---
_id: '10864'
abstract:
- lang: eng
  text: We prove that every congruence distributive variety has directed Jónsson terms,
    and every congruence modular variety has directed Gumm terms. The directed terms
    we construct witness every case of absorption witnessed by the original Jónsson
    or Gumm terms. This result is equivalent to a pair of claims about absorption
    for admissible preorders in congruence distributive and congruence modular varieties,
    respectively. For finite algebras, these absorption theorems have already seen
    significant applications, but until now, it was not clear if the theorems hold
    for general algebras as well. Our method also yields a novel proof of a result
    by P. Lipparini about the existence of a chain of terms (which we call Pixley
    terms) in varieties that are at the same time congruence distributive and k-permutable
    for some k.
acknowledgement: The second author was supported by National Science Center grant
  DEC-2011-/01/B/ST6/01006.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alexandr
  full_name: Kazda, Alexandr
  id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
  last_name: Kazda
- first_name: Marcin
  full_name: Kozik, Marcin
  last_name: Kozik
- first_name: Ralph
  full_name: McKenzie, Ralph
  last_name: McKenzie
- first_name: Matthew
  full_name: Moore, Matthew
  last_name: Moore
citation:
  ama: 'Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms.
    In: Czelakowski J, ed. <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra,
    and Computer Science</i>. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:<a
    href="https://doi.org/10.1007/978-3-319-74772-9_7">10.1007/978-3-319-74772-9_7</a>'
  apa: 'Kazda, A., Kozik, M., McKenzie, R., &#38; Moore, M. (2018). Absorption and
    directed Jónsson terms. In J. Czelakowski (Ed.), <i>Don Pigozzi on Abstract Algebraic
    Logic, Universal Algebra, and Computer Science</i> (Vol. 16, pp. 203–220). Cham:
    Springer Nature. <a href="https://doi.org/10.1007/978-3-319-74772-9_7">https://doi.org/10.1007/978-3-319-74772-9_7</a>'
  chicago: 'Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption
    and Directed Jónsson Terms.” In <i>Don Pigozzi on Abstract Algebraic Logic, Universal
    Algebra, and Computer Science</i>, edited by J Czelakowski, 16:203–20. OCTR. Cham:
    Springer Nature, 2018. <a href="https://doi.org/10.1007/978-3-319-74772-9_7">https://doi.org/10.1007/978-3-319-74772-9_7</a>.'
  ieee: 'A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson
    terms,” in <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and
    Computer Science</i>, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018,
    pp. 203–220.'
  ista: 'Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson
    terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer
    Science. vol. 16, 203–220.'
  mla: Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” <i>Don Pigozzi
    on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited
    by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:<a href="https://doi.org/10.1007/978-3-319-74772-9_7">10.1007/978-3-319-74772-9_7</a>.
  short: A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don
    Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science,
    Springer Nature, Cham, 2018, pp. 203–220.
corr_author: '1'
date_created: 2022-03-18T10:30:32Z
date_published: 2018-03-21T00:00:00Z
date_updated: 2024-10-09T21:01:50Z
day: '21'
department:
- _id: VlKo
doi: 10.1007/978-3-319-74772-9_7
editor:
- first_name: J
  full_name: Czelakowski, J
  last_name: Czelakowski
external_id:
  arxiv:
  - '1502.01072'
intvolume: '        16'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1502.01072
month: '03'
oa: 1
oa_version: Preprint
page: 203-220
place: Cham
publication: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer
  Science
publication_identifier:
  eisbn:
  - '9783319747729'
  eissn:
  - 2211-2766
  isbn:
  - '9783319747712'
  issn:
  - 2211-2758
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: OCTR
status: public
title: Absorption and directed Jónsson terms
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_id: '10880'
abstract:
- lang: eng
  text: Acquisition of evolutionary novelties is a fundamental process for adapting
    to the external environment and invading new niches and results in the diversification
    of life, which we can see in the world today. How such novel phenotypic traits
    are acquired in the course of evolution and are built up in developing embryos
    has been a central question in biology. Whole-genome duplication (WGD) is a process
    of genome doubling that supplies raw genetic materials and increases genome complexity.
    Recently, it has been gradually revealed that WGD and subsequent fate changes
    of duplicated genes can facilitate phenotypic evolution. Here, we review the current
    understanding of the relationship between WGD and the acquisition of evolutionary
    novelties. We show some examples of this link and discuss how WGD and subsequent
    duplicated genes can facilitate phenotypic evolution as well as when such genomic
    doubling can be advantageous for adaptation.
acknowledgement: This work was supported by JSPS overseas research fellowships (Y.M.)
  and SENSHIN Medical Research Foundation (K.K.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Moriyama
  full_name: Yuuta, Moriyama
  id: 4968E7C8-F248-11E8-B48F-1D18A9856A87
  last_name: Yuuta
  orcid: 0000-0002-2853-8051
- first_name: Kazuko
  full_name: Koshiba-Takeuchi, Kazuko
  last_name: Koshiba-Takeuchi
citation:
  ama: Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the
    emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>.
    2018;17(5):329-338. doi:<a href="https://doi.org/10.1093/bfgp/ely007">10.1093/bfgp/ely007</a>
  apa: Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome
    duplications on the emergence of evolutionary novelties. <i>Briefings in Functional
    Genomics</i>. Oxford University Press. <a href="https://doi.org/10.1093/bfgp/ely007">https://doi.org/10.1093/bfgp/ely007</a>
  chicago: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
    Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional
    Genomics</i>. Oxford University Press, 2018. <a href="https://doi.org/10.1093/bfgp/ely007">https://doi.org/10.1093/bfgp/ely007</a>.
  ieee: M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications
    on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>,
    vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.
  ista: Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications
    on the emergence of evolutionary novelties. Briefings in Functional Genomics.
    17(5), 329–338.
  mla: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
    Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional
    Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a
    href="https://doi.org/10.1093/bfgp/ely007">10.1093/bfgp/ely007</a>.
  short: M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018)
    329–338.
corr_author: '1'
date_created: 2022-03-18T12:40:35Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-10-09T21:01:52Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/bfgp/ely007
external_id:
  isi:
  - '000456054400004'
  pmid:
  - '29579140'
intvolume: '        17'
isi: 1
issue: '5'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1093/bfgp/ely007
month: '09'
oa: 1
oa_version: Published Version
page: 329-338
pmid: 1
publication: Briefings in Functional Genomics
publication_identifier:
  eissn:
  - 2041-2657
  issn:
  - 2041-2649
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Significance of whole-genome duplications on the emergence of evolutionary
  novelties
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2018'
...
---
_id: '10881'
abstract:
- lang: eng
  text: Strigolactones (SLs) are a relatively recent addition to the list of plant
    hormones that control different aspects of plant development. SL signalling is
    perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN
    INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called
    karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2
    1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome
    targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated
    distinct developmental roles for each, but very little is known about these repressors
    in terms of their sequence features. In this study, we performed an extensive
    comparative analysis of SMXLs and determined their phylogenetic and evolutionary
    history in the plant lineage. Our results show that SMXL family members can be
    sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1.
    Further, we identified the clade-specific motifs that have evolved and that might
    act as determinants of SL-KAR signalling specificity. These specificities resulted
    from functional diversities among the clades. Our results suggest that a gradual
    co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an
    increased specificity to both the SL perception and response in land plants.
acknowledgement: "This project received funding from the European Union’s Horizon
  2020 research and innovation programme under the Marie Skłodowska-Curie Actions
  and it is co-financed by the South Moravian Region under grant agreement No. 665860
  (SS). Access to computing and storage facilities owned by parties and projects contributing
  to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects
  of Large Infrastructure for Research, Development, and Innovations’ (LM2010005)
  was greatly appreciated (RSV). The project was funded by The Ministry of Education,
  Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601)
  (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG
  20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr
  Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore
  Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly
  the authors’ views, and the EU is not responsible for any use that may be made of
  the information it contains. "
article_processing_charge: No
article_type: original
author:
- first_name: Taraka Ramji
  full_name: Moturu, Taraka Ramji
  last_name: Moturu
- first_name: Sravankumar
  full_name: Thula, Sravankumar
  last_name: Thula
- first_name: Ravi Kumar
  full_name: Singh, Ravi Kumar
  last_name: Singh
- first_name: Tomasz
  full_name: Nodzyński, Tomasz
  last_name: Nodzyński
- first_name: Radka Svobodová
  full_name: Vařeková, Radka Svobodová
  last_name: Vařeková
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Sibu
  full_name: Simon, Sibu
  last_name: Simon
citation:
  ama: Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification
    of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378.
    doi:<a href="https://doi.org/10.1093/jxb/ery097">10.1093/jxb/ery097</a>
  apa: Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml,
    J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL
    gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a
    href="https://doi.org/10.1093/jxb/ery097">https://doi.org/10.1093/jxb/ery097</a>
  chicago: Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński,
    Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and
    Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>.
    Oxford University Press, 2018. <a href="https://doi.org/10.1093/jxb/ery097">https://doi.org/10.1093/jxb/ery097</a>.
  ieee: T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the
    SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford
    University Press, pp. 2367–2378, 2018.
  ista: Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S.
    2018. Molecular evolution and diversification of the SMXL gene family. Journal
    of Experimental Botany. 69(9), 2367–2378.
  mla: Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the
    SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford
    University Press, 2018, pp. 2367–78, doi:<a href="https://doi.org/10.1093/jxb/ery097">10.1093/jxb/ery097</a>.
  short: T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml,
    S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.
date_created: 2022-03-18T12:43:22Z
date_published: 2018-04-13T00:00:00Z
date_updated: 2025-04-15T07:48:01Z
day: '13'
department:
- _id: JiFr
doi: 10.1093/jxb/ery097
ec_funded: 1
external_id:
  isi:
  - '000430727000016'
  pmid:
  - '29538714'
intvolume: '        69'
isi: 1
issue: '9'
keyword:
- Plant Science
- Physiology
language:
- iso: eng
month: '04'
oa_version: None
page: 2367-2378
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '282300'
  name: Polarity and subcellular dynamics in plants
publication: Journal of Experimental Botany
publication_identifier:
  eissn:
  - 1460-2431
  issn:
  - 0022-0957
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular evolution and diversification of the SMXL gene family
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 69
year: '2018'
...
---
_id: '10882'
abstract:
- lang: eng
  text: 'We introduce Intelligent Annotation Dialogs for bounding box annotation.
    We train an agent to automatically choose a sequence of actions for a human annotator
    to produce a bounding box in a minimal amount of time. Specifically, we consider
    two actions: box verification [34], where the annotator verifies a box generated
    by an object detector, and manual box drawing. We explore two kinds of agents,
    one based on predicting the probability that a box will be positively verified,
    and the other based on reinforcement learning. We demonstrate that (1) our agents
    are able to learn efficient annotation strategies in several scenarios, automatically
    adapting to the image difficulty, the desired quality of the boxes, and the detector
    strength; (2) in all scenarios the resulting annotation dialogs speed up annotation
    compared to manual box drawing alone and box verification alone, while also outperforming
    any fixed combination of verification and drawing in most scenarios; (3) in a
    realistic scenario where the detector is iteratively re-trained, our agents evolve
    a series of strategies that reflect the shifting trade-off between verification
    and drawing as the detector grows stronger.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Jasper
  full_name: Uijlings, Jasper
  last_name: Uijlings
- first_name: Ksenia
  full_name: Konyushkova, Ksenia
  last_name: Konyushkova
- first_name: Christoph
  full_name: Lampert, Christoph
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
- first_name: Vittorio
  full_name: Ferrari, Vittorio
  last_name: Ferrari
citation:
  ama: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs
    for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision
    and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href="https://doi.org/10.1109/cvpr.2018.00956">10.1109/cvpr.2018.00956</a>'
  apa: 'Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning
    intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference
    on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City,
    UT, United States: IEEE. <a href="https://doi.org/10.1109/cvpr.2018.00956">https://doi.org/10.1109/cvpr.2018.00956</a>'
  chicago: Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari.
    “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF
    Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018.
    <a href="https://doi.org/10.1109/cvpr.2018.00956">https://doi.org/10.1109/cvpr.2018.00956</a>.
  ieee: J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent
    dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer
    Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp.
    9175–9184.
  ista: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent
    dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision
    and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition,
    9175–9184.'
  mla: Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.”
    <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE,
    2018, pp. 9175–84, doi:<a href="https://doi.org/10.1109/cvpr.2018.00956">10.1109/cvpr.2018.00956</a>.
  short: J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference
    on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.
conference:
  end_date: 2018-06-23
  location: Salt Lake City, UT, United States
  name: 'CVF: Conference on Computer Vision and Pattern Recognition'
  start_date: 2018-06-18
corr_author: '1'
date_created: 2022-03-18T12:45:09Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2024-10-09T21:02:26Z
day: '17'
department:
- _id: ChLa
doi: 10.1109/cvpr.2018.00956
external_id:
  arxiv:
  - '1712.08087'
  isi:
  - '000457843609036'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: ' https://doi.org/10.48550/arXiv.1712.08087'
month: '12'
oa: 1
oa_version: Preprint
page: 9175-9184
publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
  eissn:
  - 2575-7075
  isbn:
  - '9781538664209'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning intelligent dialogs for bounding box annotation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '10883'
abstract:
- lang: eng
  text: 'Solving parity games, which are equivalent to modal μ-calculus model checking,
    is a central algorithmic problem in formal methods, with applications in reactive
    synthesis, program repair, verification of branching-time properties, etc. Besides
    the standard compu- tation model with the explicit representation of games, another
    important theoretical model of computation is that of set-based symbolic algorithms.
    Set-based symbolic algorithms use basic set operations and one-step predecessor
    operations on the implicit description of games, rather than the explicit representation.
    The significance of symbolic algorithms is that they provide scalable algorithms
    for large finite-state systems, as well as for infinite-state systems with finite
    quotient. Consider parity games on graphs with n vertices and parity conditions
    with d priorities. While there is a rich literature of explicit algorithms for
    parity games, the main results for set-based symbolic algorithms are as follows:
    (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic
    space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations
    and O(n) symbolic space. In this work, our contributions are as follows: (1) We
    present a black-box set-based symbolic algorithm based on the explicit progress
    measure algorithm. Two important consequences of our algorithm are as follows:
    (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially
    many symbolic operations and O(n) symbolic space; and (b) any future improvement
    in progress measure based explicit algorithms immediately imply an efficiency
    improvement in our set-based symbolic algorithm for parity games. (2) We present
    a set-based symbolic algorithm that requires quasi-polynomially many symbolic
    operations and O(d · log n) symbolic space. Moreover, for the important special
    case of d ≤ log n, our algorithm requires only polynomially many symbolic operations
    and poly-logarithmic symbolic space.'
acknowledgement: 'A. S. is fully supported by the Vienna Science and Technology Fund
  (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund
  (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph
  Games). For M.H the research leading to these results has received funding from
  the European Research Council under the European Union’s Seventh Framework Programme
  (FP/2007-2013) /ERC Grant Agreement no. 340506.'
alternative_title:
- EPiC Series in Computing
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: Wolfgang
  full_name: Dvořák, Wolfgang
  last_name: Dvořák
- 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: Alexander
  full_name: Svozil, Alexander
  last_name: Svozil
citation:
  ama: 'Chatterjee K, Dvořák W, Henzinger M, Svozil A. Quasipolynomial set-based symbolic
    algorithms for parity games. In: <i>22nd International Conference on Logic for
    Programming, Artificial Intelligence and Reasoning</i>. Vol 57. EasyChair; 2018:233-253.
    doi:<a href="https://doi.org/10.29007/5z5k">10.29007/5z5k</a>'
  apa: 'Chatterjee, K., Dvořák, W., Henzinger, M., &#38; Svozil, A. (2018). Quasipolynomial
    set-based symbolic algorithms for parity games. In <i>22nd International Conference
    on Logic for Programming, Artificial Intelligence and Reasoning</i> (Vol. 57,
    pp. 233–253). Awassa, Ethiopia: EasyChair. <a href="https://doi.org/10.29007/5z5k">https://doi.org/10.29007/5z5k</a>'
  chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander
    Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In <i>22nd
    International Conference on Logic for Programming, Artificial Intelligence and
    Reasoning</i>, 57:233–53. EasyChair, 2018. <a href="https://doi.org/10.29007/5z5k">https://doi.org/10.29007/5z5k</a>.
  ieee: K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Quasipolynomial set-based
    symbolic algorithms for parity games,” in <i>22nd International Conference on
    Logic for Programming, Artificial Intelligence and Reasoning</i>, Awassa, Ethiopia,
    2018, vol. 57, pp. 233–253.
  ista: 'Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2018. Quasipolynomial set-based
    symbolic algorithms for parity games. 22nd International Conference on Logic for
    Programming, Artificial Intelligence and Reasoning. LPAR: Logic for Programming,
    Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.'
  mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms
    for Parity Games.” <i>22nd International Conference on Logic for Programming,
    Artificial Intelligence and Reasoning</i>, vol. 57, EasyChair, 2018, pp. 233–53,
    doi:<a href="https://doi.org/10.29007/5z5k">10.29007/5z5k</a>.
  short: K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, in:, 22nd International
    Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair,
    2018, pp. 233–253.
conference:
  end_date: 2018-11-21
  location: Awassa, Ethiopia
  name: 'LPAR: Logic for Programming, Artificial Intelligence and Reasoning'
  start_date: 2018-11-17
date_created: 2022-03-18T12:46:32Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2025-07-10T11:50:02Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29007/5z5k
ec_funded: 1
external_id:
  arxiv:
  - '1909.04983'
file:
- access_level: open_access
  checksum: 1229aa8640bd6db610c85decf2265480
  content_type: application/pdf
  creator: dernst
  date_created: 2022-05-17T07:51:08Z
  date_updated: 2022-05-17T07:51:08Z
  file_id: '11392'
  file_name: 2018_EPiCs_Chatterjee.pdf
  file_size: 720893
  relation: main_file
  success: 1
file_date_updated: 2022-05-17T07:51:08Z
has_accepted_license: '1'
intvolume: '        57'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 233-253
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11407
  name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
publication: 22nd International Conference on Logic for Programming, Artificial Intelligence
  and Reasoning
publication_identifier:
  issn:
  - 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quasipolynomial set-based symbolic algorithms for parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2018'
...
---
_id: '11'
abstract:
- lang: eng
  text: We report on a novel strategy to derive mean-field limits of quantum mechanical
    systems in which a large number of particles weakly couple to a second-quantized
    radiation field. The technique combines the method of counting and the coherent
    state approach to study the growth of the correlations among the particles and
    in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon
    system of equations from the Nelson model with ultraviolet cutoff and possibly
    massless scalar field. In particular, we prove the convergence of the reduced
    density matrices (of the nonrelativistic particles and the field bosons) associated
    with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon
    equations in trace norm. Furthermore, we derive explicit bounds on the rate of
    convergence of the one-particle reduced density matrix of the nonrelativistic
    particles in Sobolev norm.
arxiv: 1
author:
- first_name: Nikolai K
  full_name: Leopold, Nikolai K
  id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
  last_name: Leopold
  orcid: 0000-0002-0495-6822
- first_name: Peter
  full_name: Pickl, Peter
  last_name: Pickl
citation:
  ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised
    radiation fields. In: Vol 270. Springer; 2018:185-214. doi:<a href="https://doi.org/10.1007/978-3-030-01602-9_9">10.1007/978-3-030-01602-9_9</a>'
  apa: 'Leopold, N. K., &#38; Pickl, P. (2018). Mean-field limits of particles in
    interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented
    at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer.
    <a href="https://doi.org/10.1007/978-3-030-01602-9_9">https://doi.org/10.1007/978-3-030-01602-9_9</a>'
  chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in
    Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. <a
    href="https://doi.org/10.1007/978-3-030-01602-9_9">https://doi.org/10.1007/978-3-030-01602-9_9</a>.
  ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction
    with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits
    of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.'
  ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction
    with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems
    vol. 270, 185–214.'
  mla: Leopold, Nikolai K., and Peter Pickl. <i>Mean-Field Limits of Particles in
    Interaction with Quantised Radiation Fields</i>. Vol. 270, Springer, 2018, pp.
    185–214, doi:<a href="https://doi.org/10.1007/978-3-030-01602-9_9">10.1007/978-3-030-01602-9_9</a>.
  short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.
conference:
  end_date: 2017-04-01
  location: Munich, Germany
  name: 'MaLiQS: Macroscopic Limits of Quantum Systems'
  start_date: 2017-03-30
date_created: 2018-12-11T11:44:08Z
date_published: 2018-10-27T00:00:00Z
date_updated: 2021-01-12T06:48:16Z
day: '27'
department:
- _id: RoSe
doi: 10.1007/978-3-030-01602-9_9
ec_funded: 1
external_id:
  arxiv:
  - '1806.10843'
intvolume: '       270'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1806.10843
month: '10'
oa: 1
oa_version: Preprint
page: 185 - 214
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '694227'
  name: Analysis of quantum many-body systems
publication_status: published
publisher: Springer
publist_id: '8045'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mean-field limits of particles in interaction with quantised radiation fields
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2018'
...
---
OA_place: publisher
OA_type: diamond
_id: '10286'
abstract:
- lang: eng
  text: 'In this paper, we evaluate clock signals generated in ring oscillators and
    self-timed rings and the way their jitter can be transformed into random numbers.
    We show that counting the periods of the jittery clock signal produces random
    numbers of significantly better quality than the methods in which the jittery
    signal is simply sampled (the case in almost all current methods). Moreover, we
    use the counter values to characterize and continuously monitor the source of
    randomness. However, instead of using the widely used statistical variance, we
    propose to use Allan variance to do so. There are two main advantages: Allan variance
    is insensitive to low frequency noises such as flicker noise that are known to
    be autocorrelated and significantly less circuitry is required for its computation
    than that used to compute commonly used variance. We also show that it is essential
    to use a differential principle of randomness extraction from the jitter based
    on the use of two identical oscillators to avoid autocorrelations originating
    from external and internal global jitter sources and that this fact is valid for
    both kinds of rings. Last but not least, we propose a method of statistical testing
    based on high order Markov model to show the reduced dependencies when the proposed
    randomness extraction is applied.'
article_processing_charge: No
article_type: original
author:
- first_name: Elie Noumon
  full_name: Allini, Elie Noumon
  last_name: Allini
- first_name: Maciej
  full_name: Skórski, Maciej
  id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
  last_name: Skórski
- first_name: Oto
  full_name: Petura, Oto
  last_name: Petura
- first_name: Florent
  full_name: Bernard, Florent
  last_name: Bernard
- first_name: Marek
  full_name: Laban, Marek
  last_name: Laban
- first_name: Viktor
  full_name: Fischer, Viktor
  last_name: Fischer
citation:
  ama: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and
    monitoring of free running oscillators serving as source of randomness. <i>IACR
    Transactions on Cryptographic Hardware and Embedded Systems</i>. 2018;2018(3):214-242.
    doi:<a href="https://doi.org/10.13154/tches.v2018.i3.214-242">10.13154/tches.v2018.i3.214-242</a>
  apa: Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., &#38; Fischer,
    V. (2018). Evaluation and monitoring of free running oscillators serving as source
    of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>.
    International Association for Cryptologic Research. <a href="https://doi.org/10.13154/tches.v2018.i3.214-242">https://doi.org/10.13154/tches.v2018.i3.214-242</a>
  chicago: Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek
    Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators
    Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware
    and Embedded Systems</i>. International Association for Cryptologic Research,
    2018. <a href="https://doi.org/10.13154/tches.v2018.i3.214-242">https://doi.org/10.13154/tches.v2018.i3.214-242</a>.
  ieee: E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer,
    “Evaluation and monitoring of free running oscillators serving as source of randomness,”
    <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol.
    2018, no. 3. International Association for Cryptologic Research, pp. 214–242,
    2018.
  ista: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation
    and monitoring of free running oscillators serving as source of randomness. IACR
    Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.
  mla: Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators
    Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware
    and Embedded Systems</i>, vol. 2018, no. 3, International Association for Cryptologic
    Research, 2018, pp. 214–42, doi:<a href="https://doi.org/10.13154/tches.v2018.i3.214-242">10.13154/tches.v2018.i3.214-242</a>.
  short: E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR
    Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.
corr_author: '1'
date_created: 2021-11-14T23:01:25Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-05-20T09:40:25Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/tches.v2018.i3.214-242
file:
- access_level: open_access
  checksum: b816b848f046c48a8357700d9305dce5
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-11-15T10:27:29Z
  date_updated: 2021-11-15T10:27:29Z
  file_id: '10289'
  file_name: 2018_IACR_Allini.pdf
  file_size: 955755
  relation: main_file
  success: 1
file_date_updated: 2021-11-15T10:27:29Z
has_accepted_license: '1'
intvolume: '      2018'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 214-242
publication: IACR Transactions on Cryptographic Hardware and Embedded Systems
publication_identifier:
  eissn:
  - 2569-2925
publication_status: published
publisher: International Association for Cryptologic Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evaluation and monitoring of free running oscillators serving as source of
  randomness
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: 2018
year: '2018'
...
---
_id: '104'
abstract:
- lang: eng
  text: The biotrophic pathogen Ustilago maydis, the causative agent of corn smut
    disease, infects one of the most important crops worldwide – Zea mays. To successfully
    colonize its host, U. maydis secretes proteins, known as effectors, that suppress
    plant defense responses and facilitate the establishment of biotrophy. In this
    work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence
    and is upregulated during infection. Through microscopic analysis and in vitro
    assays, we show that Cce1 is secreted from hyphae during filamentous growth of
    the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection
    and induce callose deposition as a plant defense response. Cce1 is highly conserved
    among smut fungi and the Ustilago bromivora ortholog complemented the virulence
    defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core
    effector with apoplastic localization that is essential for U. maydis to infect
    its host.
acknowledgement: 'the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22],
  and the Austrian Academy of Science (OEAW).'
article_processing_charge: No
author:
- first_name: Denise
  full_name: Seitner, Denise
  last_name: Seitner
- first_name: Simon
  full_name: Uhse, Simon
  last_name: Uhse
- first_name: Michelle C
  full_name: Gallei, Michelle C
  id: 35A03822-F248-11E8-B48F-1D18A9856A87
  last_name: Gallei
  orcid: 0000-0003-1286-7368
- first_name: Armin
  full_name: Djamei, Armin
  last_name: Djamei
citation:
  ama: Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required
    for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>.
    2018;19(10):2277-2287. doi:<a href="https://doi.org/10.1111/mpp.12698">10.1111/mpp.12698</a>
  apa: Seitner, D., Uhse, S., Gallei, M. C., &#38; Djamei, A. (2018). The core effector
    Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular
    Plant Pathology</i>. Wiley. <a href="https://doi.org/10.1111/mpp.12698">https://doi.org/10.1111/mpp.12698</a>
  chicago: Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The
    Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.”
    <i>Molecular Plant Pathology</i>. Wiley, 2018. <a href="https://doi.org/10.1111/mpp.12698">https://doi.org/10.1111/mpp.12698</a>.
  ieee: D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1
    is required for early infection of maize by Ustilago maydis,” <i>Molecular Plant
    Pathology</i>, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.
  ista: Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required
    for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10),
    2277–2287.
  mla: Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection
    of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>, vol. 19, no. 10,
    Wiley, 2018, pp. 2277–87, doi:<a href="https://doi.org/10.1111/mpp.12698">10.1111/mpp.12698</a>.
  short: D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19
    (2018) 2277–2287.
date_created: 2018-12-11T11:44:39Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-19T10:06:42Z
day: '01'
ddc:
- '580'
department:
- _id: GradSch
doi: 10.1111/mpp.12698
external_id:
  isi:
  - '000445624100006'
file:
- access_level: open_access
  content_type: application/pdf
  creator: dernst
  date_created: 2018-12-18T09:46:00Z
  date_updated: 2018-12-18T09:46:00Z
  file_id: '5740'
  file_name: 2018_MolecPlantPath_Seitner.pdf
  file_size: 682335
  relation: main_file
  success: 1
file_date_updated: 2018-12-18T09:46:00Z
has_accepted_license: '1'
intvolume: '        19'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2277 - 2287
publication: Molecular Plant Pathology
publication_status: published
publisher: Wiley
publist_id: '7950'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The core effector Cce1 is required for early infection of maize by Ustilago
  maydis
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
OA_place: publisher
OA_type: hybrid
_id: '10417'
abstract:
- lang: eng
  text: "We present a new dynamic partial-order reduction method for stateless model
    checking of concurrent programs. A common approach for exploring program behaviors
    relies on enumerating the traces of the program, without storing the visited states
    (aka stateless exploration). As the number of distinct traces grows exponentially,
    dynamic partial-order reduction (DPOR) techniques have been successfully used
    to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
    with the goal of exploring only few representative traces from each class.\r\n\r\nWe
    introduce a new equivalence on traces under sequential consistency semantics,
    which we call the observation equivalence. Two traces are observationally equivalent
    if every read event observes the same write event in both traces. While the traditional
    Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
    We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
    and in many cases even exponentially coarser. We devise a DPOR exploration of
    the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
  Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
  (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
  full_name: Chalupa, Marek
  last_name: Chalupa
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Andreas
  full_name: Pavlogiannis, Andreas
  id: 49704004-F248-11E8-B48F-1D18A9856A87
  last_name: Pavlogiannis
  orcid: 0000-0002-8943-0722
- first_name: Nishant
  full_name: Sinha, Nishant
  last_name: Sinha
- first_name: Kapil
  full_name: Vaidya, Kapil
  last_name: Vaidya
citation:
  ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
    partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>.
    2018;2(POPL). doi:<a href="https://doi.org/10.1145/3158119">10.1145/3158119</a>
  apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K.
    (2018). Data-centric dynamic partial order reduction. <i>Proceedings of the ACM
    on Programming Languages</i>. Los Angeles, CA, United States: Association for
    Computing Machinery. <a href="https://doi.org/10.1145/3158119">https://doi.org/10.1145/3158119</a>'
  chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
    and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings
    of the ACM on Programming Languages</i>. Association for Computing Machinery,
    2018. <a href="https://doi.org/10.1145/3158119">https://doi.org/10.1145/3158119</a>.
  ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
    dynamic partial order reduction,” <i>Proceedings of the ACM on Programming Languages</i>,
    vol. 2, no. POPL. Association for Computing Machinery, 2018.
  ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric
    dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
    2(POPL), 31.
  mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings
    of the ACM on Programming Languages</i>, vol. 2, no. POPL, 31, Association for
    Computing Machinery, 2018, doi:<a href="https://doi.org/10.1145/3158119">10.1145/3158119</a>.
  short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
    of the ACM on Programming Languages 2 (2018).
conference:
  end_date: 2018-01-13
  location: Los Angeles, CA, United States
  name: 'POPL: Programming Languages'
  start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-05-20T09:45:10Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
  arxiv:
  - '1610.01188'
file:
- access_level: open_access
  checksum: b27ab1745f6dba2387deb785798a657c
  content_type: application/pdf
  creator: dernst
  date_created: 2025-05-20T09:44:47Z
  date_updated: 2025-05-20T09:44:47Z
  file_id: '19716'
  file_name: 2018_ACM_Chalupa.pdf
  file_size: 388891
  relation: main_file
  success: 1
file_date_updated: 2025-05-20T09:44:47Z
has_accepted_license: '1'
intvolume: '         2'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
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: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
  eissn:
  - 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
  record:
  - id: '5448'
    relation: earlier_version
    status: public
  - id: '5456'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
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: 2
year: '2018'
...
---
_id: '22'
abstract:
- lang: eng
  text: Conventional ultra-high sensitivity detectors in the millimeter-wave range
    are usually cooled as their own thermal noise at room temperature would mask the
    weak received radiation. The need for cryogenic systems increases the cost and
    complexity of the instruments, hindering the development of, among others, airborne
    and space applications. In this work, the nonlinear parametric upconversion of
    millimeter-wave radiation to the optical domain inside high-quality (Q) lithium
    niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise
    detection. We experimentally demonstrate coherent upconversion of millimeter-wave
    signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing
    the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows
    that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling
    the millimeter-wave WGM, effectively cooling the upconverted mode and allowing
    ultra-low noise detection. By theoretically estimating the sensitivity of a correlation
    radiometer based on the presented scheme, it is found that room-temperature radiometers
    with better sensitivity than state-of-the-art high-electron-mobility transistor
    (HEMT)-based radiometers can be designed. This detection paradigm can be used
    to develop room-temperature instrumentation for radio astronomy, earth observation,
    planetary missions, and imaging systems.
article_processing_charge: No
article_type: original
author:
- first_name: Gabriel
  full_name: Botello, Gabriel
  last_name: Botello
- first_name: Florian
  full_name: Sedlmeir, Florian
  last_name: Sedlmeir
- first_name: Alfredo R
  full_name: Rueda Sanchez, Alfredo R
  id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
  last_name: Rueda Sanchez
  orcid: 0000-0001-6249-5860
- first_name: Kerlos
  full_name: Abdalmalak, Kerlos
  last_name: Abdalmalak
- first_name: Elliott
  full_name: Brown, Elliott
  last_name: Brown
- first_name: Gerd
  full_name: Leuchs, Gerd
  last_name: Leuchs
- first_name: Sascha
  full_name: Preu, Sascha
  last_name: Preu
- first_name: Daniel
  full_name: Segovia Vargas, Daniel
  last_name: Segovia Vargas
- first_name: Dmitry
  full_name: Strekalov, Dmitry
  last_name: Strekalov
- first_name: Luis
  full_name: Munoz, Luis
  last_name: Munoz
- first_name: Harald
  full_name: Schwefel, Harald
  last_name: Schwefel
citation:
  ama: Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave
    photonic radiometers based on efficient electro-optic upconverters. <i>Optica</i>.
    2018;5(10):1210-1219. doi:<a href="https://doi.org/10.1364/OPTICA.5.001210">10.1364/OPTICA.5.001210</a>
  apa: Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E.,
    Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic
    radiometers based on efficient electro-optic upconverters. <i>Optica</i>. <a href="https://doi.org/10.1364/OPTICA.5.001210">https://doi.org/10.1364/OPTICA.5.001210</a>
  chicago: Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak,
    Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave
    Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” <i>Optica</i>,
    2018. <a href="https://doi.org/10.1364/OPTICA.5.001210">https://doi.org/10.1364/OPTICA.5.001210</a>.
  ieee: G. Botello <i>et al.</i>, “Sensitivity limits of millimeter-wave photonic
    radiometers based on efficient electro-optic upconverters,” <i>Optica</i>, vol.
    5, no. 10. pp. 1210–1219, 2018.
  ista: Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G,
    Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity
    limits of millimeter-wave photonic radiometers based on efficient electro-optic
    upconverters. Optica. 5(10), 1210–1219.
  mla: Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers
    Based on Efficient Electro-Optic Upconverters.” <i>Optica</i>, vol. 5, no. 10,
    2018, pp. 1210–19, doi:<a href="https://doi.org/10.1364/OPTICA.5.001210">10.1364/OPTICA.5.001210</a>.
  short: G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G.
    Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica
    5 (2018) 1210–1219.
date_created: 2018-12-11T11:44:12Z
date_published: 2018-10-20T00:00:00Z
date_updated: 2025-07-10T11:52:06Z
day: '20'
department:
- _id: JoFi
doi: 10.1364/OPTICA.5.001210
external_id:
  isi:
  - '000447853100007'
intvolume: '         5'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: 'www.doi.org/10.1364/OPTICA.5.001210 '
month: '10'
oa: 1
oa_version: Published Version
page: 1210-1219
publication: Optica
publication_identifier:
  issn:
  - 2334-2536
publication_status: published
publist_id: '8033'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensitivity limits of millimeter-wave photonic radiometers based on efficient
  electro-optic upconverters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '24'
abstract:
- lang: eng
  text: Partially-observable Markov decision processes (POMDPs) with discounted-sum
    payoff are a standard framework to model a wide range of problems related to decision
    making under uncertainty. Traditionally, the goal has been to obtain policies
    that optimize the expectation of the discounted-sum payoff. A key drawback of
    the expectation measure is that even low probability events with extreme payoff
    can significantly affect the expectation, and thus the obtained policies are not
    necessarily risk-averse. An alternate approach is to optimize the probability
    that the payoff is above a certain threshold, which allows obtaining risk-averse
    policies, but ignores optimization of the expectation. We consider the expectation
    optimization with probabilistic guarantee (EOPG) problem, where the goal is to
    optimize the expectation ensuring that the payoff is above a given threshold with
    at least a specified probability. We present several results on the EOPG problem,
    including the first algorithm to solve it.
acknowledgement: "This research was supported by the Vienna Science and Technology
  Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and
  an ERC Start Grant (279307:Graph Games).\r\n"
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: Adrian
  full_name: Elgyütt, Adrian
  id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
  last_name: Elgyütt
- first_name: Petr
  full_name: Novotny, Petr
  id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
  last_name: Novotny
- first_name: Owen
  full_name: Rouillé, Owen
  last_name: Rouillé
citation:
  ama: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with
    probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018.
    IJCAI; 2018:4692-4699. doi:<a href="https://doi.org/10.24963/ijcai.2018/652">10.24963/ijcai.2018/652</a>'
  apa: 'Chatterjee, K., Elgyütt, A., Novotný, P., &#38; Rouillé, O. (2018). Expectation
    optimization with probabilistic guarantees in POMDPs with discounted-sum objectives
    (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference
    on Artificial Intelligence, Stockholm, Sweden: IJCAI. <a href="https://doi.org/10.24963/ijcai.2018/652">https://doi.org/10.24963/ijcai.2018/652</a>'
  chicago: Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé.
    “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum
    Objectives,” 2018:4692–99. IJCAI, 2018. <a href="https://doi.org/10.24963/ijcai.2018/652">https://doi.org/10.24963/ijcai.2018/652</a>.
  ieee: 'K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization
    with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented
    at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm,
    Sweden, 2018, vol. 2018, pp. 4692–4699.'
  ista: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization
    with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI:
    International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.'
  mla: Chatterjee, Krishnendu, et al. <i>Expectation Optimization with Probabilistic
    Guarantees in POMDPs with Discounted-Sum Objectives</i>. Vol. 2018, IJCAI, 2018,
    pp. 4692–99, doi:<a href="https://doi.org/10.24963/ijcai.2018/652">10.24963/ijcai.2018/652</a>.
  short: K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp.
    4692–4699.
conference:
  end_date: 2018-07-19
  location: Stockholm, Sweden
  name: 'IJCAI: International Joint Conference on Artificial Intelligence'
  start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2025-04-14T13:51:04Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.24963/ijcai.2018/652
ec_funded: 1
external_id:
  arxiv:
  - '1804.10601'
  isi:
  - '000764175404117'
intvolume: '      2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1804.10601
month: '07'
oa: 1
oa_version: Preprint
page: 4692 - 4699
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
  grant_number: ICT15-003
  name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: IJCAI
publist_id: '8031'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum
  objectives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '25'
abstract:
- lang: eng
  text: 'Partially observable Markov decision processes (POMDPs) are the standard
    models for planning under uncertainty with both finite and infinite horizon. Besides
    the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs)
    is another classical objective for POMDPs. In this case, given a set of target
    states and a positive cost for each transition, the optimization objective is
    to minimize the expected total cost until a target state is reached. In the literature,
    RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving
    Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees,
    and HSVI may even fail to terminate its trials. We give the following contributions:
    (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they
    prevent the original HSVI from converging. (2) We present a novel algorithm inspired
    by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees.
    (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples.'
acknowledgement: '∗This work has been supported by Vienna Science and Technology Fund
  (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE),
  and ERC Starting grant (279307: Graph Games). This research was sponsored by the
  Army Research Laboratory and was accomplished under Cooperative Agreement Number
  W911NF-13-2-0045 (ARL Cyber Security CRA). '
article_processing_charge: No
author:
- first_name: Karel
  full_name: Horák, Karel
  last_name: Horák
- first_name: Branislav
  full_name: Bošanský, Branislav
  last_name: Bošanský
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
citation:
  ama: 'Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration
    for goal-POMDPs. In: <i>Proceedings of the Twenty-Seventh International Joint
    Conference on Artificial Intelligence</i>. Vol 2018-July. IJCAI; 2018:4764-4770.
    doi:<a href="https://doi.org/10.24963/ijcai.2018/662">10.24963/ijcai.2018/662</a>'
  apa: 'Horák, K., Bošanský, B., &#38; Chatterjee, K. (2018). Goal-HSVI: Heuristic
    search value iteration for goal-POMDPs. In <i>Proceedings of the Twenty-Seventh
    International Joint Conference on Artificial Intelligence</i> (Vol. 2018–July,
    pp. 4764–4770). Stockholm, Sweden: IJCAI. <a href="https://doi.org/10.24963/ijcai.2018/662">https://doi.org/10.24963/ijcai.2018/662</a>'
  chicago: 'Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI:
    Heuristic Search Value Iteration for Goal-POMDPs.” In <i>Proceedings of the Twenty-Seventh
    International Joint Conference on Artificial Intelligence</i>, 2018–July:4764–70.
    IJCAI, 2018. <a href="https://doi.org/10.24963/ijcai.2018/662">https://doi.org/10.24963/ijcai.2018/662</a>.'
  ieee: 'K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value
    iteration for goal-POMDPs,” in <i>Proceedings of the Twenty-Seventh International
    Joint Conference on Artificial Intelligence</i>, Stockholm, Sweden, 2018, vol.
    2018–July, pp. 4764–4770.'
  ista: 'Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value
    iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint
    Conference on Artificial Intelligence. IJCAI: International Joint Conference on
    Artificial Intelligence vol. 2018–July, 4764–4770.'
  mla: 'Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.”
    <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial
    Intelligence</i>, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:<a href="https://doi.org/10.24963/ijcai.2018/662">10.24963/ijcai.2018/662</a>.'
  short: K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh
    International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.
conference:
  end_date: 2018-07-19
  location: Stockholm, Sweden
  name: 'IJCAI: International Joint Conference on Artificial Intelligence'
  start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2025-04-14T13:51:04Z
day: '01'
department:
- _id: KrCh
doi: 10.24963/ijcai.2018/662
ec_funded: 1
external_id:
  isi:
  - '000764175404127'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.24963/ijcai.2018/662
month: '07'
oa: 1
oa_version: Published Version
page: 4764 - 4770
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
  grant_number: ICT15-003
  name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial
  Intelligence
publication_status: published
publisher: IJCAI
publist_id: '8030'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Goal-HSVI: Heuristic search value iteration for goal-POMDPs'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-July
year: '2018'
...
---
_id: '155'
abstract:
- lang: eng
  text: There is currently significant interest in operating devices in the quantum
    regime, where their behaviour cannot be explained through classical mechanics.
    Quantum states, including entangled states, are fragile and easily disturbed by
    excessive thermal noise. Here we address the question of whether it is possible
    to create non-reciprocal devices that encourage the flow of thermal noise towards
    or away from a particular quantum device in a network. Our work makes use of the
    cascaded systems formalism to answer this question in the affirmative, showing
    how a three-port device can be used as an effective thermal transistor, and illustrates
    how this formalism maps onto an experimentally-realisable optomechanical system.
    Our results pave the way to more resilient quantum devices and to the use of thermal
    noise as a resource.
alternative_title:
- Proceedings of SPIE
article_number: 106721N
article_processing_charge: No
arxiv: 1
author:
- first_name: André
  full_name: Xuereb, André
  last_name: Xuereb
- first_name: Matteo
  full_name: Aquilina, Matteo
  last_name: Aquilina
- first_name: Shabir
  full_name: Barzanjeh, Shabir
  id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
  last_name: Barzanjeh
  orcid: 0000-0003-0415-1423
citation:
  ama: 'Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks.
    In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a
    href="https://doi.org/10.1117/12.2309928">10.1117/12.2309928</a>'
  apa: 'Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise
    through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J.
    M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society
    for optical engineering, Strasbourg, France: SPIE. <a href="https://doi.org/10.1117/12.2309928">https://doi.org/10.1117/12.2309928</a>'
  chicago: Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal
    Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain,
    and J M Nunzi, Vol. 10672. SPIE, 2018. <a href="https://doi.org/10.1117/12.2309928">https://doi.org/10.1117/12.2309928</a>.
  ieee: 'A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through
    quantum networks,” presented at the SPIE: The international society for optical
    engineering, Strasbourg, France, 2018, vol. 10672.'
  ista: 'Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum
    networks. SPIE: The international society for optical engineering, Proceedings
    of SPIE, vol. 10672, 106721N.'
  mla: Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>.
    Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href="https://doi.org/10.1117/12.2309928">10.1117/12.2309928</a>.
  short: A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J.
    Bain, J.M. Nunzi (Eds.), SPIE, 2018.
conference:
  end_date: 2018-04-26
  location: Strasbourg, France
  name: 'SPIE: The international society for optical engineering'
  start_date: 2018-04-22
date_created: 2018-12-11T11:44:55Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-09-18T08:12:24Z
day: '04'
department:
- _id: JoFi
doi: 10.1117/12.2309928
editor:
- first_name: D L
  full_name: Andrews, D L
  last_name: Andrews
- first_name: A
  full_name: Ostendorf, A
  last_name: Ostendorf
- first_name: A J
  full_name: Bain, A J
  last_name: Bain
- first_name: J M
  full_name: Nunzi, J M
  last_name: Nunzi
external_id:
  arxiv:
  - '1806.01000'
  isi:
  - '000453298500019'
intvolume: '     10672'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1806.01000
month: '05'
oa: 1
oa_version: Preprint
publication_status: published
publisher: SPIE
publist_id: '7766'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Routing thermal noise through quantum networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10672
year: '2018'
...
---
_id: '156'
abstract:
- lang: eng
  text: 'Imprecision in timing can sometimes be beneficial: Metric interval temporal
    logic (MITL), disabling the expression of punctuality constraints, was shown to
    translate to timed automata, yielding an elementary decision procedure. We show
    how this principle extends to other forms of dense-time specification using regular
    expressions. By providing a clean, automaton-based formal framework for non-punctual
    languages, we are able to recover and extend several results in timed systems.
    Metric interval regular expressions (MIRE) are introduced, providing regular expressions
    with non-singular duration constraints. We obtain that MIRE are expressively complete
    relative to a class of one-clock timed automata, which can be determinized using
    additional clocks. Metric interval dynamic logic (MIDL) is then defined using
    MIRE as temporal modalities. We show that MIDL generalizes known extensions of
    MITL, while translating to timed automata at comparable cost.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas
  full_name: Ferrere, Thomas
  id: 40960E6E-F248-11E8-B48F-1D18A9856A87
  last_name: Ferrere
  orcid: 0000-0001-5199-3143
citation:
  ama: 'Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer;
    2018:147-164. doi:<a href="https://doi.org/10.1007/978-3-319-95582-7_9">10.1007/978-3-319-95582-7_9</a>'
  apa: 'Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951,
    pp. 147–164). Presented at the FM: Formal Methods, Oxford, UK: Springer. <a href="https://doi.org/10.1007/978-3-319-95582-7_9">https://doi.org/10.1007/978-3-319-95582-7_9</a>'
  chicago: Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64.
    Springer, 2018. <a href="https://doi.org/10.1007/978-3-319-95582-7_9">https://doi.org/10.1007/978-3-319-95582-7_9</a>.
  ieee: 'T. Ferrere, “The compound interest in relaxing punctuality,” presented at
    the FM: Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.'
  ista: 'Ferrere T. 2018. The compound interest in relaxing punctuality. FM: Formal
    Methods, LNCS, vol. 10951, 147–164.'
  mla: Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol.
    10951, Springer, 2018, pp. 147–64, doi:<a href="https://doi.org/10.1007/978-3-319-95582-7_9">10.1007/978-3-319-95582-7_9</a>.
  short: T. Ferrere, in:, Springer, 2018, pp. 147–164.
conference:
  end_date: 2018-07-17
  location: Oxford, UK
  name: 'FM: Formal Methods'
  start_date: 2018-07-15
date_created: 2018-12-11T11:44:55Z
date_published: 2018-07-12T00:00:00Z
date_updated: 2025-07-10T11:51:10Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-95582-7_9
external_id:
  isi:
  - '000489765800009'
file:
- access_level: open_access
  checksum: a045c213c42c445f1889326f8db82a0a
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-09T06:22:41Z
  date_updated: 2020-10-09T06:22:41Z
  file_id: '8637'
  file_name: 2018_LNCS_Ferrere.pdf
  file_size: 485576
  relation: main_file
  success: 1
file_date_updated: 2020-10-09T06:22:41Z
has_accepted_license: '1'
intvolume: '     10951'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 147 - 164
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: Formal methods for the design and analysis of complex systems
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '7765'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The compound interest in relaxing punctuality
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10951
year: '2018'
...
---
_id: '157'
abstract:
- lang: eng
  text: 'Social dilemmas occur when incentives for individuals are misaligned with
    group interests 1-7 . According to the ''tragedy of the commons'', these misalignments
    can lead to overexploitation and collapse of public resources. The resulting behaviours
    can be analysed with the tools of game theory 8 . The theory of direct reciprocity
    9-15 suggests that repeated interactions can alleviate such dilemmas, but previous
    work has assumed that the public resource remains constant over time. Here we
    introduce the idea that the public resource is instead changeable and depends
    on the strategic choices of individuals. An intuitive scenario is that cooperation
    increases the public resource, whereas defection decreases it. Thus, cooperation
    allows the possibility of playing a more valuable game with higher payoffs, whereas
    defection leads to a less valuable game. We analyse this idea using the theory
    of stochastic games 16-19 and evolutionary game theory. We find that the dependence
    of the public resource on previous interactions can greatly enhance the propensity
    for cooperation. For these results, the interaction between reciprocity and payoff
    feedback is crucial: neither repeated interactions in a constant environment nor
    single interactions in a changing environment yield similar cooperation rates.
    Our framework shows which feedbacks between exploitation and environment - either
    naturally occurring or designed - help to overcome social dilemmas.'
acknowledgement: "European Research Council Start Grant 279307, Austrian Science Fund
  (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme."
article_processing_charge: No
author:
- first_name: Christian
  full_name: Hilbe, Christian
  id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
  last_name: Hilbe
  orcid: 0000-0001-5116-955X
- first_name: Štepán
  full_name: Šimsa, Štepán
  last_name: Šimsa
- 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: Nowak, Martin
  last_name: Nowak
citation:
  ama: Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic
    games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href="https://doi.org/10.1038/s41586-018-0277-x">10.1038/s41586-018-0277-x</a>
  apa: Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of
    cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/s41586-018-0277-x">https://doi.org/10.1038/s41586-018-0277-x</a>
  chicago: Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak.
    “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing
    Group, 2018. <a href="https://doi.org/10.1038/s41586-018-0277-x">https://doi.org/10.1038/s41586-018-0277-x</a>.
  ieee: C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation
    in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group,
    pp. 246–249, 2018.
  ista: Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in
    stochastic games. Nature. 559(7713), 246–249.
  mla: Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>,
    vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href="https://doi.org/10.1038/s41586-018-0277-x">10.1038/s41586-018-0277-x</a>.
  short: C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-04T00:00:00Z
date_updated: 2025-04-15T06:30:08Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41586-018-0277-x
ec_funded: 1
external_id:
  isi:
  - '000438240900054'
file:
- access_level: open_access
  checksum: 011ab905cf9a410bc2b96f15174d654d
  content_type: application/pdf
  creator: dernst
  date_created: 2019-11-19T08:09:57Z
  date_updated: 2020-07-14T12:45:02Z
  file_id: '7049'
  file_name: 2018_Nature_Hilbe.pdf
  file_size: 2834442
  relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: '       559'
isi: 1
issue: '7713'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 246 - 249
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11407
  name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
- _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: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7764'
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/engineering-cooperation/
scopus_import: '1'
status: public
title: Evolution of cooperation in stochastic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 559
year: '2018'
...
---
_id: '158'
abstract:
- lang: eng
  text: 'The angiosperm seed is composed of three genetically distinct tissues: the
    diploid embryo that originates from the fertilized egg cell, the triploid endosperm
    that is produced from the fertilized central cell, and the maternal sporophytic
    integuments that develop into the seed coat1. At the onset of embryo development
    in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small
    apical embryonic cell and a larger basal cell that connects the embryo to the
    maternal tissue2. The coordinated and synchronous development of the embryo and
    the surrounding integuments, and the alignment of their growth axes, suggest communication
    between maternal tissues and the embryo. In contrast to animals, however, where
    a network of maternal factors that direct embryo patterning have been identified3,4,
    only a few maternal mutations have been described to affect embryo development
    in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of
    the phytohormone auxin in the apical cell by directed transport from the suspensor8–10.
    However, the origin of this auxin has remained obscure. Here we investigate the
    source of auxin for early embryogenesis and provide evidence that the mother plant
    coordinates seed development by supplying auxin to the early embryo from the integuments
    of the ovule. We show that auxin response increases in ovules after fertilization,
    due to upregulated auxin biosynthesis in the integuments, and this maternally
    produced auxin is required for correct embryo development.'
acknowledgement: This work was further supported by the Czech Science Foundation GACR
  (GA13-40637S) to J.F.;
article_processing_charge: No
author:
- first_name: Hélène
  full_name: Robert, Hélène
  last_name: Robert
- first_name: Chulmin
  full_name: Park, Chulmin
  last_name: Park
- first_name: Carla
  full_name: Gutièrrez, Carla
  last_name: Gutièrrez
- first_name: Barbara
  full_name: Wójcikowska, Barbara
  last_name: Wójcikowska
- first_name: Aleš
  full_name: Pěnčík, Aleš
  last_name: Pěnčík
- first_name: Ondřej
  full_name: Novák, Ondřej
  last_name: Novák
- first_name: Junyi
  full_name: Chen, Junyi
  last_name: Chen
- first_name: Wim
  full_name: Grunewald, Wim
  last_name: Grunewald
- first_name: Thomas
  full_name: Dresselhaus, Thomas
  last_name: Dresselhaus
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Thomas
  full_name: Laux, Thomas
  last_name: Laux
citation:
  ama: Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to
    early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553.
    doi:<a href="https://doi.org/10.1038/s41477-018-0204-z">10.1038/s41477-018-0204-z</a>
  apa: Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O.,
    … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning
    in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/s41477-018-0204-z">https://doi.org/10.1038/s41477-018-0204-z</a>
  chicago: Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš
    Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to
    Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing
    Group, 2018. <a href="https://doi.org/10.1038/s41477-018-0204-z">https://doi.org/10.1038/s41477-018-0204-z</a>.
  ieee: H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo
    patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing
    Group, pp. 548–553, 2018.
  ista: Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald
    W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to
    early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.
  mla: Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning
    in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group,
    2018, pp. 548–53, doi:<a href="https://doi.org/10.1038/s41477-018-0204-z">10.1038/s41477-018-0204-z</a>.
  short: H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J.
    Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018)
    548–553.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2025-04-15T07:48:03Z
day: '16'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0204-z
ec_funded: 1
external_id:
  isi:
  - '000443861300011'
  pmid:
  - '30013211'
intvolume: '         4'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pubmed/30013211
month: '07'
oa: 1
oa_version: Submitted Version
page: 548 - 553
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '282300'
  name: Polarity and subcellular dynamics in plants
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7763'
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/
scopus_import: '1'
status: public
title: Maternal auxin supply contributes to early embryo patterning in Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '159'
abstract:
- lang: eng
  text: L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction
    coupling and release of hormones from secretory cells. They are targets of antihypertensive
    and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable
    diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by
    light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell
    function and cardiac activity under optical control.
article_processing_charge: No
article_type: original
author:
- first_name: Timm
  full_name: Fehrentz, Timm
  last_name: Fehrentz
- first_name: Florian
  full_name: Huber, Florian
  last_name: Huber
- first_name: Nina
  full_name: Hartrampf, Nina
  last_name: Hartrampf
- first_name: Tobias
  full_name: Bruegmann, Tobias
  last_name: Bruegmann
- first_name: James
  full_name: Frank, James
  last_name: Frank
- first_name: Nicholas
  full_name: Fine, Nicholas
  last_name: Fine
- first_name: Daniela
  full_name: Malan, Daniela
  last_name: Malan
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Denis
  full_name: Tikhonov, Denis
  last_name: Tikhonov
- first_name: Maritn
  full_name: Sumser, Maritn
  last_name: Sumser
- first_name: Philipp
  full_name: Sasse, Philipp
  last_name: Sasse
- first_name: David
  full_name: Hodson, David
  last_name: Hodson
- first_name: Boris
  full_name: Zhorov, Boris
  last_name: Zhorov
- first_name: Nikolaj
  full_name: Klocker, Nikolaj
  last_name: Klocker
- first_name: Dirk
  full_name: Trauner, Dirk
  last_name: Trauner
citation:
  ama: Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels
    using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. 2018;14(8):764-767.
    doi:<a href="https://doi.org/10.1038/s41589-018-0090-8">10.1038/s41589-018-0090-8</a>
  apa: Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N.,
    … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem
    photoswitch. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/s41589-018-0090-8">https://doi.org/10.1038/s41589-018-0090-8</a>
  chicago: Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James
    Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels
    Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>. Nature Publishing
    Group, 2018. <a href="https://doi.org/10.1038/s41589-018-0090-8">https://doi.org/10.1038/s41589-018-0090-8</a>.
  ieee: T. Fehrentz <i>et al.</i>, “Optical control of L-type Ca2+ channels using
    a diltiazem photoswitch,” <i>Nature Chemical Biology</i>, vol. 14, no. 8. Nature
    Publishing Group, pp. 764–767, 2018.
  ista: Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl
    JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018.
    Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature
    Chemical Biology. 14(8), 764–767.
  mla: Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem
    Photoswitch.” <i>Nature Chemical Biology</i>, vol. 14, no. 8, Nature Publishing
    Group, 2018, pp. 764–67, doi:<a href="https://doi.org/10.1038/s41589-018-0090-8">10.1038/s41589-018-0090-8</a>.
  short: T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D.
    Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N.
    Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-13T09:36:35Z
day: '16'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41589-018-0090-8
external_id:
  isi:
  - '000438970200010'
file:
- access_level: open_access
  checksum: d42935094ec845f54a0688bf12986d62
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-14T12:14:09Z
  date_updated: 2020-07-14T12:45:03Z
  file_id: '7832'
  file_name: 2018_NatureChemicalBiology_Fehrentz.pdf
  file_size: 6321000
  relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: '        14'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 764 - 767
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7762'
quality_controlled: '1'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1038/s41589-021-00744-3
scopus_import: '1'
status: public
title: Optical control of L-type Ca2+ channels using a diltiazem photoswitch
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '16'
abstract:
- lang: eng
  text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic
    fluid flow between two widely spaced obstacles hindering a channel flow at Re
    1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed
    in the region between the obstacles. The mixing-layer instability arises in the
    vicinity of an inflection point on the shear velocity profile with a steep variation
    in the elastic stress. The instability results in an intermittent appearance of
    small vortices in the mixing layers and an amplification of spatiotemporal averaged
    vorticity in the elastic turbulence regime. The latter is characterized through
    scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore,
    the observations reported provide improved understanding of the stability of the
    mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1
    and oppose the current view of suppression of vorticity solely by polymer additives.
acknowledgement: This work was partially supported by the Israel Science Foundation
  (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No.
  2016145).
article_number: '103303'
article_processing_charge: No
article_type: original
author:
- first_name: Atul
  full_name: Varshney, Atul
  id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
  last_name: Varshney
  orcid: 0000-0002-3072-5999
- first_name: Victor
  full_name: Steinberg, Victor
  last_name: Steinberg
citation:
  ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification
    in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a
    href="https://doi.org/10.1103/PhysRevFluids.3.103303">10.1103/PhysRevFluids.3.103303</a>
  apa: Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity
    amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>.
    American Physical Society. <a href="https://doi.org/10.1103/PhysRevFluids.3.103303">https://doi.org/10.1103/PhysRevFluids.3.103303</a>
  chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
    Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>.
    American Physical Society, 2018. <a href="https://doi.org/10.1103/PhysRevFluids.3.103303">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.
  ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification
    in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10.
    American Physical Society, 2018.
  ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification
    in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.
  mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
    Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>,
    vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href="https://doi.org/10.1103/PhysRevFluids.3.103303">10.1103/PhysRevFluids.3.103303</a>.
  short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:10Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2025-04-14T07:44:02Z
day: '16'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103303
ec_funded: 1
external_id:
  isi:
  - '000447469200001'
file:
- access_level: open_access
  checksum: 7fc0a2322214d1c04debef36d5bf2e8a
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:13:56Z
  date_updated: 2020-07-14T12:45:04Z
  file_id: '5043'
  file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf
  file_size: 1838431
  relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: '         3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8039'
pubrep_id: '1062'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixing layer instability and vorticity amplification in a creeping viscoelastic
  flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '161'
abstract:
- lang: eng
  text: 'Which properties of metabolic networks can be derived solely from stoichiometry?
    Predictive results have been obtained by flux balance analysis (FBA), by postulating
    that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization
    of FBA to single-cell level using maximum entropy modeling, which we extend and
    test experimentally. Specifically, we define for Escherichia coli metabolism a
    flux distribution that yields the experimental growth rate: the model, containing
    FBA as a limit, provides a better match to measured fluxes and it makes a wide
    range of predictions: on flux variability, regulation, and correlations; on the
    relative importance of stoichiometry vs. optimization; on scaling relations for
    growth rate distributions. We validate the latter here with single-cell data at
    different sub-inhibitory antibiotic concentrations. The model quantifies growth
    optimization as emerging from the interplay of competitive dynamics in the population
    and regulation of metabolism at the level of single cells.'
article_number: '2988'
article_processing_charge: No
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: Andersson Anna
  full_name: Mc, Andersson Anna
  last_name: Mc
- first_name: Tobias
  full_name: Bergmiller, Tobias
  id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
  last_name: Bergmiller
  orcid: 0000-0001-5396-4346
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
citation:
  ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics
    for metabolic networks during steady state growth. <i>Nature Communications</i>.
    2018;9(1). doi:<a href="https://doi.org/10.1038/s41467-018-05417-9">10.1038/s41467-018-05417-9</a>
  apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018).
    Statistical mechanics for metabolic networks during steady state growth. <i>Nature
    Communications</i>. Springer Nature. <a href="https://doi.org/10.1038/s41467-018-05417-9">https://doi.org/10.1038/s41467-018-05417-9</a>
  chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet,
    and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady
    State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href="https://doi.org/10.1038/s41467-018-05417-9">https://doi.org/10.1038/s41467-018-05417-9</a>.
  ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical
    mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>,
    vol. 9, no. 1. Springer Nature, 2018.
  ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics
    for metabolic networks during steady state growth. Nature Communications. 9(1),
    2988.
  mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during
    Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer
    Nature, 2018, doi:<a href="https://doi.org/10.1038/s41467-018-05417-9">10.1038/s41467-018-05417-9</a>.
  short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications
    9 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2025-04-15T06:50:08Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41467-018-05417-9
ec_funded: 1
external_id:
  isi:
  - '000440149300021'
file:
- access_level: open_access
  checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18
  content_type: application/pdf
  creator: dernst
  date_created: 2018-12-17T16:44:28Z
  date_updated: 2020-07-14T12:45:06Z
  file_id: '5728'
  file_name: 2018_NatureComm_DeMartino.pdf
  file_size: 1043205
  relation: main_file
file_date_updated: 2020-07-14T12:45:06Z
has_accepted_license: '1'
intvolume: '         9'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28844-B27
  name: Biophysics of information processing in gene regulation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_status: published
publisher: Springer Nature
publist_id: '7760'
quality_controlled: '1'
related_material:
  record:
  - id: '5587'
    relation: popular_science
    status: public
scopus_import: '1'
status: public
title: Statistical mechanics for metabolic networks during steady state growth
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '162'
abstract:
- lang: eng
  text: 'Facial shape is the basis for facial recognition and categorization. Facial
    features reflect the underlying geometry of the skeletal structures. Here, we
    reveal that cartilaginous nasal capsule (corresponding to upper jaw and face)
    is shaped by signals generated by neural structures: brain and olfactory epithelium.
    Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior
    nasal capsule, whereas the formation of a capsule roof is controlled by signals
    from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule
    turned out to be important for shaping membranous facial bones during development.
    This suggests that conserved neurosensory structures could benefit from protection
    and have evolved signals inducing cranial cartilages encasing them. Experiments
    with mutant mice revealed that the genomic regulatory regions controlling production
    of SHH in the nervous system contribute to facial cartilage morphogenesis, which
    might be a mechanism responsible for the adaptive evolution of animal faces and
    snouts.'
article_number: e34465
article_processing_charge: No
author:
- first_name: Marketa
  full_name: Kaucka, Marketa
  last_name: Kaucka
- first_name: Julian
  full_name: Petersen, Julian
  last_name: Petersen
- first_name: Marketa
  full_name: Tesarova, Marketa
  last_name: Tesarova
- first_name: Bara
  full_name: Szarowska, Bara
  last_name: Szarowska
- first_name: Maria
  full_name: Kastriti, Maria
  last_name: Kastriti
- first_name: Meng
  full_name: Xie, Meng
  last_name: Xie
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
- first_name: Karl
  full_name: Annusver, Karl
  last_name: Annusver
- first_name: Maria
  full_name: Kasper, Maria
  last_name: Kasper
- first_name: Orsolya
  full_name: Symmons, Orsolya
  last_name: Symmons
- first_name: Leslie
  full_name: Pan, Leslie
  last_name: Pan
- first_name: Francois
  full_name: Spitz, Francois
  last_name: Spitz
- first_name: Jozef
  full_name: Kaiser, Jozef
  last_name: Kaiser
- first_name: Maria
  full_name: Hovorakova, Maria
  last_name: Hovorakova
- first_name: Tomas
  full_name: Zikmund, Tomas
  last_name: Zikmund
- first_name: Kazunori
  full_name: Sunadome, Kazunori
  last_name: Sunadome
- first_name: Michael P
  full_name: Matise, Michael P
  last_name: Matise
- first_name: Hui
  full_name: Wang, Hui
  last_name: Wang
- first_name: Ulrika
  full_name: Marklund, Ulrika
  last_name: Marklund
- first_name: Hind
  full_name: Abdo, Hind
  last_name: Abdo
- first_name: Patrik
  full_name: Ernfors, Patrik
  last_name: Ernfors
- first_name: Pascal
  full_name: Maire, Pascal
  last_name: Maire
- first_name: Maud
  full_name: Wurmser, Maud
  last_name: Wurmser
- first_name: Andrei S
  full_name: Chagin, Andrei S
  last_name: Chagin
- first_name: Kaj
  full_name: Fried, Kaj
  last_name: Fried
- first_name: Igor
  full_name: Adameyko, Igor
  last_name: Adameyko
citation:
  ama: Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory
    epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>.
    2018;7. doi:<a href="https://doi.org/10.7554/eLife.34465">10.7554/eLife.34465</a>
  apa: Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M.,
    … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control
    shaping of the mammalian nasal capsule cartilage. <i>ELife</i>. eLife Sciences
    Publications. <a href="https://doi.org/10.7554/eLife.34465">https://doi.org/10.7554/eLife.34465</a>
  chicago: Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
    Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory
    Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>.
    eLife Sciences Publications, 2018. <a href="https://doi.org/10.7554/eLife.34465">https://doi.org/10.7554/eLife.34465</a>.
  ieee: M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium
    control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol.
    7. eLife Sciences Publications, 2018.
  ista: Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva
    A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
    T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
    M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory
    epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7,
    e34465.
  mla: Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control
    Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465,
    eLife Sciences Publications, 2018, doi:<a href="https://doi.org/10.7554/eLife.34465">10.7554/eLife.34465</a>.
  short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A.
    Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova,
    T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors,
    P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-06-13T00:00:00Z
date_updated: 2025-04-14T07:27:30Z
day: '13'
ddc:
- '571'
department:
- _id: AnKi
doi: 10.7554/eLife.34465
ec_funded: 1
external_id:
  isi:
  - '000436227500001'
file:
- access_level: open_access
  checksum: da2378cdcf6b5461dcde194e4d608343
  content_type: application/pdf
  creator: dernst
  date_created: 2018-12-17T16:41:58Z
  date_updated: 2020-07-14T12:45:07Z
  file_id: '5727'
  file_name: 2018_eLife_Kaucka.pdf
  file_size: 9816484
  relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: '         7'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
  call_identifier: H2020
  grant_number: '680037'
  name: Coordination of Patterning And Growth In the Spinal Cord
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7759'
quality_controlled: '1'
related_material:
  record:
  - id: '9838'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Signals from the brain and olfactory epithelium control shaping of the mammalian
  nasal capsule cartilage
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
