---
_id: '4497'
abstract:
- lang: eng
text: "HyTech is a tool for the automated analysis of embedded systems. This document,
designed for the first-time user of HyTech, guides the reader through the underlying
system model, and through the input language for describing and analyzing systems.
The guide gives several examples of usage, and some hints for gaining maximal
computational efficiency from the tool.\r\nThe version of HyTech described in
this guide was released in August 1995, and is available through anonymous ftp
from ftp.cs.cornell.edu in the directory pub/tah/HyTech, and through the World-Wide
Web via HyTech's home page http:/www.cs.cornell.edu/Info/People/tah/hytech.html."
acknowledgement: This research was supported in part by the ONR YIP award N00014-95-1-0520,
by the NSF CAREER award CCR-9501708, by the NSF grants CCR-9200794 and CCR-9504469,
by the AFOSR contract F49620-93-1-0056, and by the ARPA grant NAG2-892.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Pei
full_name: Ho, Pei
last_name: Ho
- first_name: Howard
full_name: Wong Toi, Howard
last_name: Wong Toi
citation:
ama: 'Henzinger TA, Ho P, Wong Toi H. A user guide to HyTech. In: 1st International
Workshop on Tools and Algorithms for the Construction and Analysis of Systems.
Vol 1019. Springer; 1995:41-71. doi:10.1007/3-540-60630-0_3'
apa: 'Henzinger, T. A., Ho, P., & Wong Toi, H. (1995). A user guide to HyTech.
In 1st International Workshop on Tools and Algorithms for the Construction
and Analysis of Systems (Vol. 1019, pp. 41–71). Aarhus, Denmark: Springer.
https://doi.org/10.1007/3-540-60630-0_3'
chicago: Henzinger, Thomas A, Pei Ho, and Howard Wong Toi. “A User Guide to HyTech.”
In 1st International Workshop on Tools and Algorithms for the Construction
and Analysis of Systems, 1019:41–71. Springer, 1995. https://doi.org/10.1007/3-540-60630-0_3.
ieee: T. A. Henzinger, P. Ho, and H. Wong Toi, “A user guide to HyTech,” in 1st
International Workshop on Tools and Algorithms for the Construction and Analysis
of Systems, Aarhus, Denmark, 1995, vol. 1019, pp. 41–71.
ista: 'Henzinger TA, Ho P, Wong Toi H. 1995. A user guide to HyTech. 1st International
Workshop on Tools and Algorithms for the Construction and Analysis of Systems.
TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS,
vol. 1019, 41–71.'
mla: Henzinger, Thomas A., et al. “A User Guide to HyTech.” 1st International
Workshop on Tools and Algorithms for the Construction and Analysis of Systems,
vol. 1019, Springer, 1995, pp. 41–71, doi:10.1007/3-540-60630-0_3.
short: T.A. Henzinger, P. Ho, H. Wong Toi, in:, 1st International Workshop on Tools
and Algorithms for the Construction and Analysis of Systems, Springer, 1995, pp.
41–71.
conference:
end_date: 1995-05-20
location: Aarhus, Denmark
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 1995-05-19
date_created: 2018-12-11T12:09:09Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-10T09:00:05Z
day: '01'
doi: 10.1007/3-540-60630-0_3
extern: '1'
intvolume: ' 1019'
language:
- iso: eng
main_file_link:
- url: https://link.springer.com/chapter/10.1007/3-540-60630-0_3
month: '01'
oa_version: None
page: 41 - 71
publication: 1st International Workshop on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
isbn:
- '9783540606307'
publication_status: published
publisher: Springer
publist_id: '230'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A user guide to HyTech
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 1019
year: '1995'
...
---
_id: '4498'
abstract:
- lang: eng
text: We present algorithms for computing similarity relations of labeled graphs.
Similarity relations have applications for the refinement and verification of
reactive systems. For finite graphs, we present an O(mn) algorithm for computing
the similarity relation of a graph with n vertices and m edges (assuming m⩾n).
For effectively presented infinite graphs, we present a symbolic similarity-checking
procedure that terminates if a finite similarity relation exists. We show that
2D rectangular automata, which model discrete reactive systems with continuous
environments, define effectively presented infinite graphs with finite similarity
relations. It follows that the refinement problem and the ∀CTL* model-checking
problem are decidable for 2D rectangular automata
article_processing_charge: No
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Peter
full_name: Kopke, Peter
last_name: Kopke
citation:
ama: 'Henzinger M, Henzinger TA, Kopke P. Computing simulations on finite and infinite
graphs. In: Proceedings of IEEE 36th Annual Foundations of Computer Science.
IEEE; 1995:453-462. doi:10.1109/SFCS.1995.492576'
apa: 'Henzinger, M., Henzinger, T. A., & Kopke, P. (1995). Computing simulations
on finite and infinite graphs. In Proceedings of IEEE 36th Annual Foundations
of Computer Science (pp. 453–462). Milwaukee, WI, United States of America:
IEEE. https://doi.org/10.1109/SFCS.1995.492576'
chicago: Henzinger, Monika, Thomas A Henzinger, and Peter Kopke. “Computing Simulations
on Finite and Infinite Graphs.” In Proceedings of IEEE 36th Annual Foundations
of Computer Science, 453–62. IEEE, 1995. https://doi.org/10.1109/SFCS.1995.492576.
ieee: M. Henzinger, T. A. Henzinger, and P. Kopke, “Computing simulations on finite
and infinite graphs,” in Proceedings of IEEE 36th Annual Foundations of Computer
Science, Milwaukee, WI, United States of America, 1995, pp. 453–462.
ista: 'Henzinger M, Henzinger TA, Kopke P. 1995. Computing simulations on finite
and infinite graphs. Proceedings of IEEE 36th Annual Foundations of Computer Science.
FOCS: Foundations of Computer Science, 453–462.'
mla: Henzinger, Monika, et al. “Computing Simulations on Finite and Infinite Graphs.”
Proceedings of IEEE 36th Annual Foundations of Computer Science, IEEE,
1995, pp. 453–62, doi:10.1109/SFCS.1995.492576.
short: M. Henzinger, T.A. Henzinger, P. Kopke, in:, Proceedings of IEEE 36th Annual
Foundations of Computer Science, IEEE, 1995, pp. 453–462.
conference:
end_date: 1995-10-25
location: Milwaukee, WI, United States of America
name: 'FOCS: Foundations of Computer Science'
start_date: 1995-10-23
date_created: 2018-12-11T12:09:10Z
date_published: 1995-11-01T00:00:00Z
date_updated: 2024-11-06T12:02:08Z
day: '01'
doi: 10.1109/SFCS.1995.492576
extern: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 453 - 462
publication: Proceedings of IEEE 36th Annual Foundations of Computer Science
publication_identifier:
isbn:
- '0818671831'
issn:
- 0272-5428
publication_status: published
publisher: IEEE
publist_id: '231'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing simulations on finite and infinite graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '1995'
...
---
_id: '4499'
abstract:
- lang: eng
text: We describe a new implementation of HYTECH, a symbolic model checker for hybrid
systems. Given a parametric description of an embedded system as a collection
of communicating automata, HYTECH automatically computes the conditions on the
parameters under which the system satisfies its safety and timing requirements.
While the original HYTECH prototype was based on the symbolic algebra tool Mathematica,
the new implementation is written in C++ and builds on geometric algorithms instead
of formula manipulation. The new HYTECH offers a cleaner and more expressive input
language, greater portability, superior performance (typically two to three orders
of magnitude), and new features such as diagnostic error-trace generation. We
illustrate the effectiveness of the new implementation by applying HYTECH to the
automatic parametric analysis of the generic railroad crossing benchmark problem
and to an active structure control algorithm
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Pei
full_name: Ho, Pei
last_name: Ho
- first_name: Howard
full_name: Wong Toi, Howard
last_name: Wong Toi
citation:
ama: 'Henzinger TA, Ho P, Wong Toi H. HyTech: The next generation. In: Proceedings
16th IEEE Real-Time Systems Symposium. IEEE; 1995:56-65. doi:10.1109/REAL.1995.495196 '
apa: 'Henzinger, T. A., Ho, P., & Wong Toi, H. (1995). HyTech: The next generation.
In Proceedings 16th IEEE Real-Time Systems Symposium (pp. 56–65). Pisa,
Italy: IEEE. https://doi.org/10.1109/REAL.1995.495196
'
chicago: 'Henzinger, Thomas A, Pei Ho, and Howard Wong Toi. “HyTech: The next Generation.”
In Proceedings 16th IEEE Real-Time Systems Symposium, 56–65. IEEE, 1995.
https://doi.org/10.1109/REAL.1995.495196
.'
ieee: 'T. A. Henzinger, P. Ho, and H. Wong Toi, “HyTech: The next generation,” in
Proceedings 16th IEEE Real-Time Systems Symposium, Pisa, Italy, 1995, pp.
56–65.'
ista: 'Henzinger TA, Ho P, Wong Toi H. 1995. HyTech: The next generation. Proceedings
16th IEEE Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium, 56–65.'
mla: 'Henzinger, Thomas A., et al. “HyTech: The next Generation.” Proceedings
16th IEEE Real-Time Systems Symposium, IEEE, 1995, pp. 56–65, doi:10.1109/REAL.1995.495196 .'
short: T.A. Henzinger, P. Ho, H. Wong Toi, in:, Proceedings 16th IEEE Real-Time
Systems Symposium, IEEE, 1995, pp. 56–65.
conference:
end_date: 1995-12-07
location: Pisa, Italy
name: 'RTSS: Real-Time Systems Symposium'
start_date: 1995-12-05
date_created: 2018-12-11T12:09:10Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-10T09:33:19Z
day: '01'
doi: '10.1109/REAL.1995.495196 '
extern: '1'
language:
- iso: eng
main_file_link:
- url: https://ieeexplore.ieee.org/document/495196
month: '01'
oa_version: None
page: 56 - 65
publication: Proceedings 16th IEEE Real-Time Systems Symposium
publication_identifier:
isbn:
- '0818673370'
publication_status: published
publisher: IEEE
publist_id: '232'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'HyTech: The next generation'
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1995'
...
---
_id: '4500'
abstract:
- lang: eng
text: 'We investigate the expressive power of timing restrictions on labeled transition
systems. In particular, we show how constraints on clock variables together with
a uniform liveness condition—the divergence of time—can express Büchi, Muller,
Streett, Rabin, and weak and strong fairness conditions on a given labeled transition
system. We then consider the effect, on both timed and time-abstract expressiveness,
of varying the following parameters: time domain (discrete or dense), number of
clocks, number of states, and size of constants used in timing restrictions.'
acknowledgement: "This research was supported in part by the National Science Foundation
under grant CCR-9200794, by the United States Air Force Office of Scientific Research
under contract F49620-93-1-0056, by the Defense Advanced Research Projects Agency
under grant NAG2-892, and by the U.S. Army Research Office through the Mathematical
Sciences Institute of Cornell University, Contract Number DAAL03-91-C-0027.\r\nThe
full version of this paper is available from the Department of Computer Science,
Cornell University, Ithaca, NY 14853, as Technical Report TR95-1496."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Peter
full_name: Kopke, Peter
last_name: Kopke
- first_name: Howard
full_name: Wong Toi, Howard
last_name: Wong Toi
citation:
ama: 'Henzinger TA, Kopke P, Wong Toi H. The expressive power of clocks. In: 22nd
International Colloquium on Automata, Languages and Programming . Vol 944.
Springer; 1995:417-428. doi:10.1007/3-540-60084-1_93'
apa: 'Henzinger, T. A., Kopke, P., & Wong Toi, H. (1995). The expressive power
of clocks. In 22nd International Colloquium on Automata, Languages and Programming
(Vol. 944, pp. 417–428). Szeged, Hungary: Springer. https://doi.org/10.1007/3-540-60084-1_93'
chicago: Henzinger, Thomas A, Peter Kopke, and Howard Wong Toi. “The Expressive
Power of Clocks.” In 22nd International Colloquium on Automata, Languages and
Programming , 944:417–28. Springer, 1995. https://doi.org/10.1007/3-540-60084-1_93.
ieee: T. A. Henzinger, P. Kopke, and H. Wong Toi, “The expressive power of clocks,”
in 22nd International Colloquium on Automata, Languages and Programming ,
Szeged, Hungary, 1995, vol. 944, pp. 417–428.
ista: 'Henzinger TA, Kopke P, Wong Toi H. 1995. The expressive power of clocks.
22nd International Colloquium on Automata, Languages and Programming . ICALP:
Automata, Languages and Programming, LNCS, vol. 944, 417–428.'
mla: Henzinger, Thomas A., et al. “The Expressive Power of Clocks.” 22nd International
Colloquium on Automata, Languages and Programming , vol. 944, Springer, 1995,
pp. 417–28, doi:10.1007/3-540-60084-1_93.
short: T.A. Henzinger, P. Kopke, H. Wong Toi, in:, 22nd International Colloquium
on Automata, Languages and Programming , Springer, 1995, pp. 417–428.
conference:
end_date: 1995-07-14
location: Szeged, Hungary
name: 'ICALP: Automata, Languages and Programming'
start_date: 1995-07-10
date_created: 2018-12-11T12:09:10Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-09T14:58:31Z
day: '01'
doi: 10.1007/3-540-60084-1_93
extern: '1'
intvolume: ' 944'
language:
- iso: eng
main_file_link:
- url: https://link.springer.com/chapter/10.1007/3-540-60084-1_93
month: '01'
oa_version: None
page: 417 - 428
publication: '22nd International Colloquium on Automata, Languages and Programming '
publication_identifier:
isbn:
- '9783540600848'
publication_status: published
publisher: Springer
publist_id: '229'
quality_controlled: '1'
status: public
title: The expressive power of clocks
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 944
year: '1995'
...
---
_id: '4502'
abstract:
- lang: eng
text: "Hybrid automata model systems with both digital and analog components, such
as embedded control programs. Many verification tasks for such programs can be
expressed as reachability problems for hybrid automata. By improving on previous
decidability and undecidability results, we identify the precise boundary between
decidability and undecidability of the reachability problem for hybrid automata.\r\n\r\nOn
the positive side, we give an (optimal) PSPACE reachability algorithm for the
case of initialized rectangular automata, where all analog variables follow trajectories
within piecewise-linear envelopes and are reinitialized whenever the envelope
changes. Our algorithm is based on the construction of a timed automaton that
contains all reachability information about a given initialized rectangular automaton.
The translation has practical significance for verification, because it guarantees
the termination of symbolic procedures for the reachability analysis of initialized
rectangular automata. The translation also preserves the omega-languages of initialized
rectangular automata with bounded nondeterminism.\r\n\r\nOn the negative side,
we show that several slight generalizations of initialized rectangular automata
lead to an undecidable reachability problem. In particular, we prove that the
reachability problem is undecidable for timed automata augmented with a single
stopwatch."
acknowledgement: "We thank Howard Wong-Toi for a careful reading.\r\n"
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Peter
full_name: Kopke, Peter
last_name: Kopke
- first_name: Anuj
full_name: Puri, Anuj
last_name: Puri
- first_name: P.
full_name: Varaiya, P.
last_name: Varaiya
citation:
ama: 'Henzinger TA, Kopke P, Puri A, Varaiya P. What’s decidable about hybrid automata?
In: Proceedings of the 27th Annual ACM Symposium on Theory of Computing.
ACM; 1995:373-382. doi:10.1145/225058.225162'
apa: 'Henzinger, T. A., Kopke, P., Puri, A., & Varaiya, P. (1995). What’s decidable
about hybrid automata? In Proceedings of the 27th annual ACM symposium on Theory
of computing (pp. 373–382). Las Vegas, NV, United States of America: ACM.
https://doi.org/10.1145/225058.225162'
chicago: Henzinger, Thomas A, Peter Kopke, Anuj Puri, and P. Varaiya. “What’s Decidable
about Hybrid Automata?” In Proceedings of the 27th Annual ACM Symposium on
Theory of Computing, 373–82. ACM, 1995. https://doi.org/10.1145/225058.225162.
ieee: T. A. Henzinger, P. Kopke, A. Puri, and P. Varaiya, “What’s decidable about
hybrid automata?,” in Proceedings of the 27th annual ACM symposium on Theory
of computing, Las Vegas, NV, United States of America, 1995, pp. 373–382.
ista: 'Henzinger TA, Kopke P, Puri A, Varaiya P. 1995. What’s decidable about hybrid
automata? Proceedings of the 27th annual ACM symposium on Theory of computing.
STOC: Symposium on the Theory of Computing, 373–382.'
mla: Henzinger, Thomas A., et al. “What’s Decidable about Hybrid Automata?” Proceedings
of the 27th Annual ACM Symposium on Theory of Computing, ACM, 1995, pp. 373–82,
doi:10.1145/225058.225162.
short: T.A. Henzinger, P. Kopke, A. Puri, P. Varaiya, in:, Proceedings of the 27th
Annual ACM Symposium on Theory of Computing, ACM, 1995, pp. 373–382.
conference:
end_date: 1995-06-01
location: Las Vegas, NV, United States of America
name: 'STOC: Symposium on the Theory of Computing'
start_date: 1995-05-29
date_created: 2018-12-11T12:09:11Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-09T14:40:29Z
day: '01'
doi: 10.1145/225058.225162
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/225058.225162
month: '01'
oa: 1
oa_version: Published Version
page: 373 - 382
publication: Proceedings of the 27th annual ACM symposium on Theory of computing
publication_identifier:
isbn:
- '9780897917186'
publication_status: published
publisher: ACM
publist_id: '228'
quality_controlled: '1'
status: public
title: What's decidable about hybrid automata?
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1995'
...
---
_id: '4518'
abstract:
- lang: eng
text: The analysis, verification, and control of hybrid automata with finite bisimulations
can be reduced to finite-state problems. We advocate a time-abstract, phase-based
methodology for checking if a given hybrid automaton has a finite bisimulation.
First, we factor the automaton into two components, a boolean automaton with a
discrete dynamics on the finite state space B m and a euclidean automaton with
a continuous dynamics on the infinite state space n . Second, we investigate
the phase portrait of the euclidean component. In this fashion, we obtain new
decidability results for hybrid systems as well as new, uniform proofs of known
decidability results.
acknowledgement: "This research was supported in part by the NSF grant CCR-9200794,
by the AFOSR contract F49620-93-1-0056, and by the DARPA grant NAG2-892.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. Hybrid automata with finite bisimulations. In: 22nd International
Colloquium on Automata, Languages and Programming . Vol 944. Springer; 1995:324-335.
doi:10.1007/3-540-60084-1_85'
apa: 'Henzinger, T. A. (1995). Hybrid automata with finite bisimulations. In 22nd
International Colloquium on Automata, Languages and Programming (Vol. 944,
pp. 324–335). Szeged, Hungary: Springer. https://doi.org/10.1007/3-540-60084-1_85'
chicago: Henzinger, Thomas A. “Hybrid Automata with Finite Bisimulations.” In 22nd
International Colloquium on Automata, Languages and Programming , 944:324–35.
Springer, 1995. https://doi.org/10.1007/3-540-60084-1_85.
ieee: T. A. Henzinger, “Hybrid automata with finite bisimulations,” in 22nd International
Colloquium on Automata, Languages and Programming , Szeged, Hungary, 1995,
vol. 944, pp. 324–335.
ista: 'Henzinger TA. 1995. Hybrid automata with finite bisimulations. 22nd International
Colloquium on Automata, Languages and Programming . ICALP: Automata, Languages
and Programming, LNCS, vol. 944, 324–335.'
mla: Henzinger, Thomas A. “Hybrid Automata with Finite Bisimulations.” 22nd International
Colloquium on Automata, Languages and Programming , vol. 944, Springer, 1995,
pp. 324–35, doi:10.1007/3-540-60084-1_85.
short: T.A. Henzinger, in:, 22nd International Colloquium on Automata, Languages
and Programming , Springer, 1995, pp. 324–335.
conference:
end_date: 1995-07-14
location: Szeged, Hungary
name: 'ICALP: Automata, Languages and Programming'
start_date: 1995-07-10
date_created: 2018-12-11T12:09:16Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2025-06-26T08:47:29Z
day: '01'
doi: 10.1007/3-540-60084-1_85
extern: '1'
intvolume: ' 944'
language:
- iso: eng
month: '01'
oa_version: None
page: 324 - 335
publication: '22nd International Colloquium on Automata, Languages and Programming '
publication_identifier:
isbn:
- '9783540600848'
publication_status: published
publisher: Springer
publist_id: '212'
quality_controlled: '1'
status: public
title: Hybrid automata with finite bisimulations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 944
year: '1995'
...
---
_id: '4587'
abstract:
- lang: eng
text: We argue that the standard constraints on liveness conditions in nonblocking
trace models—machine closure for closed systems, and receptiveness for open systems—are
unnecessarily weak and complex, and that liveness should, instead, be specified
by augmenting transition systems with acceptance conditions that satisfy a locality
constraint. First, locality implies machine closure and receptiveness, and thus
permits the composition and modular verification of live transition systems. Second,
while machine closure and receptiveness are based on infinite games, locality
is based on repeated finite games, and thus easier to check. Third, no expressive
power is lost by the restriction to local liveness conditions. We illustrate the
appeal of local liveness using the model of Fair Reactive Systems, a nonblocking
trace model of communicating processes.
acknowledgement: Supported in part by the NSF grant CCR-9200794, by the AFOSR contract
F49620-93-1-0056, and by the DARPA grant NAG2-892.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Alur R, Henzinger TA. Local liveness for compositional modeling of fair reactive
systems. In: 7th International Conference on Computer Aided Verification.
Vol 939. Springer; 1995:166-179. doi:10.1007/3-540-60045-0_49'
apa: 'Alur, R., & Henzinger, T. A. (1995). Local liveness for compositional
modeling of fair reactive systems. In 7th International Conference on Computer
Aided Verification (Vol. 939, pp. 166–179). Liege, Belgium: Springer. https://doi.org/10.1007/3-540-60045-0_49'
chicago: Alur, Rajeev, and Thomas A Henzinger. “Local Liveness for Compositional
Modeling of Fair Reactive Systems.” In 7th International Conference on Computer
Aided Verification, 939:166–79. Springer, 1995. https://doi.org/10.1007/3-540-60045-0_49.
ieee: R. Alur and T. A. Henzinger, “Local liveness for compositional modeling of
fair reactive systems,” in 7th International Conference on Computer Aided Verification,
Liege, Belgium, 1995, vol. 939, pp. 166–179.
ista: 'Alur R, Henzinger TA. 1995. Local liveness for compositional modeling of
fair reactive systems. 7th International Conference on Computer Aided Verification.
CAV: Computer Aided Verification, LNCS, vol. 939, 166–179.'
mla: Alur, Rajeev, and Thomas A. Henzinger. “Local Liveness for Compositional Modeling
of Fair Reactive Systems.” 7th International Conference on Computer Aided Verification,
vol. 939, Springer, 1995, pp. 166–79, doi:10.1007/3-540-60045-0_49.
short: R. Alur, T.A. Henzinger, in:, 7th International Conference on Computer Aided
Verification, Springer, 1995, pp. 166–179.
conference:
end_date: 1995-07-05
location: Liege, Belgium
name: 'CAV: Computer Aided Verification'
start_date: 1995-07-03
date_created: 2018-12-11T12:09:37Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-09T14:05:04Z
day: '01'
doi: 10.1007/3-540-60045-0_49
extern: '1'
intvolume: ' 939'
language:
- iso: eng
main_file_link:
- url: https://link.springer.com/chapter/10.1007/3-540-60045-0_49
month: '01'
oa_version: None
page: 166 - 179
publication: 7th International Conference on Computer Aided Verification
publication_identifier:
isbn:
- 978-3-540-60045-9
publication_status: published
publisher: Springer
publist_id: '120'
quality_controlled: '1'
status: public
title: Local liveness for compositional modeling of fair reactive systems
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 939
year: '1995'
...
---
_id: '4613'
abstract:
- lang: eng
text: We present a general framework for the formal specification and algorithmic
analysis of hybrid systems. A hybrid system consists of a discrete program with
an analog environment. We model hybrid systems as finite automata equipped with
variables that evolve continuously with time according to dynamical laws. For
verification purposes, we restrict ourselves to linear hybrid systems, where all
variables follow piecewise-linear trajectories. We provide decidability and undecidability
results for classes of linear hybrid systems, and we show that standard program-analysis
techniques can be adapted to linear hybrid systems. In particular, we consider
symbolic model-checking and minimization procedures that are based on the reachability
analysis of an infinite state space. The procedures iteratively compute state
sets that are definable as unions of convex polyhedra in multidimensional real
space. We also present approximation techniques for dealing with systems for which
the iterative procedures do not converge.
article_processing_charge: No
article_type: original
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Costas
full_name: Courcoubetis, Costas
last_name: Courcoubetis
- first_name: Nicolas
full_name: Halbwachs, Nicolas
last_name: Halbwachs
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Pei
full_name: Ho, Pei
last_name: Ho
- first_name: Xavier
full_name: Nicollin, Xavier
last_name: Nicollin
- first_name: Alfredo
full_name: Olivero, Alfredo
last_name: Olivero
- first_name: Joseph
full_name: Sifakis, Joseph
last_name: Sifakis
- first_name: Sergio
full_name: Yovine, Sergio
last_name: Yovine
citation:
ama: Alur R, Courcoubetis C, Halbwachs N, et al. The algorithmic analysis of hybrid
systems. Theoretical Computer Science. 1995;138(1):3-34. doi:10.1016/0304-3975(94)00202-T
apa: Alur, R., Courcoubetis, C., Halbwachs, N., Henzinger, T. A., Ho, P., Nicollin,
X., … Yovine, S. (1995). The algorithmic analysis of hybrid systems. Theoretical
Computer Science. Elsevier. https://doi.org/10.1016/0304-3975(94)00202-T
chicago: Alur, Rajeev, Costas Courcoubetis, Nicolas Halbwachs, Thomas A Henzinger,
Pei Ho, Xavier Nicollin, Alfredo Olivero, Joseph Sifakis, and Sergio Yovine. “The
Algorithmic Analysis of Hybrid Systems.” Theoretical Computer Science.
Elsevier, 1995. https://doi.org/10.1016/0304-3975(94)00202-T.
ieee: R. Alur et al., “The algorithmic analysis of hybrid systems,” Theoretical
Computer Science, vol. 138, no. 1. Elsevier, pp. 3–34, 1995.
ista: Alur R, Courcoubetis C, Halbwachs N, Henzinger TA, Ho P, Nicollin X, Olivero
A, Sifakis J, Yovine S. 1995. The algorithmic analysis of hybrid systems. Theoretical
Computer Science. 138(1), 3–34.
mla: Alur, Rajeev, et al. “The Algorithmic Analysis of Hybrid Systems.” Theoretical
Computer Science, vol. 138, no. 1, Elsevier, 1995, pp. 3–34, doi:10.1016/0304-3975(94)00202-T.
short: R. Alur, C. Courcoubetis, N. Halbwachs, T.A. Henzinger, P. Ho, X. Nicollin,
A. Olivero, J. Sifakis, S. Yovine, Theoretical Computer Science 138 (1995) 3–34.
date_created: 2018-12-11T12:09:45Z
date_published: 1995-02-06T00:00:00Z
date_updated: 2022-06-09T13:40:48Z
day: '06'
doi: 10.1016/0304-3975(94)00202-T
extern: '1'
intvolume: ' 138'
issue: '1'
language:
- iso: eng
main_file_link:
- url: https://www.sciencedirect.com/science/article/pii/030439759400202T?via%3Dihub
month: '02'
oa_version: None
page: 3 - 34
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
publist_id: '94'
quality_controlled: '1'
status: public
title: The algorithmic analysis of hybrid systems
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 138
year: '1995'
...
---
_id: '6162'
abstract:
- lang: eng
text: 'The tra-1 gene is the terminal global selector of somatic sex in Caenorhabditis
elegans: High tra-1 activity elicits female somatic development while low tra-1
activity elicits male development. Previous genetic studies defined a cascade
of negatively interacting genes that regulates tra-1 activity in response to the
primary sex-determining signal. Here, we investigate the last step in this regulatory
cascade, by studying rare gain-of-function (gf) mutations of tra-1 that direct
female somatic development irrespective of the upstream sex-determining signal.
These mutations appear to abolish negative regulation of tra-1 in male tissues.
We identify the lesions associated with 29 of these mutations and find that all
affect a short stretch of amino acid residues present in both protein products
of the tra-1 gene. Twenty-six alleles are associated with single nonconservative
amino acid substitutions. Two alleles affect tra-1 RNA splicing and generate messages
that omit part or all of the exon encoding this short stretch. These results suggest
that sexual regulation of tra-1 is achieved post-translationally, by an inhibitory
protein-protein interaction. The amino acid stretch altered by the tra-1(gf) mutations
may define a site of interaction for negative regulators of tra-1. The stretch
includes a potential phosphorylation site for glycogen synthase kinase 3 and may
be conserved in the human gene GLI3, a homolog of tra-1 identified previously.'
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: D.
full_name: Zarkower, D.
last_name: Zarkower
- first_name: J.
full_name: Hodgkin, J.
last_name: Hodgkin
citation:
ama: de Bono M, Zarkower D, Hodgkin J. Dominant feminizing mutations implicate protein-protein
interactions as the main mode of regulation of the nematode sex-determining gene
tra-1. Genes and Development. 1995;9(2):155-167. doi:10.1101/gad.9.2.155
apa: de Bono, M., Zarkower, D., & Hodgkin, J. (1995). Dominant feminizing mutations
implicate protein-protein interactions as the main mode of regulation of the nematode
sex-determining gene tra-1. Genes and Development. CSH Press. https://doi.org/10.1101/gad.9.2.155
chicago: Bono, Mario de, D. Zarkower, and J. Hodgkin. “Dominant Feminizing Mutations
Implicate Protein-Protein Interactions as the Main Mode of Regulation of the Nematode
Sex-Determining Gene Tra-1.” Genes and Development. CSH Press, 1995. https://doi.org/10.1101/gad.9.2.155.
ieee: M. de Bono, D. Zarkower, and J. Hodgkin, “Dominant feminizing mutations implicate
protein-protein interactions as the main mode of regulation of the nematode sex-determining
gene tra-1,” Genes and Development, vol. 9, no. 2. CSH Press, pp. 155–167,
1995.
ista: de Bono M, Zarkower D, Hodgkin J. 1995. Dominant feminizing mutations implicate
protein-protein interactions as the main mode of regulation of the nematode sex-determining
gene tra-1. Genes and Development. 9(2), 155–167.
mla: de Bono, Mario, et al. “Dominant Feminizing Mutations Implicate Protein-Protein
Interactions as the Main Mode of Regulation of the Nematode Sex-Determining Gene
Tra-1.” Genes and Development, vol. 9, no. 2, CSH Press, 1995, pp. 155–67,
doi:10.1101/gad.9.2.155.
short: M. de Bono, D. Zarkower, J. Hodgkin, Genes and Development 9 (1995) 155–167.
date_created: 2019-03-21T11:57:40Z
date_published: 1995-01-15T00:00:00Z
date_updated: 2021-01-12T08:06:29Z
day: '15'
doi: 10.1101/gad.9.2.155
extern: '1'
external_id:
pmid:
- '7851791'
intvolume: ' 9'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 155-167
pmid: 1
publication: Genes and Development
publication_identifier:
issn:
- '08909369'
publication_status: published
publisher: CSH Press
quality_controlled: '1'
status: public
title: Dominant feminizing mutations implicate protein-protein interactions as the
main mode of regulation of the nematode sex-determining gene tra-1
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '1995'
...
---
_id: '3454'
abstract:
- lang: eng
text: The study of gene expression and regulation in the central nervous system
(CNS) is a daunting task because of the diversity of neuronal phenotypes and the
complexity of many protein classes. Molecular cloning revealed the presence of
a large number of different protein families in the CNS, each comprising several
members. Ligand-gated ion channels may serve as an example to illustrate this
point (for review, see Unwin, 1993). Heterologous expression combined with electrophysiological
analysis suggests that ligand-gated channels are multimeric proteins with functional
properties depending on the subunit composition. Very little is known, however,
about how the functional properties of the recombinant and native receptors relate
to each other. Thus, it is of eminent importance to elucidate the subunit expression
profile in different types of neurons in the CNS and to correlate this with the
functional properties of the native receptors.
article_processing_charge: No
author:
- first_name: Hannah
full_name: Monyer, Hannah
last_name: Monyer
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Monyer H, Jonas PM. Polymerase chain reaction analysis of ion channel expression
in single neurons of brain slices. In: Sakmann B, Neher E, eds. Single-Channel
Recording. Plenum; 1995:357-373. doi:10.1007/978-1-4419-1229-9_16'
apa: Monyer, H., & Jonas, P. M. (1995). Polymerase chain reaction analysis of
ion channel expression in single neurons of brain slices. In B. Sakmann &
E. Neher (Eds.), Single-channel recording (pp. 357–373). Plenum. https://doi.org/10.1007/978-1-4419-1229-9_16
chicago: Monyer, Hannah, and Peter M Jonas. “Polymerase Chain Reaction Analysis
of Ion Channel Expression in Single Neurons of Brain Slices.” In Single-Channel
Recording, edited by Bert Sakmann and Erwin Neher, 357–73. Plenum, 1995. https://doi.org/10.1007/978-1-4419-1229-9_16.
ieee: H. Monyer and P. M. Jonas, “Polymerase chain reaction analysis of ion channel
expression in single neurons of brain slices,” in Single-channel recording,
B. Sakmann and E. Neher, Eds. Plenum, 1995, pp. 357–373.
ista: 'Monyer H, Jonas PM. 1995.Polymerase chain reaction analysis of ion channel
expression in single neurons of brain slices. In: Single-channel recording. ,
357–373.'
mla: Monyer, Hannah, and Peter M. Jonas. “Polymerase Chain Reaction Analysis of
Ion Channel Expression in Single Neurons of Brain Slices.” Single-Channel Recording,
edited by Bert Sakmann and Erwin Neher, Plenum, 1995, pp. 357–73, doi:10.1007/978-1-4419-1229-9_16.
short: H. Monyer, P.M. Jonas, in:, B. Sakmann, E. Neher (Eds.), Single-Channel Recording,
Plenum, 1995, pp. 357–373.
date_created: 2018-12-11T12:03:25Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-28T09:13:01Z
day: '01'
doi: 10.1007/978-1-4419-1229-9_16
editor:
- first_name: Bert
full_name: Sakmann, Bert
last_name: Sakmann
- first_name: Erwin
full_name: Neher, Erwin
last_name: Neher
extern: '1'
language:
- iso: eng
main_file_link:
- url: https://link.springer.com/chapter/10.1007/978-1-4419-1229-9_16
month: '01'
oa_version: None
page: 357 - 373
publication: Single-channel recording
publication_identifier:
isbn:
- 978-0-306-44870-6
publication_status: published
publisher: Plenum
publist_id: '2933'
quality_controlled: '1'
status: public
title: Polymerase chain reaction analysis of ion channel expression in single neurons
of brain slices
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1995'
...
---
_id: '3455'
abstract:
- lang: eng
text: At a synapse, the transmitter is stored in synaptic vesicles and is released
into the synaptic cleft almost instantaneously upon fusion of these vesicles with
the presynaptic membrane. Subsequently, the transmitter diffuses to ligand-gated
ion channels in the postsynaptic density, binds to them, and thereby causes channel
activation. Unfortunately, we have estimates neither of the exact amount of transmitter
in the synaptic vesicle nor of the concentration in the synaptic cleft reaching
the postsynaptic receptors, and in some cases even the identity of the transmitter
is unknown. These questions may be addressed by modeling of release and diffusion.
Such a theoretical approach, however, is based on several assumptions, some of
which lack experimental evidence.
article_processing_charge: No
author:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Jonas PM. Fast application of agonists to isolated membrane patches. In: Sakmann
B, Neher E, eds. Single-Channel Recording. Plenum; 1995:231-243. doi:10.1007/978-1-4419-1229-9_10'
apa: Jonas, P. M. (1995). Fast application of agonists to isolated membrane patches.
In B. Sakmann & E. Neher (Eds.), Single-channel recording (pp. 231–243).
Plenum. https://doi.org/10.1007/978-1-4419-1229-9_10
chicago: Jonas, Peter M. “Fast Application of Agonists to Isolated Membrane Patches.”
In Single-Channel Recording, edited by Bert Sakmann and Erwin Neher, 231–43.
Plenum, 1995. https://doi.org/10.1007/978-1-4419-1229-9_10.
ieee: P. M. Jonas, “Fast application of agonists to isolated membrane patches,”
in Single-channel recording, B. Sakmann and E. Neher, Eds. Plenum, 1995,
pp. 231–243.
ista: 'Jonas PM. 1995.Fast application of agonists to isolated membrane patches.
In: Single-channel recording. , 231–243.'
mla: Jonas, Peter M. “Fast Application of Agonists to Isolated Membrane Patches.”
Single-Channel Recording, edited by Bert Sakmann and Erwin Neher, Plenum,
1995, pp. 231–43, doi:10.1007/978-1-4419-1229-9_10.
short: P.M. Jonas, in:, B. Sakmann, E. Neher (Eds.), Single-Channel Recording, Plenum,
1995, pp. 231–243.
date_created: 2018-12-11T12:03:25Z
date_published: 1995-01-01T00:00:00Z
date_updated: 2022-06-28T08:51:40Z
day: '01'
doi: 10.1007/978-1-4419-1229-9_10
editor:
- first_name: Bert
full_name: Sakmann, Bert
last_name: Sakmann
- first_name: Erwin
full_name: Neher, Erwin
last_name: Neher
extern: '1'
language:
- iso: eng
main_file_link:
- url: https://link.springer.com/chapter/10.1007/978-1-4419-1229-9_10
month: '01'
oa_version: None
page: 231 - 243
publication: Single-channel recording
publication_identifier:
isbn:
- 978-0-306-44870-6
publication_status: published
publisher: Plenum
publist_id: '2932'
quality_controlled: '1'
status: public
title: Fast application of agonists to isolated membrane patches
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1995'
...
---
_id: '3461'
article_processing_charge: No
article_type: original
author:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Nail
full_name: Burnashev, Nail
last_name: Burnashev
citation:
ama: Jonas PM, Burnashev N. Molecular mechanisms controlling calcium entry through
AMPA-type glutamate receptor channels. Neuron. 1995;15(5):987-990. doi:10.1016/0896-6273(95)90087-X
apa: Jonas, P. M., & Burnashev, N. (1995). Molecular mechanisms controlling
calcium entry through AMPA-type glutamate receptor channels. Neuron. Elsevier.
https://doi.org/10.1016/0896-6273(95)90087-X
chicago: Jonas, Peter M, and Nail Burnashev. “Molecular Mechanisms Controlling Calcium
Entry through AMPA-Type Glutamate Receptor Channels.” Neuron. Elsevier,
1995. https://doi.org/10.1016/0896-6273(95)90087-X.
ieee: P. M. Jonas and N. Burnashev, “Molecular mechanisms controlling calcium entry
through AMPA-type glutamate receptor channels,” Neuron, vol. 15, no. 5.
Elsevier, pp. 987–990, 1995.
ista: Jonas PM, Burnashev N. 1995. Molecular mechanisms controlling calcium entry
through AMPA-type glutamate receptor channels. Neuron. 15(5), 987–990.
mla: Jonas, Peter M., and Nail Burnashev. “Molecular Mechanisms Controlling Calcium
Entry through AMPA-Type Glutamate Receptor Channels.” Neuron, vol. 15,
no. 5, Elsevier, 1995, pp. 987–90, doi:10.1016/0896-6273(95)90087-X.
short: P.M. Jonas, N. Burnashev, Neuron 15 (1995) 987–990.
date_created: 2018-12-11T12:03:27Z
date_published: 1995-11-01T00:00:00Z
date_updated: 2022-06-28T08:34:36Z
day: '01'
doi: 10.1016/0896-6273(95)90087-X
extern: '1'
external_id:
pmid:
- '7576666'
intvolume: ' 15'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/089662739590087X?via%3Dihub
month: '11'
oa: 1
oa_version: Published Version
page: 987 - 990
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
publist_id: '2926'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular mechanisms controlling calcium entry through AMPA-type glutamate
receptor channels
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 15
year: '1995'
...
---
_id: '3478'
abstract:
- lang: eng
text: 1. Properties of dendritic glutamate receptor (GluR) channels were investigated
using fast application of glutamate to outside-out membrane patches isolated from
the apical dendrites of CA3 and CA1 pyramidal neurons in rat hippocampal slices.
CA3 patches were formed (15-76 μm from the soma) in the region of messy fibre
(MF) synapses, and CA1 patches (25-174 μm from the soma) in the region of Schaffer
collateral (SC) innervation. 2. Dual-component responses consisting of a rapidly
rising and decaying component followed by a second, substantially slower, component
were elicited by 1 ms pulses of 1 mM glutamate in the presence of 10 μM glycine
and absence of external Mg2+. The fast component was selectively blocked by 2-5
μM 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) and the slow component by 30 μM
D-2-amino-5-phosphonopentanoic acid (D-AP5), suggesting that the fast and slow
components were mediated by the GluR channels of the L-α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate
(AMPA) and NMDA type, respectively. The peak amplitude ratio of the NMDA to AMPA
receptor-mediated components varied between 0.03 and 0.62 in patches from both
CA3 and CA1 dendrites. Patches lacking either component were rarely observed.
3. The peak current-voltage (I-V) relationship of the fast component was almost
linear, whereas the I-V relationship of the slow component showed a region of
negative slope in the presence of 1 mM external Mg2+. The reversal potential for
both components was close to 0 mV. 4. Kainate-preferring GluR channels did not
contribute appreciably to the response to glutamate. The responses to 100 ms pulses
of 1 mM glutamate were mimicked by application of 1 mM AMPA, whereas 1 mM kainate
produced much smaller, weakly desensitizing currents. This suggests that the fast
component is primarily mediated by the action of glutamate on AMPA-preferring
receptors. 5. The mean elementary conductance of AMPA receptor channels was about
10 pS, as estimated by non-stationary fluctuation analysis. The permeability of
these channels to Ca2+ was low (~5% of the permeability to Cs+). 6. The elementary
conductance of NMDA receptor channels was larger, with a main conductance state
of about 45 pS. These channels were 3.6 times more permeable to Ca2+ than to Cs+.
7. AMPA receptor-mediated currents activated rapidly in response to 1 ms pulses
of 1 mM glutamate and deactivated with a predominant, fast time constant and a
smaller, slower component (τ1≃2 ms, τ2≃8 ms, contributing ~80 and ~20% to the
total decay amplitude, respectively). Desensitization of the current during a
100 ms pulse was best fitted by two time constants (τ1≃10 ms, ~60%; τ2≃34 ms,
~40%). 8. NMDA receptor-mediated currents in response to 1 ms pulses of 1 mM glutamate
activated and deactivated much more slowly than AMPA receptor-mediated currents.
The time course could be described by a single exponential rising phase (τ≃7 ms)
followed by a double exponential decay (τ1≃200 ms, ~80%; τ2≃1-3 s, ~20%). 9. Mg2+
blocked the NMDA component in a voltage-dependent manner, with a half-maximal
inhibitory concentration (IC50) of 21 μM at -80 mV. At physiological Mg2+ concentrations,
block of the NMDA component could be rapidly relieved with voltage jumps from
negative to positive potentials. Block of the current upon return to negative
potentials occurred almost instantaneously. 10. Zn2+ also selectively-blocked
the NMDA receptor-mediated current with an IC50 of 22 μM, but this block differed
from that of Mg2+ in that it showed little voltage dependence. Rapid application
of Zn2+ together with glutamate produced partial block of the current. More block
was observed if Zn2+ and glutamate were co-applied when NMDA receptor channels
were already open. 11. The functional properties of dendritic GluRs were similar
to those found at the soma. Knowledge of these properties facilitated simulations
investigating the contribution of coactivated AMPA and NMDA receptors to synaptic
depolarization and Ca2+ entry into dendritic spines. Because of its slow deactivation,
the NMDA receptor-mediated current contributes substantially to depolarization
and Ca2+ entry and is susceptible to modulation over a period of seconds, either
by backpropagating action potentials or by the release of Zn2+ from presynaptic
boutons.
acknowledgement: We thank M.Hausser, A.Roth, P.Ruppersberg, and G.Stuart for helpful
discussions and M.H. and G.S. for critically reading the manuscript. We also thank
M.Kaiser for expert technical assistance and F.Helmchen, M.Huke and A.Roth for computer
programming. Financial support from the Alexander von Humboldt Foundation and the
Deutsche Forschungsgemeinschaft (SFB317) is gratefully acknowledged.
article_processing_charge: No
article_type: original
author:
- first_name: Nelson
full_name: Spruston, Nelson
last_name: Spruston
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Bert
full_name: Sakmann, Bert
last_name: Sakmann
citation:
ama: Spruston N, Jonas PM, Sakmann B. Dendritic glutamate receptor channels in rat
hippocampal CA3 and CA1 pyramidal neurons. Journal of Physiology. 1995;482(Pt
2):325-352. doi:10.1113/jphysiol.1995.sp020521
apa: Spruston, N., Jonas, P. M., & Sakmann, B. (1995). Dendritic glutamate receptor
channels in rat hippocampal CA3 and CA1 pyramidal neurons. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.1995.sp020521
chicago: Spruston, Nelson, Peter M Jonas, and Bert Sakmann. “Dendritic Glutamate
Receptor Channels in Rat Hippocampal CA3 and CA1 Pyramidal Neurons.” Journal
of Physiology. Wiley-Blackwell, 1995. https://doi.org/10.1113/jphysiol.1995.sp020521.
ieee: N. Spruston, P. M. Jonas, and B. Sakmann, “Dendritic glutamate receptor channels
in rat hippocampal CA3 and CA1 pyramidal neurons,” Journal of Physiology,
vol. 482, no. Pt 2. Wiley-Blackwell, pp. 325–352, 1995.
ista: Spruston N, Jonas PM, Sakmann B. 1995. Dendritic glutamate receptor channels
in rat hippocampal CA3 and CA1 pyramidal neurons. Journal of Physiology. 482(Pt
2), 325–352.
mla: Spruston, Nelson, et al. “Dendritic Glutamate Receptor Channels in Rat Hippocampal
CA3 and CA1 Pyramidal Neurons.” Journal of Physiology, vol. 482, no. Pt
2, Wiley-Blackwell, 1995, pp. 325–52, doi:10.1113/jphysiol.1995.sp020521.
short: N. Spruston, P.M. Jonas, B. Sakmann, Journal of Physiology 482 (1995) 325–352.
date_created: 2018-12-11T12:03:32Z
date_published: 1995-01-15T00:00:00Z
date_updated: 2022-06-28T08:08:40Z
day: '15'
doi: 10.1113/jphysiol.1995.sp020521
extern: '1'
external_id:
pmid:
- '7536248'
intvolume: ' 482'
issue: Pt 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://physoc.onlinelibrary.wiley.com/doi/abs/10.1113/jphysiol.1995.sp020521
month: '01'
oa: 1
oa_version: Published Version
page: 325 - 352
pmid: 1
publication: Journal of Physiology
publication_identifier:
issn:
- 0022-3751
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2909'
quality_controlled: '1'
status: public
title: Dendritic glutamate receptor channels in rat hippocampal CA3 and CA1 pyramidal
neurons
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 482
year: '1995'
...
---
_id: '3479'
abstract:
- lang: eng
text: 1. Glutamate receptor (GluR) channels were studied in basket cells in the
dentate gyrus of rat hippocampal slices. Basket cells were identified by their
location, dendritic morphology and high frequency of action potentials generated
during sustained current injection. 2. Dual-component currents were activated
by fast application of glutamate to outside-out membrane patches isolated from
basket cell somata (10 μM glycine, no external Mg2+). The fast component was selectively
blocked by 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), the slow component by
D-2-amino-5-phosphonopentanoic acid (D-AP5). This suggests that the two components
were mediated by α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor (AMPAR)/kainate
receptor and N-methyl-D-aspartate receptor (NMDAR) channels, respectively. The
mean ratio of the peak current of the NMDAR component to that of the AMPAR/kainate
receptor component was 0.22 (1 ms pulses of 10 mM glutamate). 3. The AMPAR/kainate
receptor component, which was studied in isolation in the presence of D-AP5, was
identified as AMPAR mediated on the basis of the preferential activation by AMPA
as compared with kainate, the weak desensitization of kainate-activated currents,
the cross-desensitization between AMPA and kainate, and the reduction of desensitization
by cyclothiazide. 4. Deactivation of basket cell AMPARs following 1 ms pulses
of glutamate occurred with a time constant (τ) of 1.2 ± 0.1 ms (mean ± S.E.M.).
During 100 ms glutamate pulses, AMPARs desensitized with a τ of 3.7 ± 0.2 ms.
5. The peak current-voltage (I-V) relation of AMPAR-mediated currents in Na+-rich
extracellular solution showed a reversal potential of -4.0 ± 2.6 mV and was characterized
by a doubly rectifying shape. The conductance of single AMPAR channels was estimated
as 22.6 ± 1.6 pS using non-stationary fluctuation analysis. AMPARs expressed in
hippocampal basket cells mere highly Ca2+ permeable (P(Ca)/P(K) = 1.79). 6. NMDARs
in hippocampal basket cells were studied in isolation in the presence of CNQX.
Deactivation of NMDARs activated by glutamate pulses occurred bi-exponentially
with mean τ values of 266 ± 23 ms (76%) and 2620 ± 383 ms (24%). 7. The peak I-V
relation of the NMDAR-mediated component in Na+-rich extracellular solution showed
a reversal potential of 1.5 ± 0.6 mV and a region of negative slope at negative
membrane potentials in the presence of external Mg2+, due to voltage-dependent
block by these ions. The conductance of single NMDAR channels in the main open
state was 50.2 ± 1.8 pS. NMDARs in hippocampal basket cells were highly permeable
to Ca2+ (P(Ca)/P(K) = 6.68). 8. AMPARs in hippocampal basket cells are characterized
by about threefold faster kinetics and twentyfold higher Ca2+ permeability than
AMPARs in hippocampal granule or pyramidal cells. Simulations show that the Ca2+
influx through basket cell AMPARs is comparable to that through NMDARs at negative
membrane potentials with physiological concentrations of Ca2+ and Mg2+. This suggests
a dual pathway of synaptically mediated Ca2+ entry into interneurones.
acknowledgement: We thank Drs M.Häusser and H.Markram for critically reading the manuscript
and M.Kaiser for technical assistance. Supported by the Deutsche Forschungsgemeinschaft
(SFB-317/B14 grant to P.J. and a Graduiertenkollegstipendium to J.R.P.G.)
article_processing_charge: No
article_type: original
author:
- first_name: Duk
full_name: Koh, Duk
last_name: Koh
- first_name: Jörg
full_name: Geiger, Jörg
last_name: Geiger
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Bert
full_name: Sakmann, Bert
last_name: Sakmann
citation:
ama: Koh D, Geiger J, Jonas PM, Sakmann B. Ca(2+)-permeable AMPA and NMDA receptor
channels in basket cells of rat hippocampal dentate gyrus. Journal of Physiology.
1995;485(Pt 2):383-402. doi:10.1113/jphysiol.1995.sp020737
apa: Koh, D., Geiger, J., Jonas, P. M., & Sakmann, B. (1995). Ca(2+)-permeable
AMPA and NMDA receptor channels in basket cells of rat hippocampal dentate gyrus.
Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.1995.sp020737
chicago: Koh, Duk, Jörg Geiger, Peter M Jonas, and Bert Sakmann. “Ca(2+)-Permeable
AMPA and NMDA Receptor Channels in Basket Cells of Rat Hippocampal Dentate Gyrus.”
Journal of Physiology. Wiley-Blackwell, 1995. https://doi.org/10.1113/jphysiol.1995.sp020737.
ieee: D. Koh, J. Geiger, P. M. Jonas, and B. Sakmann, “Ca(2+)-permeable AMPA and
NMDA receptor channels in basket cells of rat hippocampal dentate gyrus,” Journal
of Physiology, vol. 485, no. Pt 2. Wiley-Blackwell, pp. 383–402, 1995.
ista: Koh D, Geiger J, Jonas PM, Sakmann B. 1995. Ca(2+)-permeable AMPA and NMDA
receptor channels in basket cells of rat hippocampal dentate gyrus. Journal of
Physiology. 485(Pt 2), 383–402.
mla: Koh, Duk, et al. “Ca(2+)-Permeable AMPA and NMDA Receptor Channels in Basket
Cells of Rat Hippocampal Dentate Gyrus.” Journal of Physiology, vol. 485,
no. Pt 2, Wiley-Blackwell, 1995, pp. 383–402, doi:10.1113/jphysiol.1995.sp020737.
short: D. Koh, J. Geiger, P.M. Jonas, B. Sakmann, Journal of Physiology 485 (1995)
383–402.
date_created: 2018-12-11T12:03:33Z
date_published: 1995-06-01T00:00:00Z
date_updated: 2022-06-28T07:54:44Z
day: '01'
doi: 10.1113/jphysiol.1995.sp020737
extern: '1'
external_id:
pmid:
- '7545230'
intvolume: ' 485'
issue: Pt 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1158000/pdf/jphysiol00319-0104.pdf
month: '06'
oa: 1
oa_version: Published Version
page: 383 - 402
pmid: 1
publication: Journal of Physiology
publication_identifier:
issn:
- 0022-3751
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2908'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ca(2+)-permeable AMPA and NMDA receptor channels in basket cells of rat hippocampal
dentate gyrus
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 485
year: '1995'
...
---
_id: '3480'
abstract:
- lang: eng
text: Recording of glutamate-activated currents in membrane patches was combine
with RT-PCR-mediated AMPA receptor (AMPAR) subunit mRNA analysis in single identified
cells of rat brain slices. Analysis of AMPARs in principal neurons end interneurons
of hippocampus and neocortex and in auditory relay neurons and Bergmann glial
cells indicates that the GluR-B subunit in its flip version determines formation
of receptors with relatively slow gating, whereas the GluR-D subunit promotes
assembly of more rapidly gated receptors. The relation between Ca 2+ permeability
of AMPAR channels and the relative GluR-B mRNA abundance is consistent with the
dominance of this subunit in determining the Ca 2+ permeability of native receptors.
The results suggest that differential expression of GluR-B and GluR-D subunit
genes, as well as splicing end editing of their mRNAs, account for the differences
in gating and Ca 2+ permeability of native AMPAR channels.
acknowledgement: "We thank Ulla Amtmann for efficient help with the molecular analysis.
We also thank M. Kaiser for technical assistance, Dr. J. G. G. Borst for advice
concerning preparation of brainstem slices, and Drs. N. Spruston and G. Stuart for
critically reading the manuscript. Funded in part by Bundesministerium für Forschung
und Technologie grant BCT 364 AZ 321/7291 (P. H. S.) and by Deutsche Forschungsgemeinschaftgrant
SFB-3171814(P. J.). J. R. P. G. and T. M. were supported by the graduate program
of Molecular and Cellular Neurobiology of the University of Heidelberg. The costs
of publication of this article were defrayed in part by the payment of page charges.
This article must therefore be hereby\r\nmarked “advertisement” in accordance with
18 USC Section 1734 solely to Indicate this fact."
article_processing_charge: No
article_type: original
author:
- first_name: Jörg
full_name: Geiger, Jörg
last_name: Geiger
- first_name: Thorsten
full_name: Melcher, Thorsten
last_name: Melcher
- first_name: Duk
full_name: Koh, Duk
last_name: Koh
- first_name: Bert
full_name: Sakmann, Bert
last_name: Sakmann
- first_name: Peter
full_name: Seeburg, Peter
last_name: Seeburg
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Hannah
full_name: Monyer, Hannah
last_name: Monyer
citation:
ama: Geiger J, Melcher T, Koh D, et al. Relative abundance of subunit mRNAs determines
gating and Ca(2+) permeability of AMPA receptors in principal neurons and interneurons
in rat CNS. Neuron. 1995;15(1):193-204. doi:10.1016/0896-6273(95)90076-4
apa: Geiger, J., Melcher, T., Koh, D., Sakmann, B., Seeburg, P., Jonas, P. M., &
Monyer, H. (1995). Relative abundance of subunit mRNAs determines gating and Ca(2+)
permeability of AMPA receptors in principal neurons and interneurons in rat CNS.
Neuron. Elsevier. https://doi.org/10.1016/0896-6273(95)90076-4
chicago: Geiger, Jörg, Thorsten Melcher, Duk Koh, Bert Sakmann, Peter Seeburg, Peter
M Jonas, and Hannah Monyer. “Relative Abundance of Subunit MRNAs Determines Gating
and Ca(2+) Permeability of AMPA Receptors in Principal Neurons and Interneurons
in Rat CNS.” Neuron. Elsevier, 1995. https://doi.org/10.1016/0896-6273(95)90076-4.
ieee: J. Geiger et al., “Relative abundance of subunit mRNAs determines gating
and Ca(2+) permeability of AMPA receptors in principal neurons and interneurons
in rat CNS,” Neuron, vol. 15, no. 1. Elsevier, pp. 193–204, 1995.
ista: Geiger J, Melcher T, Koh D, Sakmann B, Seeburg P, Jonas PM, Monyer H. 1995.
Relative abundance of subunit mRNAs determines gating and Ca(2+) permeability
of AMPA receptors in principal neurons and interneurons in rat CNS. Neuron. 15(1),
193–204.
mla: Geiger, Jörg, et al. “Relative Abundance of Subunit MRNAs Determines Gating
and Ca(2+) Permeability of AMPA Receptors in Principal Neurons and Interneurons
in Rat CNS.” Neuron, vol. 15, no. 1, Elsevier, 1995, pp. 193–204, doi:10.1016/0896-6273(95)90076-4.
short: J. Geiger, T. Melcher, D. Koh, B. Sakmann, P. Seeburg, P.M. Jonas, H. Monyer,
Neuron 15 (1995) 193–204.
date_created: 2018-12-11T12:03:33Z
date_published: 1995-07-01T00:00:00Z
date_updated: 2022-06-28T07:47:09Z
day: '01'
doi: 10.1016/0896-6273(95)90076-4
extern: '1'
external_id:
pmid:
- '7619522'
intvolume: ' 15'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/0896627395900764?via%3Dihub
month: '07'
oa: 1
oa_version: Published Version
page: 193 - 204
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
publist_id: '2907'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relative abundance of subunit mRNAs determines gating and Ca(2+) permeability
of AMPA receptors in principal neurons and interneurons in rat CNS
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 15
year: '1995'
...
---
_id: '3481'
abstract:
- lang: eng
text: 1. The influence of intracellular factors on current rectification of different
subtypes of native α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors
(AMPARs) was studied in rat brain slices by combining fast application of glutamate
with patch pipette perfusion. 2. The peak current-voltage (I-V) relation of the
AMPARs expressed in Bergmann glial cells of cerebellum and dentate gyrus (DG)
basket cells of hippocampus was weakly rectifying in outside-out patches and nystatin-perforated
vesicles, but showed a doubly rectifying shape with a region of reduced slope
between 0 and +40 mV in nucleated patches. The I-V relation of AMPARs expressed
in hippocampal CA3 pyramidal neurones was linear in all recording configurations.
3. Intracellular application of 2.5 μM spermine, a naturally occurring polyamine,
blocked outward currents in outside-oat patches from Bergmann glial cells and
DG basket cells in a voltage-dependent manner, generating I-V relations with a
doubly rectifying shape which were similar to those recorded in nucleated patches.
AMPARs in CA3 pyramidal cell patches were unaffected by 25 μM spermine. 4. The
half-maximal blocking concentration of spermine at +40 mV was 0.3 μM in Bergmann
glial cell patches and 1.5 μM in DG basket cell patches, whereas it was much higher
(≥ 100 μM) for CA3 pyramidal. cell patches. Spermidine also affected current rectification,
but with lower affinity. The block of outward current by polyamines following
voltage jumps developed within < 0.5 ms. 5. We conclude that current rectification,
rather than being an intrinsic property of the Ca2+ permeable AMPAR channel, is
generated by polyamine block.
acknowledgement: We thank Dr B.Sakmann, Dr V.Witzemann, J.Geiger, and A.Roth for helpful
discussions and Dr D.Feldmeyer and Dr A.Villarroel for reading the manuscript. We
also thank M.Kaiser for technical and H.Spiegel for secretarial assistance. Supported
by DFG grant SFB-317/B14(P.J.).
article_processing_charge: No
article_type: original
author:
- first_name: Duk
full_name: Koh, Duk
last_name: Koh
- first_name: Nail
full_name: Burnashev, Nail
last_name: Burnashev
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Koh D, Burnashev N, Jonas PM. Block of native Ca(2+)-permeable AMPA receptors
in rat brain by intracellular polyamines generates double rectification. Journal
of Physiology. 1995;486(Pt 2):305-312. doi:10.1113/jphysiol.1995.sp020813
apa: Koh, D., Burnashev, N., & Jonas, P. M. (1995). Block of native Ca(2+)-permeable
AMPA receptors in rat brain by intracellular polyamines generates double rectification.
Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.1995.sp020813
chicago: Koh, Duk, Nail Burnashev, and Peter M Jonas. “Block of Native Ca(2+)-Permeable
AMPA Receptors in Rat Brain by Intracellular Polyamines Generates Double Rectification.”
Journal of Physiology. Wiley-Blackwell, 1995. https://doi.org/10.1113/jphysiol.1995.sp020813.
ieee: D. Koh, N. Burnashev, and P. M. Jonas, “Block of native Ca(2+)-permeable AMPA
receptors in rat brain by intracellular polyamines generates double rectification,”
Journal of Physiology, vol. 486, no. Pt 2. Wiley-Blackwell, pp. 305–312,
1995.
ista: Koh D, Burnashev N, Jonas PM. 1995. Block of native Ca(2+)-permeable AMPA
receptors in rat brain by intracellular polyamines generates double rectification.
Journal of Physiology. 486(Pt 2), 305–312.
mla: Koh, Duk, et al. “Block of Native Ca(2+)-Permeable AMPA Receptors in Rat Brain
by Intracellular Polyamines Generates Double Rectification.” Journal of Physiology,
vol. 486, no. Pt 2, Wiley-Blackwell, 1995, pp. 305–12, doi:10.1113/jphysiol.1995.sp020813.
short: D. Koh, N. Burnashev, P.M. Jonas, Journal of Physiology 486 (1995) 305–312.
date_created: 2018-12-11T12:03:33Z
date_published: 1995-07-15T00:00:00Z
date_updated: 2022-06-27T14:53:16Z
day: '15'
doi: 10.1113/jphysiol.1995.sp020813
extern: '1'
external_id:
pmid:
- '7473198'
intvolume: ' 486'
issue: Pt 2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156754/
month: '07'
oa: 1
oa_version: Published Version
page: 305 - 312
pmid: 1
publication: Journal of Physiology
publication_identifier:
issn:
- 0022-3751
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2906'
quality_controlled: '1'
status: public
title: Block of native Ca(2+)-permeable AMPA receptors in rat brain by intracellular
polyamines generates double rectification
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 486
year: '1995'
...
---
_id: '3551'
abstract:
- lang: eng
text: Common geometric models for proteins and other molecules are the space filling
diagram, the solvent accessible surface, and the molecular surface. We describe
software that computes metric properties of these models, including volume and
surface area. It also measures voids or empty space enclosed by the protein, and
it keeps track of surface area contributions of individual atoms. The software
is based on 3-dimensional alpha complexes and on inclusion-exclusion formulas
with terms derived from the simplices in this complex.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Facello, Michael
last_name: Facello
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
citation:
ama: 'Edelsbrunner H, Facello M, Fu P, Liang J. Measuring proteins and voids in
proteins. In: Proceedings of the 28th Annual Hawaii International Conference
on System Sciences. IEEE; 1995:256-264. doi:10.1109/HICSS.1995.375331'
apa: 'Edelsbrunner, H., Facello, M., Fu, P., & Liang, J. (1995). Measuring proteins
and voids in proteins. In Proceedings of the 28th Annual Hawaii International
Conference on System Sciences (pp. 256–264). Wailea, HI, United States of
America: IEEE. https://doi.org/10.1109/HICSS.1995.375331'
chicago: Edelsbrunner, Herbert, Michael Facello, Ping Fu, and Jie Liang. “Measuring
Proteins and Voids in Proteins.” In Proceedings of the 28th Annual Hawaii International
Conference on System Sciences, 256–64. IEEE, 1995. https://doi.org/10.1109/HICSS.1995.375331.
ieee: H. Edelsbrunner, M. Facello, P. Fu, and J. Liang, “Measuring proteins and
voids in proteins,” in Proceedings of the 28th Annual Hawaii International
Conference on System Sciences, Wailea, HI, United States of America, 1995,
pp. 256–264.
ista: 'Edelsbrunner H, Facello M, Fu P, Liang J. 1995. Measuring proteins and voids
in proteins. Proceedings of the 28th Annual Hawaii International Conference on
System Sciences. HICSS: Hawaii International Conference on System Sciences, 256–264.'
mla: Edelsbrunner, Herbert, et al. “Measuring Proteins and Voids in Proteins.” Proceedings
of the 28th Annual Hawaii International Conference on System Sciences, IEEE,
1995, pp. 256–64, doi:10.1109/HICSS.1995.375331.
short: H. Edelsbrunner, M. Facello, P. Fu, J. Liang, in:, Proceedings of the 28th
Annual Hawaii International Conference on System Sciences, IEEE, 1995, pp. 256–264.
conference:
end_date: 1995-01-06
location: Wailea, HI, United States of America
name: 'HICSS: Hawaii International Conference on System Sciences'
start_date: 1995-01-03
date_created: 2018-12-11T12:03:55Z
date_published: 1995-01-04T00:00:00Z
date_updated: 2022-06-27T13:54:41Z
day: '04'
doi: 10.1109/HICSS.1995.375331
extern: '1'
language:
- iso: eng
main_file_link:
- url: https://ieeexplore.ieee.org/document/375331
month: '01'
oa_version: None
page: 256 - 264
publication: Proceedings of the 28th Annual Hawaii International Conference on System
Sciences
publication_identifier:
isbn:
- 0-8186-6930-6
publication_status: published
publisher: IEEE
publist_id: '2834'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Measuring proteins and voids in proteins
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1995'
...
---
_id: '3552'
abstract:
- lang: eng
text: "The concept of an α-shape of a finite set of points in R^d, with weights,
is defined and illustrated. An α-shape is a polytope which is not necessarily
convex nor connected and can be derived from the (weighted) Delaunay triangulation
of the point set, with a parameter controlling the desired level of detail. The
set of all α values leads to a descrete family of shapes capturing the intuitive
notion of ``crude'' versus ``fine'' shapes of a point set. Software that computes
such shapes in R^2 and R^3 is available via anonymous ftp from:\r\n\r\nftp://ftp.ncsa.uiuc.edu/Visualization/Alpha-shape/
\ "
article_processing_charge: No
author:
- first_name: Nataraj
full_name: Akkiraju, Nataraj
last_name: Akkiraju
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Facello, Michael
last_name: Facello
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Ernst
full_name: Mücke, Ernst
last_name: Mücke
- first_name: Carlos
full_name: Varela, Carlos
last_name: Varela
citation:
ama: 'Akkiraju N, Edelsbrunner H, Facello M, Fu P, Mücke E, Varela C. Alpha shapes:
definition and software. In: Elsevier; 1995:63-66.'
apa: 'Akkiraju, N., Edelsbrunner, H., Facello, M., Fu, P., Mücke, E., & Varela,
C. (1995). Alpha shapes: definition and software (pp. 63–66). Presented at the
GCG: International Computational Geometry Software Workshop, Elsevier.'
chicago: 'Akkiraju, Nataraj, Herbert Edelsbrunner, Michael Facello, Ping Fu, Ernst
Mücke, and Carlos Varela. “Alpha Shapes: Definition and Software,” 63–66. Elsevier,
1995.'
ieee: 'N. Akkiraju, H. Edelsbrunner, M. Facello, P. Fu, E. Mücke, and C. Varela,
“Alpha shapes: definition and software,” presented at the GCG: International Computational
Geometry Software Workshop, 1995, pp. 63–66.'
ista: 'Akkiraju N, Edelsbrunner H, Facello M, Fu P, Mücke E, Varela C. 1995. Alpha
shapes: definition and software. GCG: International Computational Geometry Software
Workshop, 63–66.'
mla: 'Akkiraju, Nataraj, et al. Alpha Shapes: Definition and Software. Elsevier,
1995, pp. 63–66.'
short: N. Akkiraju, H. Edelsbrunner, M. Facello, P. Fu, E. Mücke, C. Varela, in:,
Elsevier, 1995, pp. 63–66.
conference:
name: 'GCG: International Computational Geometry Software Workshop'
date_created: 2018-12-11T12:03:55Z
date_published: 1995-09-11T00:00:00Z
date_updated: 2022-06-27T13:20:29Z
day: '11'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.geom.uiuc.edu/software/cglist/GeomDir/shapes95def/
month: '09'
oa_version: None
page: 63 - 66
publication_status: published
publisher: Elsevier
publist_id: '2833'
quality_controlled: '1'
status: public
title: 'Alpha shapes: definition and software'
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1995'
...
---
_id: '3597'
article_processing_charge: No
author:
- first_name: Mark
full_name: Kirkpatrick, Mark
last_name: Kirkpatrick
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kirkpatrick M, Barton NH. Déjà vu all over again. Nature. 1995;377:388-389.
doi:10.1038/377388a0
apa: Kirkpatrick, M., & Barton, N. H. (1995). Déjà vu all over again. Nature.
Nature Publishing Group. https://doi.org/10.1038/377388a0
chicago: Kirkpatrick, Mark, and Nicholas H Barton. “Déjà vu All over Again.” Nature.
Nature Publishing Group, 1995. https://doi.org/10.1038/377388a0.
ieee: M. Kirkpatrick and N. H. Barton, “Déjà vu all over again,” Nature,
vol. 377. Nature Publishing Group, pp. 388–389, 1995.
ista: Kirkpatrick M, Barton NH. 1995. Déjà vu all over again. Nature. 377, 388–389.
mla: Kirkpatrick, Mark, and Nicholas H. Barton. “Déjà vu All over Again.” Nature,
vol. 377, Nature Publishing Group, 1995, pp. 388–89, doi:10.1038/377388a0.
short: M. Kirkpatrick, N.H. Barton, Nature 377 (1995) 388–389.
date_created: 2018-12-11T12:04:09Z
date_published: 1995-10-05T00:00:00Z
date_updated: 2022-06-27T13:00:10Z
day: '05'
doi: 10.1038/377388a0
extern: '1'
external_id:
pmid:
- '7566112 '
intvolume: ' 377'
language:
- iso: eng
main_file_link:
- url: https://www.nature.com/articles/377388a0
month: '10'
oa_version: None
page: 388 - 389
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '2786'
quality_controlled: '1'
status: public
title: Déjà vu all over again
type: review
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 377
year: '1995'
...
---
_id: '3636'
abstract:
- lang: eng
text: 'Observations on the means, variances, and covariances of quantitative traits
across hybrid zones can give information similar to that from Mendelian markers.
In addition, they can identify particular traits through which the cline is maintained.
We describe a survey of six traits across the hybrid zone between Bombina bombina
and Bombina variegata (Amphibia: Discoglossidae) near Pescenica in Croatia. We
obtained laboratory measuments of the belly pattern, skin thickness, mating call,
skeletal form, egg size, and the developmental time of tadpoles. Although offspring
from hybrid populations showed no evidence of reduced viability, a third of the
F1 families failed completely, irrespective of the direction of the cross. All
traits differed significantly between the taxa. Clines in belly pattern, skin
thickness, mating call, and skeletal form were closely concordant with clines
in four diagnostic enzyme loci. However, the cline in developmental time was displaced
towards bombina, and the cline in egg size was displaced towards variegata. This
discordance could be because the traits are not inherited additively or because
they are subject to different selection pressures. We favor the latter explanation
in the case of developmental time. We show that moderate selection acting directly
on a trait suffices to shift its position; rather stronger selection is needed
to change its width appreciably. Within hybrid populations, there are significant
associations among quantitative traits, and between traits and enzymes. Phenotypic
variances also increase in hybrid populations. These observations can be explained
by linkage disequilibria among the underlying loci. However, the average magnitude
of the covariance between traits is about half that expected from the linkage
disequilibria between enzyme loci. The discrepancy is not readily explained by
nonadditive gene action. This puzzle is now unresolved and calls for further investigation.'
acknowledgement: 'The project would not have been possible without F. Perovic''s extensive
knowledge of the natural history of the Pegdenica area, and his assistance in the
field. Particular thanks are due to the Perovie family for their generous hospitality.
The Croatian Museum of Natural History and the Croatian Ministry of the Environment
were helpful in granting all the necessary permits. J. Szymura assisted with allozyme
tech-niques and in sharing unpublished data from his original survey of the area.
M. Davidson and K. Grant prepared the histological specimens, and G. Patterson volunteered
time and expertise in X-raying our toads. All members of L. Partridge''s lab generously
provided us with toad food on a daily basis, in the form of uncountably many spare
Drosophila. G. Malarky and M. Oh stoically coped with much tedious toad care. We
thank W. G. Hill, L. Kruuk, D. Rand, J. Szymura, and an anonymous reviewer for helpful
comments on the manuscript. This research was supported by a grant from the Natural
Environment Research Council (GR3/8002) to N.B. '
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Catriona
full_name: Maccallum, Catriona
last_name: Maccallum
- first_name: Jason
full_name: Gilchrist, Jason
last_name: Gilchrist
- first_name: Michael
full_name: Appleby, Michael
last_name: Appleby
citation:
ama: Nürnberger B, Barton NH, Maccallum C, Gilchrist J, Appleby M. Natural selection
on quantitative traits in the Bombina hybrid zone. Evolution. 1995;49(6):1224-1238.
doi:10.1111/j.1558-5646.1995.tb04449.x
apa: Nürnberger, B., Barton, N. H., Maccallum, C., Gilchrist, J., & Appleby,
M. (1995). Natural selection on quantitative traits in the Bombina hybrid zone.
Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.1995.tb04449.x
chicago: Nürnberger, Beate, Nicholas H Barton, Catriona Maccallum, Jason Gilchrist,
and Michael Appleby. “Natural Selection on Quantitative Traits in the Bombina
Hybrid Zone.” Evolution. Wiley-Blackwell, 1995. https://doi.org/10.1111/j.1558-5646.1995.tb04449.x.
ieee: B. Nürnberger, N. H. Barton, C. Maccallum, J. Gilchrist, and M. Appleby, “Natural
selection on quantitative traits in the Bombina hybrid zone,” Evolution,
vol. 49, no. 6. Wiley-Blackwell, pp. 1224–1238, 1995.
ista: Nürnberger B, Barton NH, Maccallum C, Gilchrist J, Appleby M. 1995. Natural
selection on quantitative traits in the Bombina hybrid zone. Evolution. 49(6),
1224–1238.
mla: Nürnberger, Beate, et al. “Natural Selection on Quantitative Traits in the
Bombina Hybrid Zone.” Evolution, vol. 49, no. 6, Wiley-Blackwell, 1995,
pp. 1224–38, doi:10.1111/j.1558-5646.1995.tb04449.x.
short: B. Nürnberger, N.H. Barton, C. Maccallum, J. Gilchrist, M. Appleby, Evolution
49 (1995) 1224–1238.
date_created: 2018-12-11T12:04:22Z
date_published: 1995-12-01T00:00:00Z
date_updated: 2022-06-27T12:58:02Z
day: '01'
doi: 10.1111/j.1558-5646.1995.tb04449.x
extern: '1'
intvolume: ' 49'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1558-5646.1995.tb04449.x
month: '12'
oa: 1
oa_version: Published Version
page: 1224 - 1238
publication: Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2747'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural selection on quantitative traits in the Bombina hybrid zone
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 49
year: '1995'
...