---
_id: '1171'
article_processing_charge: No
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. Understanding regulatory networks requires more than computing a
multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005'
apa: 'Tkačik, G. (2016). Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005'
chicago: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than
Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural
Features in Gene Regulatory Networks: From Biophysical Constraints to Biological
Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier,
2016. https://doi.org/10.1016/j.plrev.2016.06.005.'
ieee: 'G. Tkačik, “Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp.
166–167, 2016.'
ista: 'Tkačik G. 2016. Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.'
mla: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing
a Multitude of Graph Statistics: Comment on "Drivers of Structural Features
in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"
by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016,
pp. 166–67, doi:10.1016/j.plrev.2016.06.005.'
short: G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
date_created: 2018-12-11T11:50:32Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-09-22T09:50:37Z
day: '01'
department:
- _id: GaTk
doi: 10.1016/j.plrev.2016.06.005
external_id:
isi:
- '000381544100033'
intvolume: ' 17'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 166 - 167
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6185'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Understanding regulatory networks requires more than computing a multitude
of graph statistics: Comment on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function" by O. C. Martin
et al.'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2016'
...
---
_id: '1172'
abstract:
- lang: eng
text: A central issue in cell biology is the physico-chemical basis of organelle
biogenesis in intracellular trafficking pathways, its most impressive manifestation
being the biogenesis of Golgi cisternae. At a basic level, such morphologically
and chemically distinct compartments should arise from an interplay between the
molecular transport and chemical maturation. Here, we formulate analytically tractable,
minimalist models, that incorporate this interplay between transport and chemical
progression in physical space, and explore the conditions for de novo biogenesis
of distinct cisternae. We propose new quantitative measures that can discriminate
between the various models of transport in a qualitative manner-this includes
measures of the dynamics in steady state and the dynamical response to perturbations
of the kind amenable to live-cell imaging.
acknowledgement: H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund
Thattai for critical discussions and suggestions.
article_number: '38840'
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Mustansir
full_name: Barma, Mustansir
last_name: Barma
- first_name: Madan
full_name: Rao, Madan
last_name: Rao
citation:
ama: Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 2016;6.
doi:10.1038/srep38840
apa: Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of
de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep38840
chicago: Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description
of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.
ieee: H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo
biogenesis and transport through Golgi-like cisternae,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.
mla: Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis
and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6,
38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.
short: H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:32Z
date_published: 2016-12-19T00:00:00Z
date_updated: 2025-09-22T09:49:53Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1038/srep38840
external_id:
isi:
- '000389885900001'
file:
- access_level: open_access
checksum: cb378732da885ea4959ec5b845fb6e52
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:56Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4977'
file_name: IST-2017-737-v1+1_srep38840.pdf
file_size: 760967
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6183'
pubrep_id: '737'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonequilibrium description of de novo biogenesis and transport through Golgi-like
cisternae
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '1177'
abstract:
- lang: eng
text: Boldyreva, Palacio and Warinschi introduced a multiple forking game as an
extension of general forking. The notion of (multiple) forking is a useful abstraction
from the actual simulation of cryptographic scheme to the adversary in a security
reduction, and is achieved through the intermediary of a so-called wrapper algorithm.
Multiple forking has turned out to be a useful tool in the security argument of
several cryptographic protocols. However, a reduction employing multiple forking
incurs a significant degradation of (Formula presented.) , where (Formula presented.)
denotes the upper bound on the underlying random oracle calls and (Formula presented.)
, the number of forkings. In this work we take a closer look at the reasons for
the degradation with a tighter security bound in mind. We nail down the exact
set of conditions for success in the multiple forking game. A careful analysis
of the cryptographic schemes and corresponding security reduction employing multiple
forking leads to the formulation of ‘dependence’ and ‘independence’ conditions
pertaining to the output of the wrapper in different rounds. Based on the (in)dependence
conditions we propose a general framework of multiple forking and a General Multiple
Forking Lemma. Leveraging (in)dependence to the full allows us to improve the
degradation factor in the multiple forking game by a factor of (Formula presented.).
By implication, the cost of a single forking involving two random oracles (augmented
forking) matches that involving a single random oracle (elementary forking). Finally,
we study the effect of these observations on the concrete security of existing
schemes employing multiple forking. We conclude that by careful design of the
protocol (and the wrapper in the security reduction) it is possible to harness
our observations to the full extent.
acknowledgement: "We are grateful to the anonymous reviewers for their insightful
comments. The\r\ndetailed reports helped us a lot to address the technical mistakes
as well as to improve the overall presentation of the paper."
article_processing_charge: No
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Sanjit
full_name: Chatterjee, Sanjit
last_name: Chatterjee
citation:
ama: 'Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging
(in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362.
doi:10.1007/s00453-015-9997-6'
apa: 'Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. Springer.
https://doi.org/10.1007/s00453-015-9997-6'
chicago: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer,
2016. https://doi.org/10.1007/s00453-015-9997-6.'
ieee: 'C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74,
no. 4. Springer, pp. 1321–1362, 2016.'
ista: 'Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.'
mla: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74,
no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.'
short: C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.
date_created: 2018-12-11T11:50:33Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2025-09-22T09:49:20Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00453-015-9997-6
external_id:
isi:
- '000373640000005'
intvolume: ' 74'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2013/651
month: '04'
oa: 1
oa_version: Submitted Version
page: 1321 - 1362
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6177'
quality_controlled: '1'
status: public
title: 'A closer look at multiple-forking: Leveraging (in)dependence for a tighter
bound'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 74
year: '2016'
...
---
_id: '1179'
abstract:
- lang: eng
text: "Computational notions of entropy have recently found many applications, including
leakage-resilient cryptography, deterministic encryption or memory delegation.
The two main types of results which make computational notions so useful are (1)
Chain rules, which quantify by how much the computational entropy of a variable
decreases if conditioned on some other variable (2) Transformations, which quantify
to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and
transformations typically lose a significant amount in quality of the entropy,
and are the reason why applying these results one gets rather weak quantitative
security bounds. In this paper we for the first time prove lower bounds in this
context, showing that existing results for transformations are, unfortunately,
basically optimal for non-adaptive black-box reductions (and it’s hard to imagine
how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable
X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y
with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby
distinguishing circuits of size s. A weaker notion is Metric entropy, where we
switch quantifiers, and only require that for every distinguisher of size s, such
a Y exists.\r\n\r\nWe first describe our result concerning transformations. By
definition, HILL implies Metric without any loss in quality. Metric entropy often
comes up in applications, but must be transformed to HILL for meaningful security
guarantees. The best known result states that if a variable X has k bits of Metric
entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2).
We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary.
In fact, we show the stronger result that this loss is already necessary when
transforming so called deterministic real valued Metric entropy to randomised
boolean Metric (both these variants of Metric entropy are implied by HILL without
loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has
k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length
m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We
show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still
leaves a gap of ϵ between the known bound and our lower bound."
acknowledgement: "K. Pietrzak—Supported by the European Research Council consolidator
grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland
(2015/17/N/ST6/03564)."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Skorski
full_name: Maciej, Skorski
last_name: Maciej
citation:
ama: 'Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations.
In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8'
apa: 'Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for
chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC:
Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8'
chicago: 'Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.'
ieee: 'K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules
and transformations,” presented at the TCC: Theory of Cryptography Conference,
Beijing, China, 2016, vol. 9985, pp. 183–203.'
ista: 'Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules
and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985,
183–203.'
mla: 'Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203,
doi:10.1007/978-3-662-53641-4_8.'
short: K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.
conference:
end_date: 2016-11-03
location: Beijing, China
name: 'TCC: Theory of Cryptography Conference'
start_date: 2016-10-31
date_created: 2018-12-11T11:50:34Z
date_published: 2016-10-22T00:00:00Z
date_updated: 2025-09-22T09:48:49Z
day: '22'
department:
- _id: KrPi
doi: 10.1007/978-3-662-53641-4_8
ec_funded: 1
external_id:
isi:
- '000390176000008'
intvolume: ' 9985'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/159
month: '10'
oa: 1
oa_version: Preprint
page: 183 - 203
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6175'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Pseudoentropy: Lower-bounds for chain rules and transformations'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9985
year: '2016'
...
---
_id: '1181'
abstract:
- lang: eng
text: 'This review accompanies a 2016 SFN mini-symposium presenting examples of
current studies that address a central question: How do neural stem cells (NSCs)
divide in different ways to produce heterogeneous daughter types at the right
time and in proper numbers to build a cerebral cortex with the appropriate size
and structure? We will focus on four aspects of corticogenesis: cytokinesis events
that follow apical mitoses of NSCs; coordinating abscission with delamination
from the apical membrane; timing of neurogenesis and its indirect regulation through
emergence of intermediate progenitors; and capacity of single NSCs to generate
the correct number and laminar fate of cortical neurons. Defects in these mechanisms
can cause microcephaly and other brain malformations, and understanding them is
critical to designing diagnostic tools and preventive and corrective therapies.'
acknowledgement: This work was supported by National Institutes of Health Grants R01NS089795
and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777
to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444
and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from
the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent
to L.N. The authors apologize to colleagues whose work could not be cited due to
space limitations.
article_processing_charge: No
author:
- first_name: Noelle
full_name: Dwyer, Noelle
last_name: Dwyer
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Shen
full_name: Chou, Shen
last_name: Chou
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Laurent
full_name: Nguyen, Laurent
last_name: Nguyen
- first_name: Troy
full_name: Ghashghaei, Troy
last_name: Ghashghaei
citation:
ama: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem
cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and
productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016'
apa: 'Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei,
T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating
progenitor behavior and productivity. Journal of Neuroscience. Society
for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016'
chicago: 'Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen,
and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience.
Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016.'
ieee: 'N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei,
“Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society
for Neuroscience, pp. 11394–11401, 2016.'
ista: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural
stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior
and productivity. Journal of Neuroscience. 36(45), 11394–11401.'
mla: 'Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience,
vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016.'
short: N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal
of Neuroscience 36 (2016) 11394–11401.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-11-09T00:00:00Z
date_updated: 2025-09-22T09:48:17Z
day: '09'
department:
- _id: SiHi
doi: 10.1523/JNEUROSCI.2359-16.2016
external_id:
isi:
- '000391054300003'
intvolume: ' 36'
isi: 1
issue: '45'
language:
- iso: eng
month: '11'
oa_version: None
page: 11394 - 11401
project:
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '6172'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2016'
...
---
_id: '1182'
abstract:
- lang: eng
text: 'Balanced knockout tournaments are ubiquitous in sports competitions and are
also used in decisionmaking and elections. The traditional computational question,
that asks to compute a draw (optimal draw) that maximizes the winning probability
for a distinguished player, has received a lot of attention. Previous works consider
the problem where the pairwise winning probabilities are known precisely, while
we study how robust is the winning probability with respect to small errors in
the pairwise winning probabilities. First, we present several illuminating examples
to establish: (a) there exist deterministic tournaments (where the pairwise winning
probabilities are 0 or 1) where one optimal draw is much more robust than the
other; and (b) in general, there exist tournaments with slightly suboptimal draws
that are more robust than all the optimal draws. The above examples motivate the
study of the computational problem of robust draws that guarantee a specified
winning probability. Second, we present a polynomial-time algorithm for approximating
the robustness of a draw for sufficiently small errors in pairwise winning probabilities,
and obtain that the stated computational problem is NP-complete. We also show
that two natural cases of deterministic tournaments where the optimal draw could
be computed in polynomial time also admit polynomial-time algorithms to compute
robust optimal draws.'
article_processing_charge: No
arxiv: 1
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: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout
tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in
balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the
IJCAI: International Joint Conference on Artificial Intelligence, New York, NY,
USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust
Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced
knockout tournaments,” presented at the IJCAI: International Joint Conference
on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.'
ista: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout
tournaments. IJCAI: International Joint Conference on Artificial Intelligence
vol. 2016–January, 172–179.'
mla: Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments.
Vol. 2016–January, AAAI Press, 2016, pp. 172–79.
short: K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.
conference:
end_date: 2016-07-15
location: New York, NY, USA
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2016-07-09
corr_author: '1'
date_created: 2018-12-11T11:50:35Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-04-22T13:42:22Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1604.05090'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05090
month: '01'
oa: 1
oa_version: Preprint
page: 172 - 179
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _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
publication_status: published
publisher: AAAI Press
publist_id: '6171'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: https://www.ijcai.org/proceedings/2016
scopus_import: '1'
status: public
title: Robust draws in balanced knockout tournaments
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-January
year: '2016'
...
---
_id: '11834'
abstract:
- lang: eng
text: "We present a deterministic incremental algorithm for exactly maintaining
the size of a minimum cut with ~O(1) amortized time per edge insertion and O(1)
query time. This result partially answers an open question posed by Thorup [Combinatorica
2007]. It also stays in sharp contrast to a polynomial conditional lower-bound
for the fully-dynamic weighted minimum cut problem. Our algorithm is obtained
by combining a recent sparsification technique of Kawarabayashi and Thorup [STOC
2015] and an exact incremental algorithm of Henzinger [J. of Algorithm 1997].\r\n\r\nWe
also study space-efficient incremental algorithms for the minimum cut problem.
Concretely, we show that there exists an O(n log n/epsilon^2) space Monte-Carlo
algorithm that can process a stream of edge insertions starting from an empty
graph, and with high probability, the algorithm maintains a (1+epsilon)-approximation
to the minimum cut. The algorithm has ~O(1) amortized update-time and constant
query-time."
alternative_title:
- LIPIcs
article_number: '46'
article_processing_charge: No
arxiv: 1
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Mikkel
full_name: Thorup, Mikkel
last_name: Thorup
citation:
ama: 'Goranci G, Henzinger M, Thorup M. Incremental exact min-cut in poly-logarithmic
amortized update time. In: 24th Annual European Symposium on Algorithms.
Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ESA.2016.46'
apa: 'Goranci, G., Henzinger, M., & Thorup, M. (2016). Incremental exact min-cut
in poly-logarithmic amortized update time. In 24th Annual European Symposium
on Algorithms (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.ESA.2016.46'
chicago: Goranci, Gramoz, Monika Henzinger, and Mikkel Thorup. “Incremental Exact
Min-Cut in Poly-Logarithmic Amortized Update Time.” In 24th Annual European
Symposium on Algorithms, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPICS.ESA.2016.46.
ieee: G. Goranci, M. Henzinger, and M. Thorup, “Incremental exact min-cut in poly-logarithmic
amortized update time,” in 24th Annual European Symposium on Algorithms,
Aarhus, Denmark, 2016, vol. 57.
ista: 'Goranci G, Henzinger M, Thorup M. 2016. Incremental exact min-cut in poly-logarithmic
amortized update time. 24th Annual European Symposium on Algorithms. ESA: Annual
European Symposium on Algorithms, LIPIcs, vol. 57, 46.'
mla: Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Poly-Logarithmic Amortized
Update Time.” 24th Annual European Symposium on Algorithms, vol. 57, 46,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ESA.2016.46.
short: G. Goranci, M. Henzinger, M. Thorup, in:, 24th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2022-08-12T10:58:32Z
date_published: 2016-08-18T00:00:00Z
date_updated: 2024-11-06T11:58:55Z
day: '18'
doi: 10.4230/LIPICS.ESA.2016.46
extern: '1'
external_id:
arxiv:
- '1611.06500'
intvolume: ' 57'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2016.46
month: '08'
oa: 1
oa_version: Published Version
publication: 24th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- 978-3-95977-015-6
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental exact min-cut in poly-logarithmic amortized update time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '11835'
abstract:
- lang: eng
text: "During the last 10 years it has become popular to study dynamic graph problems
in a emergency planning or sensitivity setting: Instead of considering the general
fully dynamic problem, we only have to process a single batch update of size d;
after the update we have to answer queries.\r\n\r\nIn this paper, we consider
the dynamic subgraph connectivity problem with sensitivity d: We are given a graph
of which some vertices are activated and some are deactivated. After that we get
a single update in which the states of up to $d$ vertices are changed. Then we
get a sequence of connectivity queries in the subgraph of activated vertices.\r\n\r\nWe
present the first fully dynamic algorithm for this problem which has an update
and query time only slightly worse than the best decremental algorithm. In addition,
we present the first incremental algorithm which is tight with respect to the
best known conditional lower bound; moreover, the algorithm is simple and we believe
it is implementable and efficient in practice."
alternative_title:
- LIPIcs
article_number: '48'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan
full_name: Neumann, Stefan
last_name: Neumann
citation:
ama: 'Henzinger M, Neumann S. Incremental and fully dynamic subgraph connectivity
for emergency planning. In: 24th Annual European Symposium on Algorithms.
Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ESA.2016.48'
apa: 'Henzinger, M., & Neumann, S. (2016). Incremental and fully dynamic subgraph
connectivity for emergency planning. In 24th Annual European Symposium on Algorithms
(Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ESA.2016.48'
chicago: Henzinger, Monika, and Stefan Neumann. “Incremental and Fully Dynamic Subgraph
Connectivity for Emergency Planning.” In 24th Annual European Symposium on
Algorithms, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
https://doi.org/10.4230/LIPICS.ESA.2016.48.
ieee: M. Henzinger and S. Neumann, “Incremental and fully dynamic subgraph connectivity
for emergency planning,” in 24th Annual European Symposium on Algorithms,
Aarhus, Denmark, 2016, vol. 57.
ista: 'Henzinger M, Neumann S. 2016. Incremental and fully dynamic subgraph connectivity
for emergency planning. 24th Annual European Symposium on Algorithms. ESA: Annual
European Symposium on Algorithms, LIPIcs, vol. 57, 48.'
mla: Henzinger, Monika, and Stefan Neumann. “Incremental and Fully Dynamic Subgraph
Connectivity for Emergency Planning.” 24th Annual European Symposium on Algorithms,
vol. 57, 48, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ESA.2016.48.
short: M. Henzinger, S. Neumann, in:, 24th Annual European Symposium on Algorithms,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2022-08-12T11:05:41Z
date_published: 2016-08-18T00:00:00Z
date_updated: 2024-11-06T11:59:06Z
day: '18'
doi: 10.4230/LIPICS.ESA.2016.48
extern: '1'
external_id:
arxiv:
- '1611.05248'
intvolume: ' 57'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2016.48
month: '08'
oa: 1
oa_version: Published Version
publication: 24th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- 978-3-95977-015-6
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental and fully dynamic subgraph connectivity for emergency planning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '11836'
abstract:
- lang: eng
text: "Given a graph where vertices are partitioned into k terminals and non-terminals,
the goal is to compress the graph (i.e., reduce the number of non-terminals) using
minor operations while preserving terminal distances approximately. The distortion
of a compressed graph is the maximum multiplicative blow-up of distances between
all pairs of terminals. We study the trade-off between the number of non-terminals
and the distortion. This problem generalizes the Steiner Point Removal (SPR) problem,
in which all non-terminals must be removed.\r\n\r\nWe introduce a novel black-box
reduction to convert any lower bound on distortion for the SPR problem into a
super-linear lower bound on the number of non-terminals, with the same distortion,
for our problem. This allows us to show that there exist graphs such that every
minor with distortion less than 2 / 2.5 / 3 must have Omega(k^2) / Omega(k^{5/4})
/ Omega(k^{6/5}) non-terminals, plus more trade-offs in between. The black-box
reduction has an interesting consequence: if the tight lower bound on distortion
for the SPR problem is super-constant, then allowing any O(k) non-terminals will
not help improving the lower bound to a constant.\r\n\r\nWe also build on the
existing results on spanners, distance oracles and connected 0-extensions to show
a number of upper bounds for general graphs, planar graphs, graphs that exclude
a fixed minor and bounded treewidth graphs. Among others, we show that any graph
admits a minor with O(log k) distortion and O(k^2) non-terminals, and any planar
graph admits a minor with\r\n1 + epsilon distortion and ~O((k/epsilon)^2) non-terminals."
alternative_title:
- LIPIcs
article_number: '131'
article_processing_charge: No
arxiv: 1
author:
- first_name: Yun Kuen
full_name: Cheung, Yun Kuen
last_name: Cheung
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Cheung YK, Goranci G, Henzinger M. Graph minors for preserving terminal distances
approximately - lower and upper bounds. In: 43rd International Colloquium on
Automata, Languages, and Programming. Vol 55. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2016. doi:10.4230/LIPICS.ICALP.2016.131'
apa: 'Cheung, Y. K., Goranci, G., & Henzinger, M. (2016). Graph minors for preserving
terminal distances approximately - lower and upper bounds. In 43rd International
Colloquium on Automata, Languages, and Programming (Vol. 55). Rome, Italy:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2016.131'
chicago: Cheung, Yun Kuen, Gramoz Goranci, and Monika Henzinger. “Graph Minors for
Preserving Terminal Distances Approximately - Lower and Upper Bounds.” In 43rd
International Colloquium on Automata, Languages, and Programming, Vol. 55.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPICS.ICALP.2016.131.
ieee: Y. K. Cheung, G. Goranci, and M. Henzinger, “Graph minors for preserving terminal
distances approximately - lower and upper bounds,” in 43rd International Colloquium
on Automata, Languages, and Programming, Rome, Italy, 2016, vol. 55.
ista: 'Cheung YK, Goranci G, Henzinger M. 2016. Graph minors for preserving terminal
distances approximately - lower and upper bounds. 43rd International Colloquium
on Automata, Languages, and Programming. ICALP: International Colloquium on Automata,
Languages, and Programming, LIPIcs, vol. 55, 131.'
mla: Cheung, Yun Kuen, et al. “Graph Minors for Preserving Terminal Distances Approximately
- Lower and Upper Bounds.” 43rd International Colloquium on Automata, Languages,
and Programming, vol. 55, 131, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPICS.ICALP.2016.131.
short: Y.K. Cheung, G. Goranci, M. Henzinger, in:, 43rd International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2016.
conference:
end_date: 2016-07-15
location: Rome, Italy
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2016-07-12
date_created: 2022-08-12T11:16:01Z
date_published: 2016-08-23T00:00:00Z
date_updated: 2024-11-06T11:58:15Z
day: '23'
doi: 10.4230/LIPICS.ICALP.2016.131
extern: '1'
external_id:
arxiv:
- '1604.08342'
intvolume: ' 55'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPICS.ICALP.2016.131
month: '08'
oa: 1
oa_version: Published Version
publication: 43rd International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- 978-3-95977-013-2
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Graph minors for preserving terminal distances approximately - lower and upper
bounds
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1184'
abstract:
- lang: eng
text: Across multicellular organisms, the costs of reproduction and self-maintenance
result in a life history trade-off between fecundity and longevity. Queens of
perennial social Hymenoptera are both highly fertile and long-lived, and thus,
this fundamental trade-off is lacking. Whether social insect males similarly evade
the fecundity/longevity trade-off remains largely unstudied. Wingless males of
the ant genus Cardiocondyla stay in their natal colonies throughout their relatively
long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla
obscurior males that were allowed to mate with large numbers of female sexuals
had a shortened life span compared to males that mated at a low frequency or virgin
males. Although frequent mating negatively affects longevity, males clearly benefit
from a “live fast, die young strategy” by inseminating as many female sexuals
as possible at a cost to their own survival.
acknowledgement: 'German Science Foundation. Grant Number: SCHR 1135/2-1. We thank
M. Adam for handling part of the setups and J. Zoellner for behavioral observations.'
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology
and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474
apa: Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in
ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474
chicago: Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity
in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474.
ieee: S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,”
Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906,
2016.
ista: Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males.
Ecology and Evolution. 6(24), 8903–8906.
mla: Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution,
vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.
short: S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-09-22T09:47:16Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1002/ece3.2474
external_id:
isi:
- '000392063300022'
file:
- access_level: open_access
checksum: 789026eb9e1be2a0da08376f29f569cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:12Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5062'
file_name: IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf
file_size: 328414
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 8903 - 8906
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6169'
pubrep_id: '736'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mating and longevity in ant males
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '1185'
abstract:
- lang: eng
text: The developmental programme of the pistil is under the control of both auxin
and cytokinin. Crosstalk between these factors converges on regulation of the
auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription
factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length
and ovule number were reduced. PIN1 expression was also lower in the triple mutant
and the phenotypes could not be rescued by exogenous cytokinin application. pin1
complementation studies using genomic PIN1 constructs showed that the pistil phenotypes
were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without
this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating
the pivotal role of CRFs in auxin-cytokinin crosstalk.
acknowledgement: M.C. was funded by a PhD fellowship from the Università degli Studi
di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca
(MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would
like to thank Andrew MacCabe and Edward Kiegle for editing the paper.
article_processing_charge: No
author:
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Silvia
full_name: Manrique, Silvia
last_name: Manrique
- first_name: Andrea
full_name: Guazzotti, Andrea
last_name: Guazzotti
- first_name: Nadia
full_name: Quadrelli, Nadia
last_name: Quadrelli
- first_name: Marta
full_name: Mendes, Marta
last_name: Mendes
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate
auxin and cytokinin pathways for female reproductive organ development. Development.
2016;143(23):4419-4424. doi:10.1242/dev.143545
apa: Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková,
E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin
pathways for female reproductive organ development. Development. Company
of Biologists. https://doi.org/10.1242/dev.143545
chicago: Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta
Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate
Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development.
Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.
ieee: M. Cucinotta et al., “Cytokinin response factors integrate auxin and
cytokinin pathways for female reproductive organ development,” Development,
vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.
ista: Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo
L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for
female reproductive organ development. Development. 143(23), 4419–4424.
mla: Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin
Pathways for Female Reproductive Organ Development.” Development, vol.
143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.
short: M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková,
L. Colombo, Development 143 (2016) 4419–4424.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-09-22T09:46:43Z
day: '01'
department:
- _id: EvBe
doi: 10.1242/dev.143545
external_id:
isi:
- '000393454100012'
intvolume: ' 143'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 4419 - 4424
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6168'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin response factors integrate auxin and cytokinin pathways for female
reproductive organ development
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 143
year: '2016'
...
---
_id: '1186'
abstract:
- lang: eng
text: The human pathogen Streptococcus pneumoniae is decorated with a special class
of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine
(PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography,
NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies,
we provide structural information of choline-binding protein L (CbpL) and demonstrate
its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated
three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported
in this work for the very first time-, (ii) an unprecedented anchorage module
showing alternate disposition of canonical and non-canonical choline-binding sites
that allows vine-like binding of fully-PCho-substituted teichoic acids (with two
choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural
and infection assays indicate an important role of the whole multimodular protein
allowing both to locate CbpL at specific places on the cell wall and to interact
with host components in order to facilitate pneumococcal lung infection and transmigration
from nasopharynx to the lungs and blood. CbpL implication in both resistance against
killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein
as relevant among the pathogenic arsenal of the pneumococcus.
acknowledgement: We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann,
for technical assistance and Lothar Petruschka for in silico analysis (all Dept.
of Genetics, University of Greifswald). We are further grateful to the staff from
SLS synchrotron beamline for help in data collection. This work was supported by
grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish
Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P
to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to
JAH and FG).
article_number: '38094'
article_processing_charge: No
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Malek
full_name: Saleh, Malek
last_name: Saleh
- first_name: Martín
full_name: Alcorlo, Martín
last_name: Alcorlo
- first_name: Alejandro
full_name: Gómez Mejóa, Alejandro
last_name: Gómez Mejóa
- first_name: David
full_name: Pantoja Uceda, David
last_name: Pantoja Uceda
- first_name: Miguel
full_name: Treviño, Miguel
last_name: Treviño
- first_name: Franziska
full_name: Vob, Franziska
last_name: Vob
- first_name: Mohammed
full_name: Abdullah, Mohammed
last_name: Abdullah
- first_name: Sergio
full_name: Galán Bartual, Sergio
last_name: Galán Bartual
- first_name: Jolien
full_name: Seinen, Jolien
last_name: Seinen
- first_name: Pedro
full_name: Sánchez Murcia, Pedro
last_name: Sánchez Murcia
- first_name: Federico
full_name: Gago, Federico
last_name: Gago
- first_name: Marta
full_name: Bruix, Marta
last_name: Bruix
- first_name: Sven
full_name: Hammerschmidt, Sven
last_name: Hammerschmidt
- first_name: Juan
full_name: Hermoso, Juan
last_name: Hermoso
citation:
ama: Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and
unique teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094
apa: Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda,
D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094
chicago: Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez
Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture
and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL
Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature
Publishing Group, 2016. https://doi.org/10.1038/srep38094.
ieee: J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.
ista: Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D,
Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago
F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique
teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 6, 38094.
mla: Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic
Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal
Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group,
2016, doi:10.1038/srep38094.
short: J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja
Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez
Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6
(2016).
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-05T00:00:00Z
date_updated: 2025-09-22T09:46:12Z
day: '05'
ddc:
- '576'
- '610'
department:
- _id: LeSa
doi: 10.1038/srep38094
external_id:
isi:
- '000389129100001'
file:
- access_level: open_access
checksum: e007d78b483bc59bf5ab98e9d42a6ec1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:18Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4804'
file_name: IST-2017-735-v1+1_srep38094.pdf
file_size: 2716045
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6167'
pubrep_id: '735'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modular architecture and unique teichoic acid recognition features of choline-binding
protein L CbpL contributing to pneumococcal pathogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '11866'
abstract:
- lang: eng
text: "We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time
algorithm for solving the single-source shortest paths problem on distributed
weighted networks (the CONGEST model); here n is the number of nodes in the network
and D is its (hop) diameter. This is the first non-trivial deterministic algorithm
for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation
Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large
as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s
Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running
time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al.
STOC 2011] modulo some lower-order terms, thus essentially settling the status
of this problem which was raised at least a decade ago [Elkin SIGACT News 2004].
It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for
approximating a network’s weighted diameter which almost matches the lower bound
by Holzer et al. [PODC 2012].\r\n\r\nIn achieving this result, we develop two
techniques which might be of independent interest and useful in other settings:
(i) a deterministic process that replaces the “hitting set argument” commonly
used for shortest paths computation in various settings, and (ii) a simple, deterministic,
construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these
techniques with many distributed algorithmic techniques, some of which from problems
that are not directly related to shortest paths, e.g. ruling sets [Goldberg et
al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance
estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads
to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation
O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation
O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights
are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC
2014]. The second result partially answers an open problem raised by McGregor
in 2006 [sublinear.info
, Problem 14]."
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger M, Krinninger S, Nanongkai D. A deterministic almost-tight distributed
algorithm for approximating single-source shortest paths. In: 48th Annual ACM
SIGACT Symposium on Theory of Computing. Association for Computing Machinery;
2016:489-498. doi:10.1145/2897518.2897638'
apa: 'Henzinger, M., Krinninger, S., & Nanongkai, D. (2016). A deterministic
almost-tight distributed algorithm for approximating single-source shortest paths.
In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 489–498).
Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897638'
chicago: Henzinger, Monika, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic
Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.”
In 48th Annual ACM SIGACT Symposium on Theory of Computing, 489–98. Association
for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897638.
ieee: M. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight
distributed algorithm for approximating single-source shortest paths,” in 48th
Annual ACM SIGACT Symposium on Theory of Computing, Cambridge, MA, United
States, 2016, pp. 489–498.
ista: 'Henzinger M, Krinninger S, Nanongkai D. 2016. A deterministic almost-tight
distributed algorithm for approximating single-source shortest paths. 48th Annual
ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing,
489–498.'
mla: Henzinger, Monika, et al. “A Deterministic Almost-Tight Distributed Algorithm
for Approximating Single-Source Shortest Paths.” 48th Annual ACM SIGACT Symposium
on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–98,
doi:10.1145/2897518.2897638.
short: M. Henzinger, S. Krinninger, D. Nanongkai, in:, 48th Annual ACM SIGACT Symposium
on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–498.
conference:
end_date: 2016-06-21
location: Cambridge, MA, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2016-06-19
date_created: 2022-08-16T09:19:31Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-11-06T12:19:26Z
day: '01'
doi: 10.1145/2897518.2897638
extern: '1'
external_id:
arxiv:
- '1504.07056'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.07056
month: '06'
oa: 1
oa_version: Preprint
page: 489 - 498
publication: 48th Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145034132-5
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A deterministic almost-tight distributed algorithm for approximating single-source
shortest paths
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '11867'
abstract:
- lang: eng
text: We present two deterministic dynamic algorithms for the maximum matching problem.
(1) An algorithm that maintains a (2+є)-approximate maximum matching in general
graphs with O(poly(logn, 1/є)) update time. (2) An algorithm that maintains an
αK approximation of the value of the maximum matching with O(n2/K) update time
in bipartite graphs, for every sufficiently large constant positive integer K.
Here, 1≤ αK < 2 is a constant determined by the value of K. Result (1) is the
first deterministic algorithm that can maintain an o(logn)-approximate maximum
matching with polylogarithmic update time, improving the seminal result of Onak
et al. [STOC 2010]. Its approximation guarantee almost matches the guarantee of
the best randomized polylogarithmic update time algorithm [Baswana et al. FOCS
2011]. Result (2) achieves a better-than-two approximation with arbitrarily small
polynomial update time on bipartite graphs. Previously the best update time for
this problem was O(m1/4) [Bernstein et al. ICALP 2015], where m is the current
number of edges in the graph.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Bhattacharya S, Henzinger M, Nanongkai D. New deterministic approximation
algorithms for fully dynamic matching. In: 48th Annual ACM SIGACT Symposium
on Theory of Computing. Association for Computing Machinery; 2016:398-411.
doi:10.1145/2897518.2897568'
apa: 'Bhattacharya, S., Henzinger, M., & Nanongkai, D. (2016). New deterministic
approximation algorithms for fully dynamic matching. In 48th Annual ACM SIGACT
Symposium on Theory of Computing (pp. 398–411). Cambridge, MA, United States:
Association for Computing Machinery. https://doi.org/10.1145/2897518.2897568'
chicago: Bhattacharya, Sayan, Monika Henzinger, and Danupon Nanongkai. “New Deterministic
Approximation Algorithms for Fully Dynamic Matching.” In 48th Annual ACM SIGACT
Symposium on Theory of Computing, 398–411. Association for Computing Machinery,
2016. https://doi.org/10.1145/2897518.2897568.
ieee: S. Bhattacharya, M. Henzinger, and D. Nanongkai, “New deterministic approximation
algorithms for fully dynamic matching,” in 48th Annual ACM SIGACT Symposium
on Theory of Computing, Cambridge, MA, United States, 2016, pp. 398–411.
ista: 'Bhattacharya S, Henzinger M, Nanongkai D. 2016. New deterministic approximation
algorithms for fully dynamic matching. 48th Annual ACM SIGACT Symposium on Theory
of Computing. STOC: Symposium on Theory of Computing, 398–411.'
mla: Bhattacharya, Sayan, et al. “New Deterministic Approximation Algorithms for
Fully Dynamic Matching.” 48th Annual ACM SIGACT Symposium on Theory of Computing,
Association for Computing Machinery, 2016, pp. 398–411, doi:10.1145/2897518.2897568.
short: S. Bhattacharya, M. Henzinger, D. Nanongkai, in:, 48th Annual ACM SIGACT
Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp.
398–411.
conference:
end_date: 2016-06-21
location: Cambridge, MA, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2016-06-19
date_created: 2022-08-16T09:27:35Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-11-06T12:19:37Z
day: '01'
doi: 10.1145/2897518.2897568
extern: '1'
external_id:
arxiv:
- '1604.05765'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05765
month: '06'
oa: 1
oa_version: Preprint
page: 398 - 411
publication: 48th Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145034132-5
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: New deterministic approximation algorithms for fully dynamic matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1188'
abstract:
- lang: eng
text: "We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic constraints-based
modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with
the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation
is solved for the steady state in the WKB\r\napproximation that maps it into the
ground state of a quantum particle in an\r\nAiry potential plus a centrifugal
term. We retrieve scaling laws for growth rate\r\nfluctuations and time response
with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal
populations can have a faster response\r\nto perturbations."
acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant
agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011.
D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa
for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano
and Vera Luz Masoero for useful discussions, also late at night.
article_number: '123502'
article_processing_charge: No
arxiv: 1
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Davide
full_name: Masoero, Davide
last_name: Masoero
citation:
ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics:
Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f'
apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness
maximization, applied to metabolism & growth. Journal of Statistical
Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f'
chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy
Fitness Maximization, Applied to Metabolism & Growth.” Journal of
Statistical Mechanics: Theory and Experiment. IOP Publishing, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.'
ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.'
ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics: Theory
and Experiment. 2016(12), 123502.'
mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness
Maximization, Applied to Metabolism & Growth.” Journal of Statistical
Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing,
2016, doi:10.1088/1742-5468/aa4e8f.'
short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and
Experiment 2016 (2016).'
date_created: 2018-12-11T11:50:37Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2025-09-22T09:45:38Z
day: '30'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa4e8f
ec_funded: 1
external_id:
arxiv:
- '1606.09048'
isi:
- '000391973900001'
intvolume: ' 2016'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.09048
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_status: published
publisher: IOP Publishing
publist_id: '6165'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asymptotic analysis of noisy fitness maximization, applied to metabolism &
growth
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2016
year: '2016'
...
---
_id: '1189'
abstract:
- lang: eng
text: "Within the scope of this thesis, we show that a driven-dissipative system
with\r\nfew ultracold atoms can exhibit dissipatively bound states, even if the
atom-atom\r\ninteraction is purely repulsive. This bond arises due to the dipole-dipole
inter-\r\naction, which is restricted to one of the lower electronic energy states,
resulting\r\nin the distance-dependent coherent population trapping. The quality
of this al-\r\nready established method of dissipative binding is improved and
the application\r\nis extended to higher dimensions and a larger number of atoms.
\ Here, we simu-\r\nlate two- and three-atom systems using an adapted approach
to the Monte Carlo\r\nwave-function method and analyse the results. Finally,
\ we examine the possi-\r\nbility of finding a setting allowing trimer
\ states but prohibiting dimer states.\r\nIn the context of open quantum systems,
such a three-body bound states corre-\r\nsponds to the driven-dissipative analogue
of a Borromean state. These states can\r\nbe detected in modern experiments with
dipolar and Rydberg-dressed ultracold\r\natomic gases.\r\n"
article_processing_charge: No
author:
- first_name: Clemens
full_name: Jochum, Clemens
last_name: Jochum
citation:
ama: Jochum C. Dissipative Few-Body Quantum Systems. 2016.
apa: Jochum, C. (2016). Dissipative Few-Body Quantum Systems. Technical University
Vienna.
chicago: Jochum, Clemens. “Dissipative Few-Body Quantum Systems.” Technical University
Vienna, 2016.
ieee: C. Jochum, “Dissipative Few-Body Quantum Systems,” Technical University Vienna,
2016.
ista: Jochum C. 2016. Dissipative Few-Body Quantum Systems. Technical University
Vienna.
mla: Jochum, Clemens. Dissipative Few-Body Quantum Systems. Technical University
Vienna, 2016.
short: C. Jochum, Dissipative Few-Body Quantum Systems, Technical University Vienna,
2016.
date_created: 2018-12-11T11:50:37Z
date_published: 2016-11-28T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '28'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repositum.tuwien.ac.at/obvutwhs/content/titleinfo/1517088
month: '11'
oa: 1
oa_version: Published Version
page: '94'
publication_status: published
publisher: Technical University Vienna
publist_id: '6164'
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Peter
full_name: Rabl, Peter
last_name: Rabl
title: Dissipative Few-Body Quantum Systems
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '11891'
abstract:
- lang: eng
text: "We study dynamic (1+\U0001D716)-approximation algorithms for the all-pairs
shortest paths problem in unweighted undirected \U0001D45B-node \U0001D45A-edge
graphs under edge deletions. The fastest algorithm for this problem is a randomized
algorithm with a total update time of \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716)
and constant query time by Roditty and Zwick [SIAM J. Comput., 41 (2012), pp.
670--683]. The fastest deterministic algorithm is from a 1981 paper by Even and
Shiloach [J. ACM, 28 (1981), pp. 1--4]; it has a total update time of \U0001D442(\U0001D45A\U0001D45B2)
and constant query time. We improve these results as follows: (1) We present an
algorithm with a total update time of \U0001D442̃ (\U0001D45B5/2/\U0001D716) and
constant query time that has an additive error of 2 in addition to the 1+\U0001D716
multiplicative error. This beats the previous \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716)
time when \U0001D45A=Ω(\U0001D45B3/2). Note that the additive error is unavoidable
since, even in the static case, an \U0001D442(\U0001D45B3−\U0001D6FF)-time (a
so-called truly subcubic) combinatorial algorithm with 1+\U0001D716 multiplicative
error cannot have an additive error less than 2−\U0001D716, unless we make a major
breakthrough for Boolean matrix multiplication [D. Dor, S. Halrepin, and U. Zwick,
SIAM J. Comput., 29 (2000), pp. 1740--1759] and many other long-standing problems
[V. Vassilevska Williams and R. Williams, Proceedings of the 2010 IEEE 51st Annual
Symposium on Foundations of Computer Science, 2010, pp. 645--654]. The algorithm
can also be turned into a (2+\U0001D716)-approximation algorithm (without an additive
error) with the same time guarantees, improving the recent (3+\U0001D716)-approximation
algorithm with \U0001D442̃ (\U0001D45B5/2+\U0001D442(log(1/\U0001D716)/log\U0001D45B√))
running time of Bernstein and Roditty [Proceedings of the Twenty-Second Annual
ACM-SIAM Symposium on Discrete Algorithms, 2011, pp. 1355--1365] in terms of both
approximation and time guarantees. (2) We present a deterministic algorithm with
a total update time of \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716) and a query
time of \U0001D442(loglog\U0001D45B). The algorithm has a multiplicative error
of 1+\U0001D716 and gives the first improved deterministic algorithm since 1981.
It also answers an open question raised by Bernstein in [Proceedings of the Forty-Fifth
Annual ACM Symposium on Theory of Computing, 2013, pp. 725--734]. The deterministic
algorithm can be turned into a deterministic fully dynamic (1+\U0001D716)-approximation
with an amortized update time of \U0001D442̃ (\U0001D45A\U0001D45B/(\U0001D716\U0001D461))
and a query time of \U0001D442̃ (\U0001D461) for every \U0001D461≤\U0001D45B√.
In order to achieve our results, we introduce two new techniques: (i) A monotone
Even--Shiloach tree algorithm which maintains a bounded-distance shortest-paths
tree on a certain type of emulator called a locally persevering emulator. (ii)
A derandomization technique based on moving Even--Shiloach trees as a way to derandomize
the standard random set argument. These techniques might be of independent interest."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger M, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest
paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing.
2016;45(3):947-1006. doi:10.1137/140957299'
apa: 'Henzinger, M., Krinninger, S., & Nanongkai, D. (2016). Dynamic approximate
all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM
Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140957299'
chicago: 'Henzinger, Monika, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic
Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.”
SIAM Journal on Computing. Society for Industrial & Applied Mathematics,
2016. https://doi.org/10.1137/140957299.'
ieee: 'M. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization,” SIAM Journal
on Computing, vol. 45, no. 3. Society for Industrial & Applied Mathematics,
pp. 947–1006, 2016.'
ista: 'Henzinger M, Krinninger S, Nanongkai D. 2016. Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on
Computing. 45(3), 947–1006.'
mla: 'Henzinger, Monika, et al. “Dynamic Approximate All-Pairs Shortest Paths: Breaking
the O(Mn) Barrier and Derandomization.” SIAM Journal on Computing, vol.
45, no. 3, Society for Industrial & Applied Mathematics, 2016, pp. 947–1006,
doi:10.1137/140957299.'
short: M. Henzinger, S. Krinninger, D. Nanongkai, SIAM Journal on Computing 45 (2016)
947–1006.
date_created: 2022-08-17T08:37:00Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2024-11-06T12:23:06Z
day: '01'
doi: 10.1137/140957299
extern: '1'
external_id:
arxiv:
- '1308.0776'
intvolume: ' 45'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1308.0776
month: '05'
oa: 1
oa_version: Preprint
page: 947-1006
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and
derandomization'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2016'
...
---
_id: '1193'
abstract:
- lang: eng
text: We consider the recent formulation of the Algorithmic Lovász Local Lemma [1],
[2] for finding objects that avoid "bad features", or "flaws".
It extends the Moser-Tardos resampling algorithm [3] to more general discrete
spaces. At each step the method picks a flaw present in the current state and
"resamples" it using a "resampling oracle" provided by the
user. However, it is less flexible than the Moser-Tardos method since [1], [2]
require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and
thus can potentially be implemented more efficiently). We formulate a new "commutativity"
condition, and prove that it is sufficient for an arbitrary rule to work. It also
enables an efficient parallelization under an additional assumption. We then show
that existing resampling oracles for perfect matchings and permutations do satisfy
this condition. Finally, we generalize the precondition in [2] (in the case of
symmetric potential causality graphs). This unifies special cases that previously
were treated separately.
acknowledgement: European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no 616160
article_number: '7782993'
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings
- Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December.
IEEE; 2016. doi:10.1109/FOCS.2016.88'
apa: 'Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma.
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science
(Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88'
chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88.
ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings
- Annual IEEE Symposium on Foundations of Computer Science, New Brunswick,
NJ, USA , 2016, vol. 2016–December.
ista: 'Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma.
Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS:
Foundations of Computer Science vol. 2016–December, 7782993.'
mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.
short: V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of
Computer Science, IEEE, 2016.
conference:
end_date: 2016-09-11
location: 'New Brunswick, NJ, USA '
name: 'FOCS: Foundations of Computer Science'
start_date: 2016-09-09
date_created: 2018-12-11T11:50:38Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2025-09-22T09:44:20Z
day: '15'
department:
- _id: VlKo
doi: 10.1109/FOCS.2016.88
ec_funded: 1
external_id:
arxiv:
- '1506.08547'
isi:
- '000391198500082'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.08547v7
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings - Annual IEEE Symposium on Foundations of Computer Science
publication_status: published
publisher: IEEE
publist_id: '6158'
quality_controlled: '1'
related_material:
record:
- id: '5975'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Commutativity in the algorithmic Lovasz local lemma
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2016-December
year: '2016'
...
---
_id: '1195'
abstract:
- lang: eng
text: 'The genetic analysis of experimentally evolving populations typically relies
on short reads from pooled individuals (Pool-Seq). While this method provides
reliable allele frequency estimates, the underlying haplotype structure remains
poorly characterized. With small population sizes and adaptive variants that start
from low frequencies, the interpretation of selection signatures in most Evolve
and Resequencing studies remains challenging. To facilitate the characterization
of selection targets, we propose a new approach that reconstructs selected haplotypes
from replicated time series, using Pool-Seq data. We identify selected haplotypes
through the correlated frequencies of alleles carried by them. Computer simulations
indicate that selected haplotype-blocks of several Mb can be reconstructed with
high confidence and low error rates, even when allele frequencies change only
by 20% across three replicates. Applying this method to real data from D. melanogaster
populations adapting to a hot environment, we identify a selected haplotype-block
of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations
by experimental haplotyping, demonstrating the power and accuracy of our haplotype
reconstruction from Pool-Seq data. We propose that the combination of allele frequency
estimates with haplotype information will provide the key to understanding the
dynamics of adaptive alleles. '
acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics
for discussion and support on the project and par-\r\nticularly N. Barghi for helpful
comments on earlier versions of\r\nthe manuscript. This work was supported
\ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”."
article_processing_charge: No
author:
- first_name: Susan
full_name: Franssen, Susan
last_name: Franssen
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
citation:
ama: Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected
during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184.
doi:10.1093/molbev/msw210
apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of
haplotype-blocks selected during experimental evolution. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210
chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction
of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology
and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.
ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks
selected during experimental evolution.,” Molecular Biology and Evolution,
vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.
ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks
selected during experimental evolution. Molecular Biology and Evolution. 34(1),
174–184.
mla: Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during
Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no.
1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.
short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution
34 (2016) 174–184.
date_created: 2018-12-11T11:50:39Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2025-09-22T09:43:41Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1093/molbev/msw210
ec_funded: 1
external_id:
isi:
- '000396772000009'
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file_name: IST-2017-770-v1+6_Fig5.pdf
file_size: 50705
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has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 174 - 184
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6155'
pubrep_id: '770'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstruction of haplotype-blocks selected during experimental evolution.
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 34
year: '2016'
...
---
_id: '1197'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation
(http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation
(https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National
Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science
Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler
for helpful comments on the manuscript.
article_number: e1005855
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes
of the retinal population code. PLoS Computational Biology. 2016;12(11).
doi:10.1371/journal.pcbi.1005148
apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2016). Error-robust modes of the retinal population code. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148
chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS
Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust
modes of the retinal population code,” PLoS Computational Biology, vol.
12, no. 11. Public Library of Science, 2016.
ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust
modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.”
PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of
Science, 2016, doi:10.1371/journal.pcbi.1005148.
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational
Biology 12 (2016).
date_created: 2018-12-11T11:50:40Z
date_published: 2016-11-17T00:00:00Z
date_updated: 2025-09-22T09:43:12Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005148
external_id:
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- '000391230900008'
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checksum: 47b08cbd4dbf32b25ba161f5f4b262cc
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date_created: 2019-01-25T10:35:00Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5884'
file_name: 2016_PLOS_Prentice.pdf
file_size: 4492021
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language:
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month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6153'
quality_controlled: '1'
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relation: research_data
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scopus_import: '1'
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title: Error-robust modes of the retinal population code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2016'
...