. 8, no. 18. Bentham Science, pp. 1763–1797, 2005. ista: Witt D, Klajn R, Barski P, Grzybowski B. 2005. Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers. Current Organic Chemistry. 8(18), 1763–1797. mla: Witt, Dariusz, et al. “Applications, Properties and Synthesis of w-Functionalized n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.” Current Organic Chemistry, vol. 8, no. 18, Bentham Science, 2005, pp. 1763–97, doi:10.2174/1385272043369421. short: D. Witt, R. Klajn, P. Barski, B. Grzybowski, Current Organic Chemistry 8 (2005) 1763–1797. date_created: 2023-08-01T10:38:58Z date_published: 2005-12-01T00:00:00Z date_updated: 2023-08-08T12:39:52Z day: '01' doi: 10.2174/1385272043369421 extern: '1' intvolume: ' 8' issue: '18' keyword: - Organic Chemistry language: - iso: eng month: '12' oa_version: None page: 1763-1797 publication: Current Organic Chemistry publication_identifier: eissn: - 1875-5348 issn: - 1385-2728 publication_status: published publisher: Bentham Science quality_controlled: '1' scopus_import: '1' status: public title: Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2005' ... --- _id: '13432' abstract: - lang: eng text: A new experimental technique is described that uses reaction−diffusion phenomena as a means of one-step microfabrication of complex, multilevel surface reliefs. Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically micropatterned with a solution of silver nitrate delivered from an agarose stamp. Precipitation reaction between the two salts causes the surface to deform. The mechanism of surface deformation is shown to involve a sequence of reactions, diffusion, and gel swelling/contraction. This mechanism is established experimentally and provides a basis of a theoretical lattice-gas model that allows prediction surface topographies emerging from arbitrary geometries of the stamped features. The usefulness of the technique is demonstrated by using it to rapidly prepare two types of mold for passive microfluidic mixers. article_processing_charge: No article_type: original author: - first_name: Christopher J. full_name: Campbell, Christopher J. last_name: Campbell - 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: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. One-step multilevel microfabrication by reaction−diffusion. Langmuir. 2005;21(1):418-423. doi:10.1021/la0487747 apa: Campbell, C. J., Klajn, R., Fialkowski, M., & Grzybowski, B. A. (2005). One-step multilevel microfabrication by reaction−diffusion. Langmuir. American Chemical Society. https://doi.org/10.1021/la0487747 chicago: Campbell, Christopher J., Rafal Klajn, Marcin Fialkowski, and Bartosz A. Grzybowski. “One-Step Multilevel Microfabrication by Reaction−diffusion.” Langmuir. American Chemical Society, 2005. https://doi.org/10.1021/la0487747. ieee: C. J. Campbell, R. Klajn, M. Fialkowski, and B. A. Grzybowski, “One-step multilevel microfabrication by reaction−diffusion,” Langmuir, vol. 21, no. 1. American Chemical Society, pp. 418–423, 2005. ista: Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. 2005. One-step multilevel microfabrication by reaction−diffusion. Langmuir. 21(1), 418–423. mla: Campbell, Christopher J., et al. “One-Step Multilevel Microfabrication by Reaction−diffusion.” Langmuir, vol. 21, no. 1, American Chemical Society, 2005, pp. 418–23, doi:10.1021/la0487747. short: C.J. Campbell, R. Klajn, M. Fialkowski, B.A. Grzybowski, Langmuir 21 (2005) 418–423. date_created: 2023-08-01T10:38:29Z date_published: 2005-01-21T00:00:00Z date_updated: 2023-08-08T12:15:48Z day: '21' doi: 10.1021/la0487747 extern: '1' external_id: pmid: - '15620333' intvolume: ' 21' issue: '1' keyword: - Electrochemistry - Spectroscopy - Surfaces and Interfaces - Condensed Matter Physics - General Materials Science language: - iso: eng month: '01' oa_version: None page: 418-423 pmid: 1 publication: Langmuir publication_identifier: eissn: - 1520-5827 issn: - 0743-7463 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: One-step multilevel microfabrication by reaction−diffusion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2005' ...