---
_id: '5419'
abstract:
- lang: eng
text: "We consider the reachability and shortest path problems on low tree-width
graphs, with n nodes, m edges, and tree-width t, on a standard RAM with wordsize
W. We use O to hide polynomial factors of the inverse of the Ackermann function.
Our main contributions are three fold:\r\n1. For reachability, we present an algorithm
that requires O(n·t2·log(n/t)) preprocessing time, O(n·(t·log(n/t))/W) space,
and O(t/W) time for pair queries and O((n·t)/W) time for single-source queries.
Note that for constant t our algorithm uses O(n·logn) time for preprocessing;
and O(n/W) time for single-source queries, which is faster than depth first search/breath
first search (after the preprocessing).\r\n2. We present an algorithm for shortest
path that requires O(n·t2) preprocessing time, O(n·t) space, and O(t2) time for
pair queries and O(n·t) time single-source queries.\r\n3. We give a space versus
query time trade-off algorithm for shortest path that, given any constant >0,
requires O(n·t2) preprocessing time, O(n·t2) space, and O(n1−·t2) time for pair
queries.\r\nOur algorithms improve all existing results, and use very simple data
structures."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Improved Algorithms for Reachability
and Shortest Path on Low Tree-Width Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-187-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Improved
algorithms for reachability and shortest path on low tree-width graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2014-187-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-187-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Improved algorithms
for reachability and shortest path on low tree-width graphs. IST Austria,
2014.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Improved algorithms for
reachability and shortest path on low tree-width graphs, IST Austria, 34p.
mla: Chatterjee, Krishnendu, et al. Improved Algorithms for Reachability and
Shortest Path on Low Tree-Width Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-187-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Improved Algorithms for
Reachability and Shortest Path on Low Tree-Width Graphs, IST Austria, 2014.
date_created: 2018-12-12T11:39:13Z
date_published: 2014-04-14T00:00:00Z
date_updated: 2021-01-12T08:02:03Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-187-v1-1
file:
- access_level: open_access
checksum: c608e66030a4bf51d2d99b451f539b99
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5548'
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file_size: 670031
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
fulldoi: https://doi.org/10.15479/AT:IST-2014-187-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '34'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '187'
status: public
title: Improved algorithms for reachability and shortest path on low tree-width graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5420'
abstract:
- lang: eng
text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player
(player 1 vs player 2) zero-sum games on finite-state graphs where every transition
is assigned a reward between 0 and 1, and the payoff function is the long-run
average of the rewards. The value is the maximal expected payoff that player 1
can guarantee against all strategies of player 2. We consider the computation
of the set of states with value 1 under finite-memory strategies for player 1,
and our main results for the problem are as follows: (1) we present a polynomial-time
algorithm; (2) we show that whenever there is a finite-memory strategy, there
is a stationary strategy that does not need memory at all; and (3) we present
an optimal bound (which is double exponential) on the patience of stationary strategies
(where patience of a distribution is the inverse of the smallest positive probability
and represents a complexity measure of a stationary strategy).'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: Chatterjee K, Ibsen-Jensen R. The Value 1 Problem for Concurrent Mean-Payoff
Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-191-v1-1
apa: Chatterjee, K., & Ibsen-Jensen, R. (2014). The value 1 problem for concurrent
mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2014-191-v1-1
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem
for Concurrent Mean-Payoff Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-191-v1-1.
ieee: K. Chatterjee and R. Ibsen-Jensen, The value 1 problem for concurrent mean-payoff
games. IST Austria, 2014.
ista: Chatterjee K, Ibsen-Jensen R. 2014. The value 1 problem for concurrent mean-payoff
games, IST Austria, 49p.
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem for
Concurrent Mean-Payoff Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-191-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, The Value 1 Problem for Concurrent Mean-Payoff
Games, IST Austria, 2014.
date_created: 2018-12-12T11:39:14Z
date_published: 2014-04-14T00:00:00Z
date_updated: 2021-01-12T08:02:05Z
day: '14'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-191-v1-1
file:
- access_level: open_access
checksum: 49e0fd3e62650346daf7dc04604f7a0a
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:58Z
date_updated: 2020-07-14T12:46:50Z
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fulldoi: https://doi.org/10.15479/AT:IST-2014-191-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '49'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '191'
status: public
title: The value 1 problem for concurrent mean-payoff games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5421'
abstract:
- lang: eng
text: 'Evolution occurs in populations of reproducing individuals. The structure
of the population affects the outcome of the evolutionary process. Evolutionary
graph theory is a powerful approach to study this phenomenon. There are two graphs.
The interaction graph specifies who interacts with whom in the context of evolution.
The replacement graph specifies who competes with whom for reproduction. The vertices
of the two graphs are the same, and each vertex corresponds to an individual.
A key quantity is the fixation probability of a new mutant. It is defined as the
probability that a newly introduced mutant (on a single vertex) generates a lineage
of offspring which eventually takes over the entire population of resident individuals.
The basic computational questions are as follows: (i) the qualitative question
asks whether the fixation probability is positive; and (ii) the quantitative approximation
question asks for an approximation of the fixation probability. Our main results
are: (1) We show that the qualitative question is NP-complete and the quantitative
approximation question is #P-hard in the special case when the interaction and
the replacement graphs coincide and even with the restriction that the resident
individuals do not reproduce (which corresponds to an invading population taking
over an empty structure). (2) We show that in general the qualitative question
is PSPACE-complete and the quantitative approximation question is PSPACE-hard
and can be solved in exponential time.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolution on Graphs.
IST Austria; 2014. doi:10.15479/AT:IST-2014-190-v2-2
apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2014). The complexity
of evolution on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-190-v2-2
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity
of Evolution on Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-190-v2-2.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolution
on graphs. IST Austria, 2014.
ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2014. The complexity of evolution on
graphs, IST Austria, 27p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Evolution on Graphs.
IST Austria, 2014, doi:10.15479/AT:IST-2014-190-v2-2.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolution on
Graphs, IST Austria, 2014.
date_created: 2018-12-12T11:39:14Z
date_published: 2014-04-18T00:00:00Z
date_updated: 2023-02-23T12:26:33Z
day: '18'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-190-v2-2
file:
- access_level: open_access
checksum: 42f3d8b563286eb0d903832bd9a848d3
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:16Z
date_updated: 2020-07-14T12:46:50Z
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content_type: application/pdf
creator: kschuh
date_created: 2019-09-06T07:30:20Z
date_updated: 2020-07-14T12:46:50Z
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file_name: IST-2014-190-v1+1_main_full.pdf
file_size: 440911
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has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '190'
related_material:
record:
- id: '5432'
relation: later_version
status: public
- id: '5440'
relation: later_version
status: public
status: public
title: The complexity of evolution on graphs
type: technical_report
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5423'
abstract:
- lang: eng
text: 'We present a flexible framework for the automated competitive analysis of
on-line scheduling algorithms for firm- deadline real-time tasks based on multi-objective
graphs: Given a taskset and an on-line scheduling algorithm specified as a labeled
transition system, along with some optional safety, liveness, and/or limit-average
constraints for the adversary, we automatically compute the competitive ratio
of the algorithm w.r.t. a clairvoyant scheduler. We demonstrate the flexibility
and power of our approach by comparing the competitive ratio of several on-line
algorithms, including D(over), that have been proposed in the past, for various
tasksets. Our experimental results reveal that none of these algorithms is universally
optimal, in the sense that there are tasksets where other schedulers provide better
performance. Our framework is hence a very useful design tool for selecting optimal
algorithms for a given application. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Alexander
full_name: Kössler, Alexander
last_name: Kössler
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. A Framework for Automated
Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria;
2014. doi:10.15479/AT:IST-2014-300-v1-1
apa: Chatterjee, K., Kössler, A., Pavlogiannis, A., & Schmid, U. (2014). A
framework for automated competitive analysis of on-line scheduling of firm-deadline
tasks. IST Austria. https://doi.org/10.15479/AT:IST-2014-300-v1-1
chicago: Chatterjee, Krishnendu, Alexander Kössler, Andreas Pavlogiannis, and Ulrich
Schmid. A Framework for Automated Competitive Analysis of On-Line Scheduling
of Firm-Deadline Tasks. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-300-v1-1.
ieee: K. Chatterjee, A. Kössler, A. Pavlogiannis, and U. Schmid, A framework
for automated competitive analysis of on-line scheduling of firm-deadline tasks.
IST Austria, 2014.
ista: Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. 2014. A framework for automated
competitive analysis of on-line scheduling of firm-deadline tasks, IST Austria,
14p.
mla: Chatterjee, Krishnendu, et al. A Framework for Automated Competitive Analysis
of On-Line Scheduling of Firm-Deadline Tasks. IST Austria, 2014, doi:10.15479/AT:IST-2014-300-v1-1.
short: K. Chatterjee, A. Kössler, A. Pavlogiannis, U. Schmid, A Framework for Automated
Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks, IST Austria,
2014.
date_created: 2018-12-12T11:39:15Z
date_published: 2014-07-29T00:00:00Z
date_updated: 2025-09-29T13:15:35Z
day: '29'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-300-v1-1
file:
- access_level: open_access
checksum: 4b8fde4d9ef6653837f6803921d83032
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5514'
file_name: IST-2014-300-v1+1_main.pdf
file_size: 1270021
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
fulldoi: https://doi.org/10.15479/AT:IST-2014-300-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '14'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '300'
related_material:
record:
- id: '1714'
relation: later_version
status: public
status: public
title: A framework for automated competitive analysis of on-line scheduling of firm-deadline
tasks
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5424'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs), that
are a standard framework for robotics applications to model uncertainties present
in the real world, with temporal logic specifications. All temporal logic specifications
in linear-time temporal logic (LTL) can be expressed as parity objectives. We
study the qualitative analysis problem for POMDPs with parity objectives that
asks whether there is a controller (policy) to ensure that the objective holds
with probability 1 (almost-surely). While the qualitative analysis of POMDPs with
parity objectives is undecidable, recent results show that when restricted to
finite-memory policies the problem is EXPTIME-complete. While the problem is intractable
in theory, we present a practical approach to solve the qualitative analysis problem.
We designed several heuristics to deal with the exponential complexity, and have
used our implementation on a number of well-known POMDP examples for robotics
applications. Our results provide the first practical approach to solve the qualitative
analysis of robot motion planning with LTL properties in the presence of uncertainty.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs
with Temporal Logic Specifications for Robotics Applications. IST Austria;
2014. doi:10.15479/AT:IST-2014-305-v1-1
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative
analysis of POMDPs with temporal logic specifications for robotics applications.
IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v1-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics
Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v1-1.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis
of POMDPs with temporal logic specifications for robotics applications. IST
Austria, 2014.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of
POMDPs with temporal logic specifications for robotics applications, IST Austria,
12p.
mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal
Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v1-1.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of
POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria,
2014.
date_created: 2018-12-12T11:39:15Z
date_published: 2014-09-09T00:00:00Z
date_updated: 2025-04-15T07:55:41Z
day: '09'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-305-v1-1
file:
- access_level: open_access
checksum: 35009d5fad01198341e6c1a3353481b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:51Z
date_updated: 2020-07-14T12:46:51Z
file_id: '5512'
file_name: IST-2014-305-v1+1_main.pdf
file_size: 655774
relation: main_file
file_date_updated: 2020-07-14T12:46:51Z
fulldoi: https://doi.org/10.15479/AT:IST-2014-305-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '12'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '305'
related_material:
record:
- id: '5426'
relation: later_version
status: public
- id: '1732'
relation: later_version
status: public
status: public
title: Qualitative analysis of POMDPs with temporal logic specifications for robotics
applications
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5426'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs), that
are a standard framework for robotics applications to model uncertainties present
in the real world, with temporal logic specifications. All temporal logic specifications
in linear-time temporal logic (LTL) can be expressed as parity objectives. We
study the qualitative analysis problem for POMDPs with parity objectives that
asks whether there is a controller (policy) to ensure that the objective holds
with probability 1 (almost-surely). While the qualitative analysis of POMDPs with
parity objectives is undecidable, recent results show that when restricted to
finite-memory policies the problem is EXPTIME-complete. While the problem is intractable
in theory, we present a practical approach to solve the qualitative analysis problem.
We designed several heuristics to deal with the exponential complexity, and have
used our implementation on a number of well-known POMDP examples for robotics
applications. Our results provide the first practical approach to solve the qualitative
analysis of robot motion planning with LTL properties in the presence of uncertainty.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs
with Temporal Logic Specifications for Robotics Applications. IST Austria;
2014. doi:10.15479/AT:IST-2014-305-v2-1
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative
analysis of POMDPs with temporal logic specifications for robotics applications.
IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v2-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics
Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v2-1.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis
of POMDPs with temporal logic specifications for robotics applications. IST
Austria, 2014.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of
POMDPs with temporal logic specifications for robotics applications, IST Austria,
10p.
mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal
Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v2-1.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of
POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria,
2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-09-29T00:00:00Z
date_updated: 2025-04-15T07:55:41Z
day: '29'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-305-v2-1
file:
- access_level: open_access
checksum: 730c0a8e97cf2712a884b2cc423f3919
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:15Z
date_updated: 2020-07-14T12:46:51Z
file_id: '5537'
file_name: IST-2014-305-v2+1_main2.pdf
file_size: 656019
relation: main_file
file_date_updated: 2020-07-14T12:46:51Z
fulldoi: https://doi.org/10.15479/AT:IST-2014-305-v2-1
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '10'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '311'
related_material:
record:
- id: '5424'
relation: earlier_version
status: public
- id: '1732'
relation: later_version
status: public
status: public
title: Qualitative analysis of POMDPs with temporal logic specifications for robotics
applications
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5427'
abstract:
- lang: eng
text: 'We consider graphs with n nodes together with their tree-decomposition that
has b = O ( n ) bags and width t , on the standard RAM computational model with
wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution
is an algorithm that given a graph and its tree-decomposition as input, computes
a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph
in O ( b ) time and space, improving a long-standing (from 1992) bound of O (
n · log n ) time for constant treewidth graphs. Our second contribution is on
reachability queries for low treewidth graphs. We build on our tree-balancing
algorithm and present a data-structure for graph reachability that requires O
( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time
for pair queries, and O ( n · t · log t/ log n ) time for single-source queries.
For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time
for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically)
optimal and is faster than DFS/BFS when answering more than a constant number
of single-source queries.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal Tree-Decomposition
Balancing and Reachability on Low Treewidth Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-314-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Optimal
tree-decomposition balancing and reachability on low treewidth graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2014-314-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs.
IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-314-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Optimal tree-decomposition
balancing and reachability on low treewidth graphs. IST Austria, 2014.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Optimal tree-decomposition
balancing and reachability on low treewidth graphs, IST Austria, 24p.
mla: Chatterjee, Krishnendu, et al. Optimal Tree-Decomposition Balancing and
Reachability on Low Treewidth Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-314-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Optimal Tree-Decomposition
Balancing and Reachability on Low Treewidth Graphs, IST Austria, 2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-11-05T00:00:00Z
date_updated: 2021-01-12T08:02:09Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2014-314-v1-1
file:
- access_level: open_access
checksum: 9d3b90bf4fff74664f182f2d95ef727a
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:10Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5471'
file_name: IST-2014-314-v1+1_long.pdf
file_size: 405561
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
fulldoi: https://doi.org/10.15479/AT:IST-2014-314-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '314'
status: public
title: Optimal tree-decomposition balancing and reachability on low treewidth graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5428'
abstract:
- lang: eng
text: "Simulation is an attractive alternative for language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. For non-deterministic automata, while language inclusion is PSPACE-complete,
simulation can be computed in polynomial time. Simulation has also been extended
in two orthogonal directions, namely, (1) fair simulation, for simulation over
specified set of infinite runs; and (2) quantitative simulation, for simulation
between weighted automata. Again, while fair trace inclusion is PSPACE-complete,
fair simulation can be computed in polynomial time. For weighted automata, the
(quantitative) language inclusion problem is undecidable for mean-payoff automata
and the decidability is open for discounted-sum automata, whereas the (quantitative)
simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial
time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted
automata with Büchi acceptance conditions, i.e., we generalize fair simulation
from non-weighted automata to weighted automata. We show that imposing Büchi acceptance
conditions on weighted automata changes many fundamental properties of the simulation
games. For example, whereas for mean-payoff and discounted-sum games, the players
do not need memory to play optimally; we show in contrast that for simulation
games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal
strategies for both players require infinite memory in general, and (ii) for discounted-sum
objectives, optimal strategies need not exist for both players. While the simulation
games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory
requirements for mean-payoff objectives) as compared to their counterpart without
Büchi acceptance conditions, we still present pseudo-polynomial time algorithms
to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff
and weighted discounted-sum automata."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation
Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative
fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair
simulation games. IST Austria, 2014.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation
games, IST Austria, 26p.
mla: Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST
Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation
Games, IST Austria, 2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2026-06-18T08:47:00Z
day: '05'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.15479/AT:IST-2014-315-v1-1
file:
- access_level: open_access
checksum: b1d573bc04365625ff9974880c0aa807
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:59Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5521'
file_name: IST-2014-315-v1+1_report.pdf
file_size: 531046
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
fulldoi: https://doi.org/10.15479/AT:IST-2014-315-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '315'
related_material:
record:
- id: '1066'
relation: later_version
status: public
status: public
title: Quantitative fair simulation games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '6178'
abstract:
- lang: eng
text: Mechanically coupled cells can generate forces driving cell and tissue morphogenesis
during development. Visualization and measuring of these forces is of major importance
to better understand the complexity of the biomechanic processes that shape cells
and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively
assess mechanical tension in different tissues of the developing zebrafish and
in cultures of primary germ layer progenitor cells ex vivo.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation
to measure cell and tissue-generated forces in the zebrafish embryo in vivo and
ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. MIMB. New York:
Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15'
apa: 'Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P.
J. (2014). UV laser ablation to measure cell and tissue-generated forces in the
zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis
(Vol. 1189, pp. 219–235). New York: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15'
chicago: 'Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and
Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis,
edited by Celeste Nelson, 1189:219–35. MIMB. New York: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.'
ieee: 'M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg,
“UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson,
Ed. New York: Springer, 2014, pp. 219–235.'
ista: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser
ablation to measure cell and tissue-generated forces in the zebrafish embryo in
vivo and ex vivo. In: Tissue Morphogenesis. Methods in Molecular Biology, vol.
1189, 219–235.'
mla: Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis,
edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.
short: M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:,
C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, 2014, pp. 219–235.
corr_author: '1'
date_created: 2019-03-26T08:55:59Z
date_published: 2014-08-22T00:00:00Z
date_updated: 2026-04-16T10:31:19Z
day: '22'
department:
- _id: CaHe
doi: 10.1007/978-1-4939-1164-6_15
editor:
- first_name: Celeste
full_name: Nelson, Celeste
last_name: Nelson
external_id:
pmid:
- '25245697'
fulldoi: https://doi.org/10.1007/978-1-4939-1164-6_15
intvolume: ' 1189'
language:
- iso: eng
month: '08'
oa_version: None
page: 219-235
place: New York
pmid: 1
publication: Tissue Morphogenesis
publication_identifier:
eisbn:
- '9781493911646'
eissn:
- 1940-6029
isbn:
- '9781493911639'
issn:
- 1064-3745
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: MIMB
status: public
title: UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo
type: book_chapter
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 1189
year: '2014'
...
---
_id: '1994'
abstract:
- lang: eng
text: The emergence and radiation of multicellular land plants was driven by crucial
innovations to their body plans [1]. The directional transport of the phytohormone
auxin represents a key, plant-specific mechanism for polarization and patterning
in complex seed plants [2-5]. Here, we show that already in the early diverging
land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport
by PIN transporters is operational and diversified into ER-localized and plasma
membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses
revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates
crucial developmental transitions in tip-growing filaments and waves of polarization
and differentiation in leaf-like structures. Plasma membrane PIN proteins localize
in a polar manner to the tips of moss filaments, revealing an unexpected relation
between polarization mechanisms in moss tip-growing cells and multicellular tissues
of seed plants. Our results trace the origins of polarization and auxin-mediated
patterning mechanisms and highlight the crucial role of polarized auxin transport
during the evolution of multicellular land plants.
article_processing_charge: No
author:
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Katarina
full_name: Landberg, Katarina
last_name: Landberg
- first_name: Mattias
full_name: Thelander, Mattias
last_name: Thelander
- first_name: Eva
full_name: Medvecka, Eva
last_name: Medvecka
- first_name: Eric
full_name: Pederson, Eric
last_name: Pederson
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Endymion
full_name: Cooper, Endymion
last_name: Cooper
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Charles
full_name: Delwiche, Charles
last_name: Delwiche
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Eva
full_name: Sundberg, Eva
last_name: Sundberg
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Viaene T, Landberg K, Thelander M, et al. Directional auxin transport mechanisms
in early diverging land plants. Current Biology. 2014;24(23):2786-2791.
doi:10.1016/j.cub.2014.09.056
apa: Viaene, T., Landberg, K., Thelander, M., Medvecka, E., Pederson, E., Feraru,
E., … Friml, J. (2014). Directional auxin transport mechanisms in early diverging
land plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.09.056
chicago: Viaene, Tom, Katarina Landberg, Mattias Thelander, Eva Medvecka, Eric Pederson,
Elena Feraru, Endymion Cooper, et al. “Directional Auxin Transport Mechanisms
in Early Diverging Land Plants.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.09.056.
ieee: T. Viaene et al., “Directional auxin transport mechanisms in early
diverging land plants,” Current Biology, vol. 24, no. 23. Cell Press, pp.
2786–2791, 2014.
ista: Viaene T, Landberg K, Thelander M, Medvecka E, Pederson E, Feraru E, Cooper
E, Karimi M, Delwiche C, Ljung K, Geisler M, Sundberg E, Friml J. 2014. Directional
auxin transport mechanisms in early diverging land plants. Current Biology. 24(23),
2786–2791.
mla: Viaene, Tom, et al. “Directional Auxin Transport Mechanisms in Early Diverging
Land Plants.” Current Biology, vol. 24, no. 23, Cell Press, 2014, pp. 2786–91,
doi:10.1016/j.cub.2014.09.056.
short: T. Viaene, K. Landberg, M. Thelander, E. Medvecka, E. Pederson, E. Feraru,
E. Cooper, M. Karimi, C. Delwiche, K. Ljung, M. Geisler, E. Sundberg, J. Friml,
Current Biology 24 (2014) 2786–2791.
corr_author: '1'
date_created: 2018-12-11T11:55:06Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2025-09-29T12:07:20Z
day: '01'
department:
- _id: JiFr
doi: 10.1016/j.cub.2014.09.056
ec_funded: 1
external_id:
isi:
- '000345808700019'
fulldoi: https://doi.org/10.1016/j.cub.2014.09.056
intvolume: ' 24'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 2786 - 2791
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5088'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directional auxin transport mechanisms in early diverging land plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 24
year: '2014'
...
---
_id: '1995'
abstract:
- lang: eng
text: 'Optical transport represents a natural route towards fast communications,
and it is currently used in large scale data transfer. The progressive miniaturization
of devices for information processing calls for the microscopic tailoring of light
transport and confinement at length scales appropriate for upcoming technologies.
With this goal in mind, we present a theoretical analysis of a one-dimensional
Fabry-Perot interferometer built with two highly saturable nonlinear mirrors:
a pair of two-level systems. Our approach captures nonlinear and nonreciprocal
effects of light transport that were not reported previously. Remarkably, we show
that such an elementary device can operate as a microscopic integrated optical
rectifier.'
article_number: '243601'
article_processing_charge: No
arxiv: 1
author:
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Eduardo
full_name: Mascarenhas, Eduardo
last_name: Mascarenhas
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Jean
full_name: Poizat, Jean
last_name: Poizat
- first_name: Daniel
full_name: Valente, Daniel
last_name: Valente
- first_name: Alexia
full_name: Auffèves, Alexia
last_name: Auffèves
- first_name: Dario
full_name: Gerace, Dario
last_name: Gerace
- first_name: Marcelo
full_name: Santos, Marcelo
last_name: Santos
citation:
ama: 'Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with
quantum mirrors: Nonlinear light transport and rectification. Physical Review
Letters. 2014;113(24). doi:10.1103/PhysRevLett.113.243601'
apa: 'Fratini, F., Mascarenhas, E., Safari, L., Poizat, J., Valente, D., Auffèves,
A., … Santos, M. (2014). Fabry-Perot interferometer with quantum mirrors: Nonlinear
light transport and rectification. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.113.243601'
chicago: 'Fratini, Filippo, Eduardo Mascarenhas, Laleh Safari, Jean Poizat, Daniel
Valente, Alexia Auffèves, Dario Gerace, and Marcelo Santos. “Fabry-Perot Interferometer
with Quantum Mirrors: Nonlinear Light Transport and Rectification.” Physical
Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.243601.'
ieee: 'F. Fratini et al., “Fabry-Perot interferometer with quantum mirrors:
Nonlinear light transport and rectification,” Physical Review Letters,
vol. 113, no. 24. American Physical Society, 2014.'
ista: 'Fratini F, Mascarenhas E, Safari L, Poizat J, Valente D, Auffèves A, Gerace
D, Santos M. 2014. Fabry-Perot interferometer with quantum mirrors: Nonlinear
light transport and rectification. Physical Review Letters. 113(24), 243601.'
mla: 'Fratini, Filippo, et al. “Fabry-Perot Interferometer with Quantum Mirrors:
Nonlinear Light Transport and Rectification.” Physical Review Letters,
vol. 113, no. 24, 243601, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.243601.'
short: F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves,
D. Gerace, M. Santos, Physical Review Letters 113 (2014).
date_created: 2018-12-11T11:55:06Z
date_published: 2014-12-08T00:00:00Z
date_updated: 2025-09-29T12:06:45Z
day: '08'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.113.243601
ec_funded: 1
external_id:
arxiv:
- '1410.5972'
isi:
- '000346049700005'
fulldoi: https://doi.org/10.1103/PhysRevLett.113.243601
intvolume: ' 113'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5972
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5085'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport
and rectification'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 113
year: '2014'
...
---
_id: '1996'
abstract:
- lang: eng
text: Auxin polar transport, local maxima, and gradients have become an importantmodel
system for studying self-organization. Auxin distribution is regulated by auxin-dependent
positive feedback loops that are not well-understood at the molecular level. Previously,
we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY
active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are
posttranscriptionally repressed at the site of maximum auxin accumulation at the
root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential
for regulating formation of auxin local maxima and gradients. ICR1 levels increase
concomitant with increase in auxin response in lateral root primordia, cotyledon
tips, and provascular tissues. However, in the embryo hypophysis and root meristem,
when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB)
[SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent
auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo
hypophysis resulted in reduction of auxin accumulation and concomitant root growth
arrest. ICR1 disappeared during root regeneration and lateral root initiation
concomitantly with the formation of a local auxin maximum in response to external
auxin treatments and transiently after gravitropic stimulation. Destabilization
of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome
function, and protein synthesis. A mathematical model based on these findings
shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward
reflux can be simulated without assuming preexisting tissue polarity. Our experimental
results and mathematical modeling indicate that regulation of auxin distribution
is tightly associated with auxin-dependent ICR1 levels.
article_processing_charge: No
author:
- first_name: Ora
full_name: Hazak, Ora
last_name: Hazak
- first_name: Uri
full_name: Obolski, Uri
last_name: Obolski
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Lilach
full_name: Hadany, Lilach
last_name: Hadany
- first_name: Shaul
full_name: Yalovsky, Shaul
last_name: Yalovsky
citation:
ama: Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. Bimodal regulation
of ICR1 levels generates self-organizing auxin distribution. PNAS. 2014;111(50):E5471-E5479.
doi:10.1073/pnas.1413918111
apa: Hazak, O., Obolski, U., Prat, T., Friml, J., Hadany, L., & Yalovsky, S.
(2014). Bimodal regulation of ICR1 levels generates self-organizing auxin distribution.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1413918111
chicago: Hazak, Ora, Uri Obolski, Tomas Prat, Jiří Friml, Lilach Hadany, and Shaul
Yalovsky. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.”
PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1413918111.
ieee: O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, and S. Yalovsky, “Bimodal
regulation of ICR1 levels generates self-organizing auxin distribution,” PNAS,
vol. 111, no. 50. National Academy of Sciences, pp. E5471–E5479, 2014.
ista: Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. 2014. Bimodal regulation
of ICR1 levels generates self-organizing auxin distribution. PNAS. 111(50), E5471–E5479.
mla: Hazak, Ora, et al. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing
Auxin Distribution.” PNAS, vol. 111, no. 50, National Academy of Sciences,
2014, pp. E5471–79, doi:10.1073/pnas.1413918111.
short: O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111
(2014) E5471–E5479.
date_created: 2018-12-11T11:55:07Z
date_published: 2014-12-16T00:00:00Z
date_updated: 2025-09-29T12:06:13Z
day: '16'
department:
- _id: JiFr
doi: 10.1073/pnas.1413918111
external_id:
isi:
- '000346366500020'
fulldoi: https://doi.org/10.1073/pnas.1413918111
intvolume: ' 111'
isi: 1
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/
month: '12'
oa: 1
oa_version: Submitted Version
page: E5471 - E5479
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5083'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bimodal regulation of ICR1 levels generates self-organizing auxin distribution
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 111
year: '2014'
...
---
_id: '1998'
abstract:
- lang: eng
text: Immune systems are able to protect the body against secondary infection with
the same parasite. In insect colonies, this protection is not restricted to the
level of the individual organism, but also occurs at the societal level. Here,
we review recent evidence for and insights into the mechanisms underlying individual
and social immunisation in insects. We disentangle general immune-protective effects
from specific immune memory (priming), and examine immunisation in the context
of the lifetime of an individual and that of a colony, and of transgenerational
immunisation that benefits offspring. When appropriate, we discuss parallels with
disease defence strategies in human societies. We propose that recurrent parasitic
threats have shaped the evolution of both the individual immune systems and colony-level
social immunity in insects.
acknowledgement: "This work was funded by an ERC Starting Grant by the European Research
Council (to S.C.) and the ISTFELLOW program (Co-fund Marie Curie Actions of the
European Commission; to L.M.).\r\nWe thank Christopher D. Pull, Sophie A.O. Armitage,
Hinrich Schulenburg, Line V. Ugelvig, Matthias Konrad, Matthias Fürst, Miriam Stock,
Barbara Casillas-Perez and three anonymous referees for comments on the manuscript. "
article_processing_charge: No
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: El Masri L, Cremer S. Individual and social immunisation in insects. Trends
in Immunology. 2014;35(10):471-482. doi:10.1016/j.it.2014.08.005
apa: El Masri, L., & Cremer, S. (2014). Individual and social immunisation in
insects. Trends in Immunology. Elsevier. https://doi.org/10.1016/j.it.2014.08.005
chicago: El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation
in Insects.” Trends in Immunology. Elsevier, 2014. https://doi.org/10.1016/j.it.2014.08.005.
ieee: L. El Masri and S. Cremer, “Individual and social immunisation in insects,”
Trends in Immunology, vol. 35, no. 10. Elsevier, pp. 471–482, 2014.
ista: El Masri L, Cremer S. 2014. Individual and social immunisation in insects.
Trends in Immunology. 35(10), 471–482.
mla: El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in
Insects.” Trends in Immunology, vol. 35, no. 10, Elsevier, 2014, pp. 471–82,
doi:10.1016/j.it.2014.08.005.
short: L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.
corr_author: '1'
date_created: 2018-12-11T11:55:07Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2025-09-29T12:05:29Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.it.2014.08.005
external_id:
isi:
- '000343632600006'
fulldoi: https://doi.org/10.1016/j.it.2014.08.005
intvolume: ' 35'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 471 - 482
publication: Trends in Immunology
publication_status: published
publisher: Elsevier
publist_id: '5081'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Individual and social immunisation in insects
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2014'
...
---
OA_type: closed access
_id: '19994'
abstract:
- lang: eng
text: Firing patterns of hippocampal principal cells are thought to participate
in the formation of mnemonic representations of place, which ultimately can be
used to guide the behavior of animals in space. Past studies have suggested that
place-selective activity in the hippocampus can emphasize the representation of
discrete locations associated with a strong behavioral salience. In the first
part of this book chapter, we review work that has described how that hippocampal
neuronal activity patterns reorganize during spatial learning. These studies revealed
that new hippocampal maps emerge during spatial learning to represent the location
of goal locations and demonstrated that, during recall, the reinstatement of these
maps predicts successful memory performance. In the second part of this chapter,
we discuss the role of sleep in memory consolidation in the context of goal-oriented
spatial learning. We summarize work that has demonstrated the replay of goal-oriented
neuronal assembly patterns that predict subsequent memory recall. Moreover, we
argue that the initial strengthening of new maps may in fact take place during
learning, triggered by waking sharp-wave/ripple patterns occurring at goal locations.
These reviewed studies highlight that the reorganization and replay of place cell
firing patterns might constitute a circuit signature for the expression of newly
acquired hippocampal engrams.
alternative_title:
- Springer Series in Computational Neuroscience
article_processing_charge: No
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: 'Dupret D, Csicsvari JL. Reorganization of Hippocampal Place-Selective Patterns
During Goal-Directed Learning and Their Reactivation During Sleep. In: Analysis
and Modeling of Coordinated Multi-Neuronal Activity. Vol 12. NEUROSCI. Springer
Nature; 2014. doi:10.1007/978-1-4939-1969-7_6'
apa: Dupret, D., & Csicsvari, J. L. (2014). Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep. In
Analysis and Modeling of Coordinated Multi-neuronal Activity (Vol. 12).
Springer Nature. https://doi.org/10.1007/978-1-4939-1969-7_6
chicago: Dupret, David, and Jozsef L Csicsvari. “Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep.” In
Analysis and Modeling of Coordinated Multi-Neuronal Activity, Vol. 12.
NEUROSCI. Springer Nature, 2014. https://doi.org/10.1007/978-1-4939-1969-7_6.
ieee: D. Dupret and J. L. Csicsvari, “Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep,” in
Analysis and Modeling of Coordinated Multi-neuronal Activity, vol. 12,
Springer Nature, 2014.
ista: 'Dupret D, Csicsvari JL. 2014.Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep. In:
Analysis and Modeling of Coordinated Multi-neuronal Activity. Springer Series
in Computational Neuroscience, vol. 12.'
mla: Dupret, David, and Jozsef L. Csicsvari. “Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep.” Analysis
and Modeling of Coordinated Multi-Neuronal Activity, vol. 12, Springer Nature,
2014, doi:10.1007/978-1-4939-1969-7_6.
short: D. Dupret, J.L. Csicsvari, in:, Analysis and Modeling of Coordinated Multi-Neuronal
Activity, Springer Nature, 2014.
date_created: 2025-07-10T14:06:05Z
date_published: 2014-10-30T00:00:00Z
date_updated: 2025-09-23T09:36:44Z
day: '30'
department:
- _id: JoCs
doi: 10.1007/978-1-4939-1969-7_6
fulldoi: https://doi.org/10.1007/978-1-4939-1969-7_6
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa_version: None
publication: Analysis and Modeling of Coordinated Multi-neuronal Activity
publication_identifier:
eisbn:
- '9781493919697'
eissn:
- 2197-1919
isbn:
- '9781493919680'
issn:
- 2197-1900
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: NEUROSCI
status: public
title: Reorganization of Hippocampal Place-Selective Patterns During Goal-Directed
Learning and Their Reactivation During Sleep
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2014'
...
---
_id: '2001'
abstract:
- lang: eng
text: Antibiotics affect bacterial cell physiology at many levels. Rather than just
compensating for the direct cellular defects caused by the drug, bacteria respond
to antibiotics by changing their morphology, macromolecular composition, metabolism,
gene expression and possibly even their mutation rate. Inevitably, these processes
affect each other, resulting in a complex response with changes in the expression
of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive
understanding of bacterial responses to antibiotics. In addition, a combination
of experimental and theoretical approaches is needed for identifying general principles
that underlie these responses. Here, we review recent progress in our understanding
of bacterial responses to antibiotics and their combinations, focusing on effects
at the levels of growth rate and gene expression. We concentrate on studies performed
in controlled laboratory conditions, which combine promising experimental techniques
with quantitative data analysis and mathematical modeling. While these basic research
approaches are not immediately applicable in the clinic, uncovering the principles
and mechanisms underlying bacterial responses to antibiotics may, in the long
term, contribute to the development of new treatment strategies to cope with and
prevent the rise of resistant pathogenic bacteria.
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations.
Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190
apa: Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics
and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190
chicago: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014.
https://doi.org/10.1111/1758-2229.12190.
ieee: K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their
combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley,
pp. 545–557, 2014.
ista: Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their
combinations. Environmental Microbiology Reports. 6(6), 545–557.
mla: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports, vol. 6, no.
6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190.
short: K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014)
545–557.
corr_author: '1'
date_created: 2018-12-11T11:55:08Z
date_published: 2014-06-22T00:00:00Z
date_updated: 2026-04-08T14:21:56Z
day: '22'
department:
- _id: ToBo
doi: 10.1111/1758-2229.12190
ec_funded: 1
external_id:
isi:
- '000345702700002'
fulldoi: https://doi.org/10.1111/1758-2229.12190
intvolume: ' 6'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 545 - 557
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Environmental Microbiology Reports
publication_status: published
publisher: Wiley
publist_id: '5076'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Bacterial responses to antibiotics and their combinations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2014'
...
---
_id: '2002'
abstract:
- lang: eng
text: Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus
play a key role in feedback inhibition and in the control of network activity.
However, how these cells are efficiently activated in the network remains unclear.
To address this question, I performed recordings from CA1 pyramidal neuron axons,
the presynaptic fibers that provide feedback innervation of these interneurons.
Two forms of axonal action potential (AP) modulation were identified. First, repetitive
stimulation resulted in activity-dependent AP broadening. Broadening showed fast
onset, with marked changes in AP shape following a single AP. Second, tonic depolarization
in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced
broadening summated with activity-dependent broadening. Outsideout patch recordings
from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive,
inactivating K+ channels, suggesting that K+ channel inactivation mechanistically
contributes to AP broadening. To examine the functional consequences of axonal
AP modulation for synaptic transmission, I performed paired recordings between
synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal
neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation
during both repetitive stimulation and tonic depolarization of the presynaptic
neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they
were mediated by K+ channel inactivation. Therefore, axonal AP modulation can
greatly facilitate the activation of O-LM interneurons. In conclusion, modulation
of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy
of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons
in recurrent inhibitory microcircuits.
article_number: '0113124'
article_processing_charge: No
author:
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
citation:
ama: Kim S. Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus.
PLoS One. 2014;9(11). doi:10.1371/journal.pone.0113124
apa: Kim, S. (2014). Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0113124
chicago: Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons
Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of
Rat Hippocampus.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0113124.
ieee: S. Kim, “Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus,”
PLoS One, vol. 9, no. 11. Public Library of Science, 2014.
ista: Kim S. 2014. Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus.
PLoS One. 9(11), 0113124.
mla: Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates
OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.”
PLoS One, vol. 9, no. 11, 0113124, Public Library of Science, 2014, doi:10.1371/journal.pone.0113124.
short: S. Kim, PLoS One 9 (2014).
corr_author: '1'
date_created: 2018-12-11T11:55:09Z
date_published: 2014-11-19T00:00:00Z
date_updated: 2025-09-29T12:03:47Z
day: '19'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0113124
ec_funded: 1
external_id:
isi:
- '000345533200070'
file:
- access_level: open_access
checksum: 85e4f4ea144f827272aaf376b2830564
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:52Z
date_updated: 2020-07-14T12:45:24Z
file_id: '5107'
file_name: IST-2016-434-v1+1_journal.pone.0113124.pdf
file_size: 5179993
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
fulldoi: https://doi.org/10.1371/journal.pone.0113124
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5074'
pubrep_id: '434'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron
activation in recurrent inhibitory microcircuits of rat hippocampus
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2014'
...
---
_id: '2003'
abstract:
- lang: eng
text: Learning can be facilitated by previous knowledge when it is organized into
relational representations forming schemas. In this issue of Neuron, McKenzie
et al. (2014) demonstrate that the hippocampus rapidly forms interrelated, hierarchical
memory representations to support schema-based learning.
article_processing_charge: No
author:
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: O’Neill J, Csicsvari JL. Learning by example in the hippocampus. Neuron.
2014;83(1):8-10. doi:10.1016/j.neuron.2014.06.013
apa: O’Neill, J., & Csicsvari, J. L. (2014). Learning by example in the hippocampus.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.06.013
chicago: O’Neill, Joseph, and Jozsef L Csicsvari. “Learning by Example in the Hippocampus.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.06.013.
ieee: J. O’Neill and J. L. Csicsvari, “Learning by example in the hippocampus,”
Neuron, vol. 83, no. 1. Elsevier, pp. 8–10, 2014.
ista: O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron.
83(1), 8–10.
mla: O’Neill, Joseph, and Jozsef L. Csicsvari. “Learning by Example in the Hippocampus.”
Neuron, vol. 83, no. 1, Elsevier, 2014, pp. 8–10, doi:10.1016/j.neuron.2014.06.013.
short: J. O’Neill, J.L. Csicsvari, Neuron 83 (2014) 8–10.
corr_author: '1'
date_created: 2018-12-11T11:55:09Z
date_published: 2014-07-02T00:00:00Z
date_updated: 2025-09-29T12:03:17Z
day: '02'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2014.06.013
external_id:
isi:
- '000340476800004'
fulldoi: https://doi.org/10.1016/j.neuron.2014.06.013
intvolume: ' 83'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 8 - 10
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5073'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning by example in the hippocampus
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 83
year: '2014'
...
---
_id: '2004'
abstract:
- lang: eng
text: We have assembled a network of cell-fate determining transcription factors
that play a key role in the specification of the ventral neuronal subtypes of
the spinal cord on the basis of published transcriptional interactions. Asynchronous
Boolean modelling of the network was used to compare simulation results with reported
experimental observations. Such comparison highlighted the need to include additional
regulatory connections in order to obtain the fixed point attractors of the model
associated with the five known progenitor cell types located in the ventral spinal
cord. The revised gene regulatory network reproduced previously observed cell
state switches between progenitor cells observed in knock-out animal models or
in experiments where the transcription factors were overexpressed. Furthermore
the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was
tested experimentally. Our results provide evidence for the existence of an as
yet undescribed inhibitory connection which could potentially have significance
beyond the ventral spinal cord. The work presented in this paper demonstrates
the strength of Boolean modelling for identifying gene regulatory networks.
article_number: e111430
article_processing_charge: No
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen
full_name: Byrne, Helen
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory
connections between transcription factors orchestrating the development of the
ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács,
K. (2014). Boolean modelling reveals new regulatory connections between transcription
factors orchestrating the development of the ventral spinal cord. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0111430
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András
Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections
between Transcription Factors Orchestrating the Development of the Ventral Spinal
Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.
ieee: A. Lovrics et al., “Boolean modelling reveals new regulatory connections
between transcription factors orchestrating the development of the ventral spinal
cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean
modelling reveals new regulatory connections between transcription factors orchestrating
the development of the ventral spinal cord. PLoS One. 9(11), e111430.
mla: Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections
between Transcription Factors Orchestrating the Development of the Ventral Spinal
Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014,
doi:10.1371/journal.pone.0111430.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács,
PLoS One 9 (2014).
date_created: 2018-12-11T11:55:09Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2025-09-29T12:02:48Z
day: '14'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430
ec_funded: 1
external_id:
isi:
- '000345558500017'
file:
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checksum: a2289b843f7463eb1233f9ce45e6a943
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:58Z
date_updated: 2020-07-14T12:45:24Z
file_id: '4850'
file_name: IST-2016-435-v1+1_journal.pone.0111430.pdf
file_size: 829363
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
fulldoi: https://doi.org/10.1371/journal.pone.0111430
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5072'
pubrep_id: '435'
quality_controlled: '1'
related_material:
record:
- id: '9722'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Boolean modelling reveals new regulatory connections between transcription
factors orchestrating the development of the ventral spinal cord
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2014'
...
---
_id: '2005'
abstract:
- lang: eng
text: By eliciting a natural exploratory behavior in rats, head scanning, a study
reveals that hippocampal place cells form new, stable firing fields in those locations
where the behavior has just occurred.
article_processing_charge: No
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Dupret D, Csicsvari JL. Turning heads to remember places. Nature Neuroscience.
2014;17(5):643-644. doi:10.1038/nn.3700
apa: Dupret, D., & Csicsvari, J. L. (2014). Turning heads to remember places.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3700
chicago: Dupret, David, and Jozsef L Csicsvari. “Turning Heads to Remember Places.”
Nature Neuroscience. Nature Publishing Group, 2014. https://doi.org/10.1038/nn.3700.
ieee: D. Dupret and J. L. Csicsvari, “Turning heads to remember places,” Nature
Neuroscience, vol. 17, no. 5. Nature Publishing Group, pp. 643–644, 2014.
ista: Dupret D, Csicsvari JL. 2014. Turning heads to remember places. Nature Neuroscience.
17(5), 643–644.
mla: Dupret, David, and Jozsef L. Csicsvari. “Turning Heads to Remember Places.”
Nature Neuroscience, vol. 17, no. 5, Nature Publishing Group, 2014, pp.
643–44, doi:10.1038/nn.3700.
short: D. Dupret, J.L. Csicsvari, Nature Neuroscience 17 (2014) 643–644.
corr_author: '1'
date_created: 2018-12-11T11:55:09Z
date_published: 2014-04-25T00:00:00Z
date_updated: 2025-09-29T12:02:14Z
day: '25'
department:
- _id: JoCs
doi: 10.1038/nn.3700
external_id:
isi:
- '000335016200003'
fulldoi: https://doi.org/10.1038/nn.3700
intvolume: ' 17'
isi: 1
issue: '5'
language:
- iso: eng
month: '04'
oa_version: None
page: 643 - 644
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '5071'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Turning heads to remember places
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2014'
...
---
_id: '2007'
abstract:
- lang: eng
text: Maximum likelihood estimation under relational models, with or without the
overall effect. For more information see the reference manual
article_processing_charge: No
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: 'Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for
relational models. 2014.'
apa: 'Klimova, A., & Rudas, T. (2014). gIPFrm: Generalized iterative proportional
fitting for relational models. The Comprehensive R Archive Network.'
chicago: 'Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional
Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.'
ieee: 'A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting
for relational models.” The Comprehensive R Archive Network, 2014.'
ista: 'Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting
for relational models, The Comprehensive R Archive Network.'
mla: 'Klimova, Anna, and Tamás Rudas. GIPFrm: Generalized Iterative Proportional
Fitting for Relational Models. The Comprehensive R Archive Network, 2014.'
short: A. Klimova, T. Rudas, (2014).
corr_author: '1'
date_created: 2018-12-11T11:55:10Z
date_published: 2014-03-20T00:00:00Z
date_updated: 2024-10-09T20:55:44Z
day: '20'
department:
- _id: CaUh
main_file_link:
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url: 'https://CRAN.R-project.org/package=gIPFrm '
month: '03'
oa: 1
oa_version: Published Version
publisher: The Comprehensive R Archive Network
publist_id: '5069'
status: public
title: 'gIPFrm: Generalized iterative proportional fitting for relational models'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...