---
_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: 2023-02-23T10:11:15Z
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
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: 2023-02-23T12:25:52Z
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
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: '1732'
relation: later_version
status: public
- id: '5426'
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: 2023-02-23T12:25:47Z
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
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: '1732'
relation: later_version
status: public
- id: '5424'
relation: earlier_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
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: 2023-09-20T12:07:48Z
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
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.
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. Methods in Molecular
Biology. New York, NY: 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, NY: 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. Methods in Molecular Biology. New York,
NY: 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, NY: 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. 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, NY, 2014, pp. 219–235.
date_created: 2019-03-26T08:55:59Z
date_published: 2014-08-22T00:00:00Z
date_updated: 2023-09-05T14:12:00Z
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'
intvolume: ' 1189'
language:
- iso: eng
month: '08'
oa_version: None
page: 219-235
place: New York, NY
pmid: 1
publication: Tissue Morphogenesis
publication_identifier:
eissn:
- 1940-6029
isbn:
- '9781493911639'
- '9781493911646'
issn:
- 1064-3745
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: Methods in Molecular Biology
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1189
year: '2014'
...
---
_id: '6853'
abstract:
- lang: eng
text: This monograph presents a short course in computational geometry and topology.
In the first part the book covers Voronoi diagrams and Delaunay triangulations,
then it presents the theory of alpha complexes which play a crucial role in biology.
The central part of the book is the homology theory and their computation, including
the theory of persistence which is indispensable for applications, e.g. shape
reconstruction. The target audience comprises researchers and practitioners in
mathematics, biology, neuroscience and computer science, but the book may also
be beneficial to graduate students of these fields.
alternative_title:
- SpringerBriefs in Applied Sciences and Technology
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
citation:
ama: 'Edelsbrunner H. A Short Course in Computational Geometry and Topology.
1st ed. Cham: Springer Nature; 2014. doi:10.1007/978-3-319-05957-0'
apa: 'Edelsbrunner, H. (2014). A Short Course in Computational Geometry and Topology
(1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-05957-0'
chicago: 'Edelsbrunner, Herbert. A Short Course in Computational Geometry and
Topology. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham:
Springer Nature, 2014. https://doi.org/10.1007/978-3-319-05957-0.'
ieee: 'H. Edelsbrunner, A Short Course in Computational Geometry and Topology,
1st ed. Cham: Springer Nature, 2014.'
ista: 'Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology
1st ed., Cham: Springer Nature, IX, 110p.'
mla: Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology.
1st ed., Springer Nature, 2014, doi:10.1007/978-3-319-05957-0.
short: H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st
ed., Springer Nature, Cham, 2014.
date_created: 2019-09-06T09:22:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-03-04T07:47:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-319-05957-0
edition: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: IX, 110
place: Cham
publication_identifier:
eisbn:
- 9-783-3190-5957-0
eissn:
- 2191-5318
isbn:
- 9-783-3190-5956-3
issn:
- 2191-530X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: available as eBook via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106
- description: available via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842
scopus_import: '1'
series_title: SpringerBriefs in Applied Sciences and Technology
status: public
title: A Short Course in Computational Geometry and Topology
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '10793'
abstract:
- lang: eng
text: "The Hanani–Tutte theorem is a classical result proved for the first time
in the 1930s that characterizes planar graphs as graphs that admit a drawing in
the plane in which every pair of edges not sharing a vertex cross an even number
of times. We generalize this classical result to clustered graphs with two disjoint
clusters, and show that a straightforward extension of our result to flat clustered
graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give
a new and short proof for a related result by Di Battista and Frati based on the
matroid intersection algorithm."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
- first_name: Igor
full_name: Malinović, Igor
last_name: Malinović
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: 'Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited.
In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer
Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36'
apa: 'Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered
planarity testing revisited. In International Symposium on Graph Drawing
(Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36'
chicago: 'Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered
Planarity Testing Revisited.” In International Symposium on Graph Drawing,
8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.'
ieee: R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing
revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871,
pp. 428–436.
ista: Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing
revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.
mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International
Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36,
doi:10.1007/978-3-662-45803-7_36.
short: R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium
on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.
date_created: 2022-02-25T10:32:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T10:08:04Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/978-3-662-45803-7_36
external_id:
arxiv:
- '1305.4519'
intvolume: ' 8871'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 428-436
place: Cham
publication: International Symposium on Graph Drawing
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '1642'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Clustered planarity testing revisited
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8871
year: '2014'
...
---
_id: '10811'
abstract:
- lang: eng
text: Auxin is an important signaling compound in plants and vital for plant development
and growth. The present book, Auxin and its Role in Plant Development, provides
the reader with detailed and comprehensive insight into the functioning of the
molecule on the whole and specifically in plant development. In the first part,
the functioning, metabolism and signaling pathways of auxin in plants are explained,
the second part depicts the specific role of auxin in plant development and the
third part describes the interaction and functioning of the signaling compound upon
stimuli of the environment. Each chapter is written by international experts in
the respective field and designed for scientists and researchers in plant biology,
plant development and cell biology to summarize the recent progress in understanding
the role of auxin and suggest future perspectives for auxin research.
article_processing_charge: No
citation:
ama: 'Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development.
1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8'
apa: 'Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and
Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8'
chicago: 'Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its
Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.'
ieee: 'E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in
Plant Development, 1st ed. Vienna: Springer Nature, 2014.'
ista: 'Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant
Development 1st ed., Vienna: Springer Nature, 444p.'
mla: Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development.
1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8.
short: E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant
Development, 1st ed., Springer Nature, Vienna, 2014.
date_created: 2022-03-03T11:52:44Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2022-03-04T07:38:15Z
day: '01'
department:
- _id: EvBe
doi: 10.1007/978-3-7091-1526-8
edition: '1'
editor:
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
language:
- iso: eng
month: '04'
oa_version: None
page: '444'
place: Vienna
publication_identifier:
eisbn:
- '9783709115268'
isbn:
- '9783709115251'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin and Its Role in Plant Development
type: book_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '10814'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the excitation
spectrum of bosonic quantum many-body systems. In particular, we explain how one
can rigorously establish the predictions resulting from the Bogoliubov approximation
in the mean field limit. The latter predicts that the spectrum is made up of elementary
excitations, whose energy behaves linearly in the momentum for small momentum.
This property is crucial for the superfluid behavior of the system. We also discuss
a list of open problems in this field.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht der Deutschen Mathematiker-Vereinigung. 2014;116:21-41. doi:10.1365/s13291-014-0083-9
apa: Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature.
https://doi.org/10.1365/s13291-014-0083-9
chicago: Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.”
Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature,
2014. https://doi.org/10.1365/s13291-014-0083-9.
ieee: R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,”
Jahresbericht der Deutschen Mathematiker-Vereinigung, vol. 116. Springer
Nature, pp. 21–41, 2014.
ista: Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.
mla: Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.”
Jahresbericht Der Deutschen Mathematiker-Vereinigung, vol. 116, Springer
Nature, 2014, pp. 21–41, doi:10.1365/s13291-014-0083-9.
short: R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014)
21–41.
date_created: 2022-03-04T07:54:39Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-09-05T14:19:47Z
day: '01'
department:
- _id: RoSe
doi: 10.1365/s13291-014-0083-9
intvolume: ' 116'
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 21-41
publication: Jahresbericht der Deutschen Mathematiker-Vereinigung
publication_identifier:
eissn:
- 1869-7135
issn:
- 0012-0456
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitation spectrum for Bose fluids with weak interactions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2014'
...
---
_id: '10815'
abstract:
- lang: eng
text: In the last several decades, developmental biology has clarified the molecular
mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated
that the “tool-kit genes” essential for regulating developmental processes are
not only highly conserved among species, but are also used as systems at various
times and places in an organism to control distinct developmental events. Therefore,
mutations in many of these tool-kit genes may cause congenital diseases involving
morphological abnormalities. This link between genes and abnormal morphological
phenotypes underscores the importance of understanding how cells behave and contribute
to morphogenesis as a result of gene function. Recent improvements in live imaging
and in quantitative analyses of cellular dynamics will advance our understanding
of the cellular pathogenesis of congenital diseases associated with aberrant morphologies.
In these studies, it is critical to select an appropriate model organism for the
particular phenomenon of interest.
acknowledgement: The authors thank all the members of the Division of Morphogenesis,
National Institute for Basic Biology, for their contributions to the research, their
encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical
reading of the manuscript. We also thank the Model Animal Research and Spectrography
and Bioimaging Facilities, NIBB Core Research Facilities, for technical support.
M.H. was supported by a research fellowship from the Japan Society for the Promotion
of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid
for Scientific Research on Innovative Areas from the Ministry of Education, Culture,
Sports, Science, and Technology (MEXT), Japan, to N.U.
article_processing_charge: No
article_type: original
author:
- first_name: Masakazu
full_name: Hashimoto, Masakazu
last_name: Hashimoto
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Naoto
full_name: Ueno, Naoto
last_name: Ueno
citation:
ama: Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development
underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039
apa: Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms
of development underlying congenital diseases. Congenital Anomalies. Wiley.
https://doi.org/10.1111/cga.12039
chicago: Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular
Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies.
Wiley, 2014. https://doi.org/10.1111/cga.12039.
ieee: M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of
development underlying congenital diseases,” Congenital Anomalies, vol.
54, no. 1. Wiley, pp. 1–7, 2014.
ista: Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of
development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.
mla: Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development
Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1,
Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.
short: M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.
date_created: 2022-03-04T08:17:25Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-03-04T08:26:05Z
day: '01'
department:
- _id: CaHe
doi: 10.1111/cga.12039
external_id:
pmid:
- '24666178'
intvolume: ' 54'
issue: '1'
keyword:
- Developmental Biology
- Embryology
- General Medicine
- Pediatrics
- Perinatology
- and Child Health
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/cga.12039
month: '02'
oa: 1
oa_version: None
page: 1-7
pmid: 1
publication: Congenital Anomalies
publication_identifier:
issn:
- 0914-3505
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and cellular mechanisms of development underlying congenital diseases
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2014'
...
---
_id: '9458'
abstract:
- lang: eng
text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
Their genomes are typically depleted of CG dinucleotides because of imperfect
repair of deaminated methylcytosines. Here, we extensively survey diverse species
lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
frequently present and catalyzed by a different DNA methyltransferase family,
Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
methylation occurs at unprecedented densities and directly disfavors nucleosomes,
contributing to nucleosome positioning between clusters. Dense methylation is
enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
and drives the highest CG frequencies known. Species with linker methylation have
small, transcriptionally active nuclei that approach the physical limits of chromatin
compaction. These features constitute a previously unappreciated genome architecture,
in which dense methylation influences nucleosome positions, likely facilitating
nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029
chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2014.01.029.
ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6.
Elsevier, pp. 1286–1297, 2014.
ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6,
Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.
short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
pmid:
- '24630728'
intvolume: ' 156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '9722'
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 M.
full_name: Byrne, Helen M.
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. Transition probability between TF expression
states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &
Kovács, K. (2014). Transition probability between TF expression states when Dbx2
inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András
Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.
ieee: A. Lovrics et al., “Transition probability between TF expression states
when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition
probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library
of Science, 10.1371/journal.pone.0111430.s006.
mla: Lovrics, Anna, et al. Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács,
(2014).
date_created: 2021-07-26T14:35:00Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T10:24:07Z
day: '14'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430.s006
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2004'
relation: used_in_publication
status: public
status: public
title: Transition probability between TF expression states when Dbx2 inhibits Nkx2.2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9739'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Novak, Martin
last_name: Novak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time
scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed
proofs for “The time scale of evolutionary innovation.” Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003818.s001
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak.
“Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library
of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for
‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for
“The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.
mla: Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary
Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).
date_created: 2021-07-28T08:13:57Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T10:25:37Z
day: '11'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2039'
relation: used_in_publication
status: public
status: public
title: Detailed proofs for “The time scale of evolutionary innovation”
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9740'
abstract:
- lang: eng
text: The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens.
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc'
apa: 'Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from:
Anti-pathogen protection versus survival costs mediated by an ectosymbiont in
an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc'
chicago: 'Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data
from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont
in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.'
ieee: 'M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host.”
Dryad, 2014.'
ista: 'Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad,
10.5061/dryad.vm0vc.'
mla: 'Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival
Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.'
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).
date_created: 2021-07-28T08:38:40Z
date_published: 2014-11-13T00:00:00Z
date_updated: 2023-02-23T10:23:32Z
day: '13'
department:
- _id: SyCr
doi: 10.5061/dryad.vm0vc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.vm0vc
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1993'
relation: used_in_publication
status: public
status: public
title: 'Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9741'
abstract:
- lang: eng
text: In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: 'Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. 2014.
doi:10.5061/dryad.85dn7'
apa: 'Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history
and epistatic interactions impact dynamics of adaptation to novel environmental
stresses. Dryad. https://doi.org/10.5061/dryad.85dn7'
chicago: 'Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History
and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental
Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.'
ieee: 'M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and
epistatic interactions impact dynamics of adaptation to novel environmental stresses.”
Dryad, 2014.'
ista: 'Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses, Dryad,
10.5061/dryad.85dn7.'
mla: 'Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions
Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014,
doi:10.5061/dryad.85dn7.'
short: M. Lagator, N. Colegrave, P. Neve, (2014).
date_created: 2021-07-28T08:48:06Z
date_published: 2014-08-21T00:00:00Z
date_updated: 2023-02-23T10:25:31Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.85dn7
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.85dn7
month: '08'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2036'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selection history and epistatic interactions impact dynamics of
adaptation to novel environmental stresses'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9747'
abstract:
- lang: eng
text: Understanding the effects of sex and migration on adaptation to novel environments
remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas
reinhardtii, we investigated how sex and migration affected rates of evolutionary
rescue in a sink environment, and subsequent changes in fitness following evolutionary
rescue. We show that sex and migration affect both the rate of evolutionary rescue
and subsequent adaptation. However, their combined effects change as the populations
adapt to a sink habitat. Both sex and migration independently increased rates
of evolutionary rescue, but the effect of sex on subsequent fitness improvements,
following initial rescue, changed with migration, as sex was beneficial in the
absence of migration but constraining adaptation when combined with migration.
These results suggest that sex and migration are beneficial during the initial
stages of adaptation, but can become detrimental as the population adapts to its
environment.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Andrew
full_name: Morgan, Andrew
last_name: Morgan
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
citation:
ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration
in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1'
apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from:
Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1'
chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from:
Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.'
ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex
and migration in adaptation to sink environments.” Dryad, 2014.'
ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and
migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.'
mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation
to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.'
short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).
date_created: 2021-07-28T15:32:55Z
date_published: 2014-04-17T00:00:00Z
date_updated: 2023-02-23T10:27:31Z
day: '17'
department:
- _id: CaGu
doi: 10.5061/dryad.s42n1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s42n1
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2083'
relation: used_in_publication
status: public
status: public
title: 'Data from: Role of sex and migration in adaptation to sink environments'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9752'
abstract:
- lang: eng
text: Redundancies and correlations in the responses of sensory neurons may seem
to waste neural resources, but they can also carry cues about structured stimuli
and may help the brain to correct for response errors. To investigate the effect
of stimulus structure on redundancy in retina, we measured simultaneous responses
from populations of retinal ganglion cells presented with natural and artificial
stimuli that varied greatly in correlation structure; these stimuli and recordings
are publicly available online. Responding to spatio-temporally structured stimuli
such as natural movies, pairs of ganglion cells were modestly more correlated
than in response to white noise checkerboards, but they were much less correlated
than predicted by a non-adapting functional model of retinal response. Meanwhile,
responding to stimuli with purely spatial correlations, pairs of ganglion cells
showed increased correlations consistent with a static, non-adapting receptive
field and nonlinearity. We found that in response to spatio-temporally correlated
stimuli, ganglion cells had faster temporal kernels and tended to have stronger
surrounds. These properties of individual cells, along with gain changes that
opposed changes in effective contrast at the ganglion cell input, largely explained
the pattern of pairwise correlations across stimuli where receptive field measurements
were possible.
article_processing_charge: No
author:
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Heather
full_name: Yee, Heather
last_name: Yee
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Philip
full_name: Nelson, Philip
last_name: Nelson
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: 'Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus
correlations by the retina. 2014. doi:10.5061/dryad.246qg'
apa: 'Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., …
Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations
by the retina. Dryad. https://doi.org/10.5061/dryad.246qg'
chicago: 'Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather
Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation
of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg.'
ieee: 'K. Simmons et al., “Data from: Transformation of stimulus correlations
by the retina.” Dryad, 2014.'
ista: 'Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian
V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad,
10.5061/dryad.246qg.'
mla: 'Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations
by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.'
short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson,
V. Balasubramanian, (2014).
date_created: 2021-07-30T08:13:52Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-02-23T10:35:57Z
day: '07'
department:
- _id: GaTk
doi: 10.5061/dryad.246qg
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.246qg
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2277'
relation: used_in_publication
status: public
status: public
title: 'Data from: Transformation of stimulus correlations by the retina'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...