---
_id: '1603'
abstract:
- lang: eng
text: "For deterministic systems, a counterexample to a property can simply be an
error trace, whereas counterexamples in probabilistic systems are necessarily
more complex. For instance, a set of erroneous traces with a sufficient cumulative
probability mass can be used. Since these are too large objects to understand
and manipulate, compact representations such as subchains have been considered.
In the case of probabilistic systems with non-determinism, the situation is even
more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism)
is a straightforward choice, we take a different approach. Instead, we focus on
the strategy itself, and extract the most important decisions it makes, and present
its succinct representation.\r\nThe key tools we employ to achieve this are (1)
introducing a concept of importance of a state w.r.t. the strategy, and (2) learning
using decision trees. There are three main consequent advantages of our approach.
Firstly, it exploits the quantitative information on states, stressing the more
important decisions. Secondly, it leads to a greater variability and degree of
freedom in representing the strategies. Thirdly, the representation uses a self-explanatory
data structure. In summary, our approach produces more succinct and more explainable
strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental
results show that we can extract several rules describing the strategy even for
very large systems that do not fit in memory, and based on the rules explain the
erroneous behaviour."
acknowledgement: This research was funded in part by Austrian Science Fund (FWF) Grant
No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989
(QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme
(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013)
REA Grant No 291734.
alternative_title:
- LNCS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- 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: Andreas
full_name: Fellner, Andreas
id: 42BABFB4-F248-11E8-B48F-1D18A9856A87
last_name: Fellner
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: 'Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample
explanation by learning small strategies in Markov decision processes. In: Vol
9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10'
apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J.
(2015). Counterexample explanation by learning small strategies in Markov decision
processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification,
San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner,
and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in
Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.
ieee: 'T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample
explanation by learning small strategies in Markov decision processes,” presented
at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015,
vol. 9206, pp. 158–177.'
ista: 'Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample
explanation by learning small strategies in Markov decision processes. CAV: Computer
Aided Verification, LNCS, vol. 9206, 158–177.'
mla: Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies
in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10.
short: T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer,
2015, pp. 158–177.
conference:
end_date: 2015-07-24
location: San Francisco, CA, United States
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:58Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2024-02-21T13:52:07Z
day: '16'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-21690-4_10
ec_funded: 1
intvolume: ' 9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.02834
month: '07'
oa: 1
oa_version: Preprint
page: 158 - 177
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_identifier:
eisbn:
- 978-3-319-21690-4
publication_status: published
publisher: Springer
publist_id: '5564'
quality_controlled: '1'
related_material:
record:
- id: '5549'
relation: research_paper
status: public
scopus_import: 1
status: public
title: Counterexample explanation by learning small strategies in Markov decision
processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '5549'
abstract:
- lang: eng
text: "This repository contains the experimental part of the CAV 2015 publication
Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe
extended the probabilistic model checker PRISM to represent strategies of Markov
Decision Processes as Decision Trees.\r\nThe archive contains a java executable
version of the extended tool (prism_dectree.jar) together with a few examples
of the PRISM benchmark library.\r\nTo execute the program, please have a look
at the README.txt, which provides instructions and further information on the
archive.\r\nThe archive contains scripts that (if run often enough) reproduces
the data presented in the publication."
article_processing_charge: No
author:
- first_name: Andreas
full_name: Fellner, Andreas
id: 42BABFB4-F248-11E8-B48F-1D18A9856A87
last_name: Fellner
citation:
ama: 'Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation
by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28'
apa: 'Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28'
chicago: 'Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes.” Institute
of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28.'
ieee: 'A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation
by Learning Small Strategies in Markov Decision Processes.” Institute of Science
and Technology Austria, 2015.'
ista: 'Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:28.'
mla: 'Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes. Institute
of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.'
short: A. Fellner, (2015).
contributor:
- first_name: Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
datarep_id: '28'
date_created: 2018-12-12T12:31:29Z
date_published: 2015-08-13T00:00:00Z
date_updated: 2024-02-21T13:52:07Z
day: '13'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:ISTA:28
ec_funded: 1
file:
- access_level: open_access
checksum: b8bcb43c0893023cda66c1b69c16ac62
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:31Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5597'
file_name: IST-2015-28-v1+2_Fellner_DataRep.zip
file_size: 49557109
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
keyword:
- Markov Decision Process
- Decision Tree
- Probabilistic Verification
- Counterexample Explanation
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publisher: Institute of Science and Technology Austria
publist_id: '5564'
related_material:
record:
- id: '1603'
relation: popular_science
status: public
status: public
title: 'Experimental part of CAV 2015 publication: Counterexample Explanation by Learning
Small Strategies in Markov Decision Processes'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1512'
abstract:
- lang: eng
text: 'We show that very weak topological assumptions are enough to ensure the existence
of a Helly-type theorem. More precisely, we show that for any non-negative integers
b and d there exists an integer h(b,d) such that the following holds. If F is
a finite family of subsets of R^d such that the ith reduced Betti number (with
Z_2 coefficients in singular homology) of the intersection of any proper subfamily
G of F is at most b for every non-negative integer i less or equal to (d-1)/2,
then F has Helly number at most h(b,d). These topological conditions are sharp:
not controlling any of these first Betti numbers allow for families with unbounded
Helly number. Our proofs combine homological non-embeddability results with a
Ramsey-based approach to build, given an arbitrary simplicial complex K, some
well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent
interest.'
acknowledgement: "PP, ZP and MT were partially supported by the Charles University
Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant
SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant
No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science
Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants
SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was
affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen
för matematik, Kungliga Tekniska Högskolan, then IST Austria."
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via
Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507'
apa: 'Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding
Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG:
Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507'
chicago: Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507.
ieee: 'X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly
numbers via Betti numbers,” presented at the SoCG: Symposium on Computational
Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.'
ista: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers
via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34,
507–521.'
mla: Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol.
34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.
short: X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2015, pp. 507–521.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2024-02-28T12:59:37Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SOCG.2015.507
file:
- access_level: open_access
checksum: e6881df44d87fe0c2529c9f7b2724614
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:09Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4794'
file_name: IST-2016-501-v1+1_46.pdf
file_size: 633712
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 34'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 507 - 521
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5665'
pubrep_id: '501'
quality_controlled: '1'
related_material:
record:
- id: '424'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Bounding Helly numbers via Betti numbers
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '271'
abstract:
- lang: eng
text: We show that a non-singular integral form of degree d is soluble non-trivially
over the integers if and only if it is soluble non-trivially over the reals and
the p-adic numbers, provided that the form has at least (d-\sqrt{d}/2)2^d variables.
This improves on a longstanding result of Birch.
acknowledgement: While working on this paper the authors were supported by the Leverhulme
Trust and ERC grant 306457.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Sean
full_name: Prendiville, Sean
last_name: Prendiville
citation:
ama: Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many
variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234.
doi:10.1515/crelle-2014-0122
apa: Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem
on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik.
Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122
chicago: Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem
on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik.
Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122.
ieee: T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms
in many variables,” Journal fur die Reine und Angewandte Mathematik, vol.
2017, no. 731. Walter de Gruyter, pp. 203–234.
ista: Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many
variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.
mla: Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem
on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik,
vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122.
short: T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik
2017 (n.d.) 203–234.
date_created: 2018-12-11T11:45:32Z
date_published: 2015-02-20T00:00:00Z
date_updated: 2024-03-05T12:09:22Z
day: '20'
doi: 10.1515/crelle-2014-0122
extern: '1'
external_id:
arxiv:
- '1402.4489'
intvolume: ' 2017'
issue: '731'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.4489
month: '02'
oa: 1
oa_version: Preprint
page: 203 - 234
publication: Journal fur die Reine und Angewandte Mathematik
publication_identifier:
issn:
- 0075-4102
publication_status: submitted
publisher: Walter de Gruyter
publist_id: '7631'
quality_controlled: '1'
related_material:
record:
- id: '256'
relation: later_version
status: public
status: public
title: Improvements in Birch's theorem on forms in many variables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2017
year: '2015'
...
---
_id: '1675'
abstract:
- lang: eng
text: Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as
protection to a shared resource. The basic idea is to ask the service requestor
to dedicate some non-trivial amount of computational work to every request. The
original applications included prevention of spam and protection against denial
of service attacks. More recently, PoWs have been used to prevent double spending
in the Bitcoin digital currency system. In this work, we put forward an alternative
concept for PoWs - so-called proofs of space (PoS), where a service requestor
must dedicate a significant amount of disk space as opposed to computation. We
construct secure PoS schemes in the random oracle model (with one additional mild
assumption required for the proof to go through), using graphs with high “pebbling
complexity” and Merkle hash-trees. We discuss some applications, including follow-up
work where a decentralized digital currency scheme called Spacecoin is constructed
that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending.
The main technical contribution of this work is the construction of (directed,
loop-free) graphs on N vertices with in-degree O(log logN) such that even if one
places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of
nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble
on a node if all its parents have a pebble).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th
Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29'
apa: 'Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015).
Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605).
Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29'
chicago: Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof
Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605.
Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29.
ieee: S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,”
in 35th Annual Cryptology Conference, Santa Barbara, CA, United States,
2015, vol. 9216, pp. 585–605.
ista: 'Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space.
35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference,
LNCS, vol. 9216, 585–605.'
mla: Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference,
vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29.
short: S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual
Cryptology Conference, Springer, 2015, pp. 585–605.
conference:
end_date: 2015-08-20
location: Santa Barbara, CA, United States
name: 'CRYPTO: International Cryptology Conference'
start_date: 2015-08-16
date_created: 2018-12-11T11:53:24Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2024-03-20T08:31:49Z
day: '01'
department:
- _id: VlKo
- _id: KrPi
doi: 10.1007/978-3-662-48000-7_29
ec_funded: 1
intvolume: ' 9216'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2013/796.pdf
month: '08'
oa: 1
oa_version: Preprint
page: 585 - 605
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: 35th Annual Cryptology Conference
publication_identifier:
isbn:
- '9783662479995'
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '5474'
pubrep_id: '671'
quality_controlled: '1'
related_material:
record:
- id: '2274'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Proofs of space
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9216
year: '2015'
...
---
_id: '15160'
abstract:
- lang: eng
text: The circadian clock orchestrates global changes in transcriptional regulation
on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven
by other bHLH-PAS transcription factors have a homologous repressor that modulates
activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1.
We show here that the cancer/testis antigen PASD1 fulfills this role to suppress
circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with
the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1
is restricted to germline tissues in healthy individuals but can be induced in
cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human
cancer cells significantly increases the amplitude of transcriptional oscillations
to generate more robust circadian rhythms. Our results describe a function for
a germline-specific protein in regulation of the circadian clock and provide a
molecular link from oncogenic transformation to suppression of circadian rhythms.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Stacy L.
full_name: Harvey, Stacy L.
last_name: Harvey
- first_name: Patrick J.
full_name: Sammons, Patrick J.
last_name: Sammons
- first_name: Amanda P.
full_name: Anderson, Amanda P.
last_name: Anderson
- first_name: Hema M.
full_name: Kopalle, Hema M.
last_name: Kopalle
- first_name: Alison H.
full_name: Banham, Alison H.
last_name: Banham
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences
the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031
apa: Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H.
M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences
the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031
chicago: Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson,
Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen
PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031.
ieee: A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian
clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015.
ista: Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch
CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular
Cell. 58(5), 743–754.
mla: Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian
Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.
short: A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H.
Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.
date_created: 2024-03-21T07:58:08Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2024-03-25T11:52:26Z
day: '04'
doi: 10.1016/j.molcel.2015.03.031
extern: '1'
intvolume: ' 58'
issue: '5'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2015.03.031
month: '06'
oa: 1
oa_version: Published Version
page: 743-754
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cancer/Testis antigen PASD1 silences the circadian clock
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2015'
...
---
_id: '15159'
abstract:
- lang: eng
text: It is widely recognized that BMAL1 is an essential subunit of the primary
transcription factor that drives rhythmic circadian transcription in the nucleus.
In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts
with translational machinery in the cytosol to stimulate protein synthesis in
response to mTOR signaling.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Hande
full_name: Asimgil, Hande
last_name: Asimgil
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation
factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006
apa: Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights
as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006
chicago: Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1
Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier,
2015. https://doi.org/10.1016/j.tibs.2015.07.006.
ieee: A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as
a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9.
Elsevier, pp. 489–490, 2015.
ista: Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation
factor. Trends in Biochemical Sciences. 40(9), 489–490.
mla: Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.”
Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90,
doi:10.1016/j.tibs.2015.07.006.
short: A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40
(2015) 489–490.
date_created: 2024-03-21T07:57:44Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2024-03-25T11:53:58Z
day: '01'
doi: 10.1016/j.tibs.2015.07.006
extern: '1'
intvolume: ' 40'
issue: '9'
keyword:
- Molecular Biology
- Biochemistry
language:
- iso: eng
month: '09'
oa_version: None
page: 489-490
publication: Trends in Biochemical Sciences
publication_identifier:
issn:
- 0968-0004
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytosolic BMAL1 moonlights as a translation factor
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2015'
...
---
_id: '1619'
abstract:
- lang: eng
text: The emergence of drug resistant pathogens is a serious public health problem.
It is a long-standing goal to predict rates of resistance evolution and design
optimal treatment strategies accordingly. To this end, it is crucial to reveal
the underlying causes of drug-specific differences in the evolutionary dynamics
leading to resistance. However, it remains largely unknown why the rates of resistance
evolution via spontaneous mutations and the diversity of mutational paths vary
substantially between drugs. Here we comprehensively quantify the distribution
of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics,
in the presence of eight antibiotics representing the main modes of action. Using
precise high-throughput fitness measurements for genome-wide Escherichia coli
gene deletion strains, we find that the width of the DFE varies dramatically between
antibiotics and, contrary to conventional wisdom, for some drugs the DFE width
is lower than in the absence of stress. We show that this previously underappreciated
divergence in DFE width among antibiotics is largely caused by their distinct
drug-specific dose-response characteristics. Unlike the DFE, the magnitude of
the changes in tolerated drug concentration resulting from genome-wide mutations
is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin,
i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin
than for other drugs. A population genetics model predicts that resistance evolution
for drugs with this property is severely limited and confined to reproducible
mutational paths. We tested this prediction in laboratory evolution experiments
using the “morbidostat”, a device for evolving bacteria in well-controlled drug
environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible
mutations—an almost paradoxical behavior since this drug causes DNA damage and
increases the mutation rate. Overall, we identified novel quantitative characteristics
of the evolutionary landscape that provide the conceptual foundation for predicting
the dynamics of drug resistance evolution.
article_number: e1002299
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Dravecka, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Dravecka
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay
full_name: Ayhan, Dilay
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of
evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11).
doi:10.1371/journal.pbio.1002299
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak,
E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary
dynamics leading to drug resistance. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1002299
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants
of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.
ieee: G. Chevereau et al., “Quantifying the determinants of evolutionary
dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public
Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach
MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug
resistance. PLoS Biology. 13(11), e1002299.
mla: Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary
Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299,
Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak,
M.T. Bollenbach, PLoS Biology 13 (2015).
date_created: 2018-12-11T11:53:04Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2024-03-28T23:30:28Z
day: '18'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299
ec_funded: 1
file:
- access_level: open_access
checksum: 0e82e3279f50b15c6c170c042627802b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:00Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4723'
file_name: IST-2016-468-v1+1_journal.pbio.1002299.pdf
file_size: 1387760
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5547'
pubrep_id: '468'
quality_controlled: '1'
related_material:
record:
- id: '9711'
relation: research_data
status: public
- id: '9765'
relation: research_data
status: public
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantifying the determinants of evolutionary dynamics leading to drug resistance
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2015'
...
---
_id: '10382'
abstract:
- lang: eng
text: 'Protein oligomers have been implicated as toxic agents in a wide range of
amyloid-related diseases. However, it has remained unsolved whether the oligomers
are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct.
Analogously, it has not been resolved if the amyloid nucleation process is a classical
one-step nucleation process or a two-step process involving prenucleation clusters.
We use coarse-grained computer simulations to study the effect of nonspecific
attractions between peptides on the primary nucleation process underlying amyloid
fibrillization. We find that, for peptides that do not attract, the classical
one-step nucleation mechanism is possible but only at nonphysiologically high
peptide concentrations. At low peptide concentrations, which mimic the physiologically
relevant regime, attractive interpeptide interactions are essential for fibril
formation. Nucleation then inevitably takes place through a two-step mechanism
involving prefibrillar oligomers. We show that oligomers not only help peptides
meet each other but also, create an environment that facilitates the conversion
of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically
does not proceed through the most prevalent oligomers but through an oligomer
size that is only observed in rare fluctuations, which is why such aggregates
might be hard to capture experimentally. Finally, we find that the nucleation
of amyloid fibrils cannot be described by classical nucleation theory: in the
two-step mechanism, the critical nucleus size increases with increases in both
concentration and interpeptide interactions, which is in direct contrast with
predictions from classical nucleation theory.'
acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs,
for helpful discussions. A.Š. acknowledges support from the Human Frontier Science
Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical
Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the
Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology
and Biological Sciences Research Council. D.F. acknowledges European Research Council
Advanced Grant 227758.
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Yassmine C.
full_name: Chebaro, Yassmine C.
last_name: Chebaro
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions
in amyloid nucleation. Proceedings of the National Academy of Sciences.
2014;111(50):17869-17874. doi:10.1073/pnas.1410159111
apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial
role of nonspecific interactions in amyloid nucleation. Proceedings of the
National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111
chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel.
“Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.
ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of
nonspecific interactions in amyloid nucleation,” Proceedings of the National
Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874,
2014.
ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific
interactions in amyloid nucleation. Proceedings of the National Academy of Sciences.
111(50), 17869–17874.
mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid
Nucleation.” Proceedings of the National Academy of Sciences, vol. 111,
no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.
short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National
Academy of Sciences 111 (2014) 17869–17874.
date_created: 2021-11-29T13:09:53Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-11-29T13:29:05Z
day: '01'
doi: 10.1073/pnas.1410159111
extern: '1'
external_id:
arxiv:
- '1412.0897'
pmid:
- '25453085'
intvolume: ' 111'
issue: '50'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/111/50/17869
month: '12'
oa: 1
oa_version: Published Version
page: 17869-17874
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: Crucial role of nonspecific interactions in amyloid nucleation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '10383'
abstract:
- lang: eng
text: We use numerical simulations to compute the equation of state of a suspension
of spherical self-propelled nanoparticles in two and three dimensions. We study
in detail the effect of excluded volume interactions and confinement as a function
of the system's temperature, concentration, and strength of the propulsion. We
find a striking nonmonotonic dependence of the pressure on the temperature and
provide simple scaling arguments to predict and explain the occurrence of such
anomalous behavior. We explicitly show how our results have important implications
for the effective forces on passive components suspended in a bath of active particles.
article_number: '052303'
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mallory, S. A.
last_name: Mallory
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
citation:
ama: Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties
of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303
apa: Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous
thermomechanical properties of a self-propelled colloidal fluid. Physical Review
E. American Physical Society. https://doi.org/10.1103/physreve.89.052303
chicago: Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous
Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical
Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.
ieee: S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical
properties of a self-propelled colloidal fluid,” Physical Review E, vol.
89, no. 5. American Physical Society, 2014.
ista: Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical
properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.
mla: Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled
Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical
Society, 2014, doi:10.1103/physreve.89.052303.
short: S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).
date_created: 2021-11-29T13:10:33Z
date_published: 2014-05-06T00:00:00Z
date_updated: 2021-11-29T13:29:01Z
day: '06'
doi: 10.1103/physreve.89.052303
extern: '1'
external_id:
arxiv:
- '1310.0826'
pmid:
- '25353796'
intvolume: ' 89'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.0826
month: '05'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 1550-2376
issn:
- 1539-3755
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous thermomechanical properties of a self-propelled colloidal fluid
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 89
year: '2014'
...