---
_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'
...