---
_id: '2427'
abstract:
- lang: eng
text: Intersection graphs of disks and of line segments, respectively, have been
well studied, because of both practical applications and theoretically interesting
properties of these graphs. Despite partial results, the complexity status of
the Clique problem for these two graph classes is still open. Here, we consider
the Clique problem for intersection graphs of ellipses, which, in a sense, interpolate
between disks and line segments, and show that the problem is APX-hard in that
case. Moreover, this holds even if for all ellipses, the ratio of the larger over
the smaller radius is some prescribed number. Furthermore, the reduction immediately
carries over to intersection graphs of triangles. To our knowledge, this is the
first hardness result for the Clique problem in intersection graphs of convex
objects with finite description complexity. We also describe a simple approximation
algorithm for the case of ellipses for which the ratio of radii is bounded.
author:
- first_name: Christoph
full_name: Ambühl, Christoph
last_name: Ambühl
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Ambühl C, Wagner U. The Clique problem in intersection graphs of ellipses and
triangles. Theory of Computing Systems. 2005;38(3):279-292. doi:10.1007/s00224-005-1141-6
apa: Ambühl, C., & Wagner, U. (2005). The Clique problem in intersection graphs
of ellipses and triangles. Theory of Computing Systems. Springer. https://doi.org/10.1007/s00224-005-1141-6
chicago: Ambühl, Christoph, and Uli Wagner. “The Clique Problem in Intersection
Graphs of Ellipses and Triangles.” Theory of Computing Systems. Springer,
2005. https://doi.org/10.1007/s00224-005-1141-6.
ieee: C. Ambühl and U. Wagner, “The Clique problem in intersection graphs of ellipses
and triangles,” Theory of Computing Systems, vol. 38, no. 3. Springer,
pp. 279–292, 2005.
ista: Ambühl C, Wagner U. 2005. The Clique problem in intersection graphs of ellipses
and triangles. Theory of Computing Systems. 38(3), 279–292.
mla: Ambühl, Christoph, and Uli Wagner. “The Clique Problem in Intersection Graphs
of Ellipses and Triangles.” Theory of Computing Systems, vol. 38, no. 3,
Springer, 2005, pp. 279–92, doi:10.1007/s00224-005-1141-6.
short: C. Ambühl, U. Wagner, Theory of Computing Systems 38 (2005) 279–292.
date_created: 2018-12-11T11:57:36Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T06:57:25Z
day: '01'
doi: 10.1007/s00224-005-1141-6
extern: 1
intvolume: ' 38'
issue: '3'
month: '05'
page: 279 - 292
publication: Theory of Computing Systems
publication_status: published
publisher: Springer
publist_id: '4497'
quality_controlled: 0
status: public
title: The Clique problem in intersection graphs of ellipses and triangles
type: journal_article
volume: 38
year: '2005'
...
---
_id: '2428'
abstract:
- lang: eng
text: We consider an online version of the conflict-free coloring of a set of points
on the line, where each newly inserted point must be assigned a color upon insertion,
and at all times the coloring has to be conflict-free, in the sense that in every
interval I there is a color that appears exactly once in I. We present several
deterministic and randomized algorithms for achieving this goal, and analyze their
performance, that is, the maximum number of colors that they need to use, as a
function of the number n of inserted points. We first show that a natural and
simple (deterministic) approach may perform rather poorly, requiring Ω(√n) colors
in the worst case. We then modify this approach, to obtain an efficient deterministic
algorithm that uses a maximum of Θ(log 2 n) colors. Next, we present two randomized
solutions. The first algorithm requires an expected number of at most O(log 2
n) colors, and produces a coloring which is valid with high probability, and the
second one, which is a variant of our efficient deterministic algorithm, requires
an expected number of at most O(log n log log n) colors but always produces a
valid coloring. We also analyze the performance of the simplest proposed algorithm
when the points are inserted in a random order, and present an incomplete analysis
that indicates that, with high probability, it uses only O(log n) colors. Finally,
we show that in the extension of this problem to two dimensions, where the relevant
ranges are disks, n colors may be required in the worst case. The average-case
behavior for disks, and cases involving other planar ranges, are still open.
author:
- first_name: Amos
full_name: Fiat, Amos
last_name: Fiat
- first_name: Meital
full_name: Levy, Meital B
last_name: Levy
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Elchanan
full_name: Pach, Elchanan M
last_name: Pach
- first_name: Micha
full_name: Sharir, Micha
last_name: Sharir
- first_name: Shakhar
full_name: Smorodinsky, Shakhar
last_name: Smorodinsky
- first_name: Uli
full_name: Uli Wagner
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Emo
full_name: Welzl, Emo
last_name: Welzl
citation:
ama: 'Fiat A, Levy M, Matoušek J, et al. Online conflict-free coloring for intervals.
In: SIAM; 2005:545-554. doi:10.1137/S0097539704446682'
apa: 'Fiat, A., Levy, M., Matoušek, J., Pach, E., Sharir, M., Smorodinsky, S., …
Welzl, E. (2005). Online conflict-free coloring for intervals (pp. 545–554). Presented
at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1137/S0097539704446682'
chicago: Fiat, Amos, Meital Levy, Jiří Matoušek, Elchanan Pach, Micha Sharir, Shakhar
Smorodinsky, Uli Wagner, and Emo Welzl. “Online Conflict-Free Coloring for Intervals,”
545–54. SIAM, 2005. https://doi.org/10.1137/S0097539704446682.
ieee: 'A. Fiat et al., “Online conflict-free coloring for intervals,” presented
at the SODA: Symposium on Discrete Algorithms, 2005, pp. 545–554.'
ista: 'Fiat A, Levy M, Matoušek J, Pach E, Sharir M, Smorodinsky S, Wagner U, Welzl
E. 2005. Online conflict-free coloring for intervals. SODA: Symposium on Discrete
Algorithms, 545–554.'
mla: Fiat, Amos, et al. Online Conflict-Free Coloring for Intervals. SIAM,
2005, pp. 545–54, doi:10.1137/S0097539704446682.
short: A. Fiat, M. Levy, J. Matoušek, E. Pach, M. Sharir, S. Smorodinsky, U. Wagner,
E. Welzl, in:, SIAM, 2005, pp. 545–554.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T11:57:36Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:25Z
day: '01'
doi: 10.1137/S0097539704446682
extern: 1
month: '01'
page: 545 - 554
publication_status: published
publisher: SIAM
publist_id: '4496'
quality_controlled: 0
status: public
title: Online conflict-free coloring for intervals
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: '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: '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: '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: '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: '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: '1444'
abstract:
- lang: eng
text: The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas
concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat
connections and character varieties for curves, respectively. Several new results
and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman
and Earl-Kirwan are explained. These use the representation theory of finite groups
of Lie-type via the arithmetic of character varieties and lead to an unexpected
conjecture for a Hard Lefschetz theorem for their cohomology.
alternative_title:
- Progress in Mathematics
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: 'Hausel T. Mirror symmetry and Langlands duality in the non-Abelian Hodge theory
of a curve. In: Geometric Methods in Algebra and Number Theory. Vol 235.
Springer; 2005:193-217. doi:10.1007/0-8176-4417-2_9'
apa: Hausel, T. (2005). Mirror symmetry and Langlands duality in the non-Abelian
Hodge theory of a curve. In Geometric Methods in Algebra and Number Theory
(Vol. 235, pp. 193–217). Springer. https://doi.org/10.1007/0-8176-4417-2_9
chicago: Hausel, Tamás. “Mirror Symmetry and Langlands Duality in the Non-Abelian
Hodge Theory of a Curve.” In Geometric Methods in Algebra and Number Theory,
235:193–217. Springer, 2005. https://doi.org/10.1007/0-8176-4417-2_9.
ieee: T. Hausel, “Mirror symmetry and Langlands duality in the non-Abelian Hodge
theory of a curve,” in Geometric Methods in Algebra and Number Theory,
vol. 235, Springer, 2005, pp. 193–217.
ista: 'Hausel T. 2005.Mirror symmetry and Langlands duality in the non-Abelian Hodge
theory of a curve. In: Geometric Methods in Algebra and Number Theory. Progress
in Mathematics, vol. 235, 193–217.'
mla: Hausel, Tamás. “Mirror Symmetry and Langlands Duality in the Non-Abelian Hodge
Theory of a Curve.” Geometric Methods in Algebra and Number Theory, vol.
235, Springer, 2005, pp. 193–217, doi:10.1007/0-8176-4417-2_9.
short: T. Hausel, in:, Geometric Methods in Algebra and Number Theory, Springer,
2005, pp. 193–217.
date_created: 2018-12-11T11:52:03Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:47Z
day: '01'
doi: 10.1007/0-8176-4417-2_9
extern: 1
intvolume: ' 235'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0406380
month: '01'
oa: 1
page: 193 - 217
publication: Geometric Methods in Algebra and Number Theory
publication_status: published
publisher: Springer
publist_id: '5752'
quality_controlled: 0
status: public
title: Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a
curve
type: book_chapter
volume: 235
year: '2005'
...
---
_id: '1447'
abstract:
- lang: eng
text: Building on a recent paper [8], here we argue that the combinatorics of matroids
are intimately related to the geometry and topology of toric hyperkähler varieties.
We show that just like toric varieties occupy a central role in Stanley’s proof
for the necessity of McMullen’s conjecture (or g-inequalities) about the classification
of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties
leads to new restrictions on face vectors of matroid complexes. Namely in this
paper we will give two proofs that the injectivity part of the Hard Lefschetz
theorem survives for toric hyperkähler varieties. We explain how this implies
the g-inequalities for rationally representable matroids. We show how the geometrical
intuition in the first proof, coupled with results of Chari [3], leads to a proof
of the g-inequalities for general matroid complexes, which is a recent result
of Swartz [20]. The geometrical idea in the second proof will show that a pure
O-sequence should satisfy the g-inequalities, thus showing that our result is
in fact a consequence of a long-standing conjecture of Stanley.
acknowledgement: Financial support wa s provided by a Miller Research Fellowship at
the University of California at Berkeley , and by NSF grants DMS- 0072675 and DMS-0305505.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: Hausel T. Quaternionic geometry of matroids. Open Mathematics. 2005;3(1):26-38.
doi:10.2478/BF02475653
apa: Hausel, T. (2005). Quaternionic geometry of matroids. Open Mathematics.
Central European Science Journals. https://doi.org/10.2478/BF02475653
chicago: Hausel, Tamás. “Quaternionic Geometry of Matroids.” Open Mathematics.
Central European Science Journals, 2005. https://doi.org/10.2478/BF02475653.
ieee: T. Hausel, “Quaternionic geometry of matroids,” Open Mathematics, vol.
3, no. 1. Central European Science Journals, pp. 26–38, 2005.
ista: Hausel T. 2005. Quaternionic geometry of matroids. Open Mathematics. 3(1),
26–38.
mla: Hausel, Tamás. “Quaternionic Geometry of Matroids.” Open Mathematics,
vol. 3, no. 1, Central European Science Journals, 2005, pp. 26–38, doi:10.2478/BF02475653.
short: T. Hausel, Open Mathematics 3 (2005) 26–38.
date_created: 2018-12-11T11:52:05Z
date_published: 2005-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:49Z
day: '01'
doi: 10.2478/BF02475653
extern: 1
intvolume: ' 3'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0308146
month: '03'
oa: 1
page: 26 - 38
publication: Open Mathematics
publication_status: published
publisher: Central European Science Journals
publist_id: '5749'
quality_controlled: 0
status: public
title: Quaternionic geometry of matroids
type: journal_article
volume: 3
year: '2005'
...
---
_id: '1463'
abstract:
- lang: eng
text: We study an integration theory in circle equivariant cohomology in order to
prove a theorem relating the cohomology ring of a hyperkähler quotient to the
cohomology ring of the quotient by a maximal abelian subgroup, analogous to a
theorem of Martin for symplectic quotients. We discuss applications of this theorem
to quiver varieties, and compute as an example the ordinary and equivariant cohomology
rings of a hyperpolygon space.
acknowledgement: ' Financial support was provided in part by NSF Grants DMS-0072675
and DMS-0305505.'
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Nicholas
full_name: Proudfoot, Nicholas J
last_name: Proudfoot
citation:
ama: Hausel T, Proudfoot N. Abelianization for hyperkähler quotients. Topology.
2005;44(1):231-248. doi:10.1016/j.top.2004.04.002
apa: Hausel, T., & Proudfoot, N. (2005). Abelianization for hyperkähler quotients.
Topology. Elsevier. https://doi.org/10.1016/j.top.2004.04.002
chicago: Hausel, Tamás, and Nicholas Proudfoot. “Abelianization for Hyperkähler
Quotients.” Topology. Elsevier, 2005. https://doi.org/10.1016/j.top.2004.04.002.
ieee: T. Hausel and N. Proudfoot, “Abelianization for hyperkähler quotients,” Topology,
vol. 44, no. 1. Elsevier, pp. 231–248, 2005.
ista: Hausel T, Proudfoot N. 2005. Abelianization for hyperkähler quotients. Topology.
44(1), 231–248.
mla: Hausel, Tamás, and Nicholas Proudfoot. “Abelianization for Hyperkähler Quotients.”
Topology, vol. 44, no. 1, Elsevier, 2005, pp. 231–48, doi:10.1016/j.top.2004.04.002.
short: T. Hausel, N. Proudfoot, Topology 44 (2005) 231–248.
date_created: 2018-12-11T11:52:10Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:55Z
day: '01'
doi: 10.1016/j.top.2004.04.002
extern: 1
intvolume: ' 44'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0310141
month: '01'
oa: 1
page: 231 - 248
publication: Topology
publication_status: published
publisher: Elsevier
publist_id: '5735'
quality_controlled: 0
status: public
title: Abelianization for hyperkähler quotients
type: journal_article
volume: 44
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: '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'
...
---
_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: '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: '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: '11904'
abstract:
- lang: eng
text: "Many daily activities present information in the form of a stream of text,
and often people can benefit from additional information on the topic discussed.
TV broadcast news can be treated as one such stream of text; in this paper we
discuss finding news articles on the web that are relevant to news currently being
broadcast.\r\n\r\nWe evaluated a variety of algorithms for this problem, looking
at the impact of inverse document frequency, stemming, compounds, history, and
query length on the relevance and coverage of news articles returned in real time
during a broadcast. We also evaluated several postprocessing techniques for improving
the precision, including reranking using additional terms, reranking by document
similarity, and filtering on document similarity. For the best algorithm, 84–91%
of the articles found were relevant, with at least 64% of the articles being on
the exact topic of the broadcast. In addition, a relevant article was found for
at least 70% of the topics."
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Bay-Wei
full_name: Chang, Bay-Wei
last_name: Chang
- first_name: Brian
full_name: Milch, Brian
last_name: Milch
- first_name: Sergey
full_name: Brin, Sergey
last_name: Brin
citation:
ama: Henzinger MH, Chang B-W, Milch B, Brin S. Query-free news search. World
Wide Web. 2005;8(2):101-126. doi:10.1007/s11280-004-4870-6
apa: Henzinger, M. H., Chang, B.-W., Milch, B., & Brin, S. (2005). Query-free
news search. World Wide Web. Springer Nature. https://doi.org/10.1007/s11280-004-4870-6
chicago: Henzinger, Monika H, Bay-Wei Chang, Brian Milch, and Sergey Brin. “Query-Free
News Search.” World Wide Web. Springer Nature, 2005. https://doi.org/10.1007/s11280-004-4870-6.
ieee: M. H. Henzinger, B.-W. Chang, B. Milch, and S. Brin, “Query-free news search,”
World Wide Web, vol. 8, no. 2. Springer Nature, pp. 101–126, 2005.
ista: Henzinger MH, Chang B-W, Milch B, Brin S. 2005. Query-free news search. World
Wide Web. 8(2), 101–126.
mla: Henzinger, Monika H., et al. “Query-Free News Search.” World Wide Web,
vol. 8, no. 2, Springer Nature, 2005, pp. 101–26, doi:10.1007/s11280-004-4870-6.
short: M.H. Henzinger, B.-W. Chang, B. Milch, S. Brin, World Wide Web 8 (2005) 101–126.
date_created: 2022-08-17T11:16:56Z
date_published: 2005-06-01T00:00:00Z
date_updated: 2023-02-21T16:30:56Z
day: '01'
doi: 10.1007/s11280-004-4870-6
extern: '1'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 101-126
publication: World Wide Web
publication_identifier:
eissn:
- 1573-1413
issn:
- 1386-145X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11860'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Query-free news search
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2005'
...