---
_id: '6174'
abstract:
- lang: eng
  text: We propose a scaling theory for the many-body localization (MBL) phase transition
    in one dimension, building on the idea that it proceeds via a “quantum avalanche.”
    We argue that the critical properties can be captured at a coarse-grained level
    by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological
    grounds, we identify the scaling variables as the density of thermal regions and
    the length scale that controls the decay of typical matrix elements. Within this
    KT picture, the MBL phase is a line of fixed points that terminates at the delocalization
    transition. We discuss two possible scenarios distinguished by the distribution
    of rare, fractal thermal inclusions within the MBL phase. In the first scenario,
    these regions have a stretched exponential distribution in the MBL phase. In the
    second scenario, the near-critical MBL phase hosts rare thermal regions that are
    power-law-distributed in size. This points to the existence of a second transition
    within the MBL phase, at which these power laws change to the stretched exponential
    form expected at strong disorder. We numerically simulate two different phenomenological
    RGs previously proposed to describe the MBL transition. Both RGs display a universal
    power-law length distribution of thermal regions at the transition with a critical
    exponent αc=2, and continuously varying exponents in the MBL phase consistent
    with the KT picture.
article_number: '094205'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Philipp T.
  full_name: Dumitrescu, Philipp T.
  last_name: Dumitrescu
- first_name: Anna
  full_name: Goremykina, Anna
  last_name: Goremykina
- first_name: Siddharth A.
  full_name: Parameswaran, Siddharth A.
  last_name: Parameswaran
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
- first_name: Romain
  full_name: Vasseur, Romain
  last_name: Vasseur
citation:
  ama: Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless
    scaling at many-body localization phase transitions. <i>Physical Review B</i>.
    2019;99(9). doi:<a href="https://doi.org/10.1103/physrevb.99.094205">10.1103/physrevb.99.094205</a>
  apa: Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., &#38; Vasseur,
    R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions.
    <i>Physical Review B</i>. American Physical Society. <a href="https://doi.org/10.1103/physrevb.99.094205">https://doi.org/10.1103/physrevb.99.094205</a>
  chicago: Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym
    Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization
    Phase Transitions.” <i>Physical Review B</i>. American Physical Society, 2019.
    <a href="https://doi.org/10.1103/physrevb.99.094205">https://doi.org/10.1103/physrevb.99.094205</a>.
  ieee: P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur,
    “Kosterlitz-Thouless scaling at many-body localization phase transitions,” <i>Physical
    Review B</i>, vol. 99, no. 9. American Physical Society, 2019.
  ista: Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless
    scaling at many-body localization phase transitions. Physical Review B. 99(9),
    094205.
  mla: Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization
    Phase Transitions.” <i>Physical Review B</i>, vol. 99, no. 9, 094205, American
    Physical Society, 2019, doi:<a href="https://doi.org/10.1103/physrevb.99.094205">10.1103/physrevb.99.094205</a>.
  short: P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur,
    Physical Review B 99 (2019).
date_created: 2019-03-25T07:32:08Z
date_published: 2019-03-22T00:00:00Z
date_updated: 2023-09-05T12:11:13Z
day: '22'
department:
- _id: MaSe
doi: 10.1103/physrevb.99.094205
external_id:
  arxiv:
  - '1811.03103'
  isi:
  - '000462883200001'
intvolume: '        99'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1811.03103
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
  eissn:
  - 2469-9969
  issn:
  - 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Kosterlitz-Thouless scaling at many-body localization phase transitions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 99
year: '2019'
...
---
_id: '6191'
abstract:
- lang: eng
  text: The formation of self-organized patterns is key to the morphogenesis of multicellular
    organisms, although a comprehensive theory of biological pattern formation is
    still lacking. Here, we propose a minimal model combining tissue mechanics with
    morphogen turnover and transport to explore routes to patterning. Our active description
    couples morphogen reaction and diffusion, which impact cell differentiation and
    tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase
    consists of a poroelastic cell network and the other one of a permeating extracellular
    fluid, which provides a feedback by actively transporting morphogens. While this
    model encompasses previous theories approximating tissues to inert monophasic
    media, such as Turing’s reaction–diffusion model, it overcomes some of their key
    limitations permitting pattern formation via any two-species biochemical kinetics
    due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively
    different advection-driven Keller–Segel instability which allows for the formation
    of patterns with a single morphogen and whose fundamental mode pattern robustly
    scales with tissue size. We discuss the potential relevance of these findings
    for tissue morphogenesis.
article_processing_charge: No
author:
- first_name: Pierre
  full_name: Recho, Pierre
  last_name: Recho
- first_name: Adrien
  full_name: Hallou, Adrien
  last_name: Hallou
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
citation:
  ama: Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic
    biological tissues. <i>Proceedings of the National Academy of Sciences of the
    United States of America</i>. 2019;116(12):5344-5349. doi:<a href="https://doi.org/10.1073/pnas.1813255116">10.1073/pnas.1813255116</a>
  apa: Recho, P., Hallou, A., &#38; Hannezo, E. B. (2019). Theory of mechanochemical
    patterning in biphasic biological tissues. <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>. National Academy of Sciences.
    <a href="https://doi.org/10.1073/pnas.1813255116">https://doi.org/10.1073/pnas.1813255116</a>
  chicago: Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical
    Patterning in Biphasic Biological Tissues.” <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>. National Academy of Sciences,
    2019. <a href="https://doi.org/10.1073/pnas.1813255116">https://doi.org/10.1073/pnas.1813255116</a>.
  ieee: P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning
    in biphasic biological tissues,” <i>Proceedings of the National Academy of Sciences
    of the United States of America</i>, vol. 116, no. 12. National Academy of Sciences,
    pp. 5344–5349, 2019.
  ista: Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning
    in biphasic biological tissues. Proceedings of the National Academy of Sciences
    of the United States of America. 116(12), 5344–5349.
  mla: Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological
    Tissues.” <i>Proceedings of the National Academy of Sciences of the United States
    of America</i>, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49,
    doi:<a href="https://doi.org/10.1073/pnas.1813255116">10.1073/pnas.1813255116</a>.
  short: P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of
    Sciences of the United States of America 116 (2019) 5344–5349.
corr_author: '1'
date_created: 2019-03-31T21:59:13Z
date_published: 2019-03-19T00:00:00Z
date_updated: 2025-07-10T11:53:14Z
day: '19'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1813255116
external_id:
  isi:
  - '000461679000027'
  pmid:
  - '30819884'
file:
- access_level: open_access
  checksum: 8b67eee0ea8e5db61583e4d485215258
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-03T14:10:30Z
  date_updated: 2020-07-14T12:47:23Z
  file_id: '6193'
  file_name: 2019_PNAS_Recho.pdf
  file_size: 3456045
  relation: main_file
file_date_updated: 2020-07-14T12:47:23Z
has_accepted_license: '1'
intvolume: '       116'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 5344-5349
pmid: 1
project:
- _id: 268294B6-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P31639
  name: Active mechano-chemical description of the cell cytoskeleton
publication: Proceedings of the National Academy of Sciences of the United States
  of America
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
  link:
  - relation: supplementary_material
    url: www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental
scopus_import: '1'
status: public
title: Theory of mechanochemical patterning in biphasic biological tissues
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: 116
year: '2019'
...
---
_id: '6232'
abstract:
- lang: eng
  text: 'The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary
    conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[
    SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional
    constant coefficient linear equation whose solution at the boundary is not α-Hölder
    continuous.We obtain a positive counterpart of this: under some mild regularity
    assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are
    proved to be α-Hölder continuous up to the boundary with some α>0.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mate
  full_name: Gerencser, Mate
  id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
  last_name: Gerencser
citation:
  ama: Gerencser M. Boundary regularity of stochastic PDEs. <i>Annals of Probability</i>.
    2019;47(2):804-834. doi:<a href="https://doi.org/10.1214/18-AOP1272">10.1214/18-AOP1272</a>
  apa: Gerencser, M. (2019). Boundary regularity of stochastic PDEs. <i>Annals of
    Probability</i>. Institute of Mathematical Statistics. <a href="https://doi.org/10.1214/18-AOP1272">https://doi.org/10.1214/18-AOP1272</a>
  chicago: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” <i>Annals of
    Probability</i>. Institute of Mathematical Statistics, 2019. <a href="https://doi.org/10.1214/18-AOP1272">https://doi.org/10.1214/18-AOP1272</a>.
  ieee: M. Gerencser, “Boundary regularity of stochastic PDEs,” <i>Annals of Probability</i>,
    vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.
  ista: Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability.
    47(2), 804–834.
  mla: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” <i>Annals of Probability</i>,
    vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:<a
    href="https://doi.org/10.1214/18-AOP1272">10.1214/18-AOP1272</a>.
  short: M. Gerencser, Annals of Probability 47 (2019) 804–834.
date_created: 2019-04-07T21:59:15Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2025-07-10T11:53:17Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/18-AOP1272
external_id:
  arxiv:
  - '1705.05364'
  isi:
  - '000459681900005'
intvolume: '        47'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1705.05364
month: '03'
oa: 1
oa_version: Preprint
page: 804-834
publication: Annals of Probability
publication_identifier:
  issn:
  - 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary regularity of stochastic PDEs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2019'
...
---
_id: '6259'
abstract:
- lang: eng
  text: The plant hormone auxin has crucial roles in almost all aspects of plant growth
    and development. Concentrations of auxin vary across different tissues, mediating
    distinct developmental outcomes and contributing to the functional diversity of
    auxin. However, the mechanisms that underlie these activities are poorly understood.
    Here we identify an auxin signalling mechanism, which acts in parallel to the
    canonical auxin pathway based on the transport inhibitor response1 (TIR1) and
    other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that
    translates levels of cellular auxin to mediate differential growth during apical-hook
    development. This signalling mechanism operates at the concave side of the apical
    hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase
    1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically
    interacts with and phosphorylates two non-canonical transcriptional repressors
    of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby
    regulating ARF transcription factors. In contrast to the degradation of Aux/IAA
    transcriptional repressors in the canonical pathway, the newly identified mechanism
    stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate
    gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway
    originates at the cell surface, is triggered by high levels of auxin and shares
    a partially overlapping set of transcription factors with the TIR1/AFB signalling
    pathway. This allows distinct interpretations of different concentrations of cellular
    auxin, and thus enables this versatile signalling molecule to mediate complex
    developmental outcomes.
article_processing_charge: No
article_type: original
author:
- first_name: Min
  full_name: Cao, Min
  last_name: Cao
- first_name: Rong
  full_name: Chen, Rong
  last_name: Chen
- first_name: Pan
  full_name: Li, Pan
  last_name: Li
- first_name: Yongqiang
  full_name: Yu, Yongqiang
  last_name: Yu
- first_name: Rui
  full_name: Zheng, Rui
  last_name: Zheng
- first_name: Danfeng
  full_name: Ge, Danfeng
  last_name: Ge
- first_name: Wei
  full_name: Zheng, Wei
  last_name: Zheng
- first_name: Xuhui
  full_name: Wang, Xuhui
  last_name: Wang
- first_name: Yangtao
  full_name: Gu, Yangtao
  last_name: Gu
- first_name: Zuzana
  full_name: Gelová, Zuzana
  id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
  last_name: Gelová
  orcid: 0000-0003-4783-1752
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Heng
  full_name: Zhang, Heng
  last_name: Zhang
- first_name: Renyi
  full_name: Liu, Renyi
  last_name: Liu
- first_name: Jun
  full_name: He, Jun
  last_name: He
- first_name: Tongda
  full_name: Xu, Tongda
  last_name: Xu
citation:
  ama: Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential
    growth of the apical hook. <i>Nature</i>. 2019;568:240-243. doi:<a href="https://doi.org/10.1038/s41586-019-1069-7">10.1038/s41586-019-1069-7</a>
  apa: Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated
    auxin signalling regulates differential growth of the apical hook. <i>Nature</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41586-019-1069-7">https://doi.org/10.1038/s41586-019-1069-7</a>
  chicago: Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng,
    et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical
    Hook.” <i>Nature</i>. Springer Nature, 2019. <a href="https://doi.org/10.1038/s41586-019-1069-7">https://doi.org/10.1038/s41586-019-1069-7</a>.
  ieee: M. Cao <i>et al.</i>, “TMK1-mediated auxin signalling regulates differential
    growth of the apical hook,” <i>Nature</i>, vol. 568. Springer Nature, pp. 240–243,
    2019.
  ista: Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z,
    Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates
    differential growth of the apical hook. Nature. 568, 240–243.
  mla: Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth
    of the Apical Hook.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 240–43,
    doi:<a href="https://doi.org/10.1038/s41586-019-1069-7">10.1038/s41586-019-1069-7</a>.
  short: M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu,
    Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.
date_created: 2019-04-09T08:37:05Z
date_published: 2019-04-11T00:00:00Z
date_updated: 2025-04-14T07:45:04Z
day: '11'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41586-019-1069-7
ec_funded: 1
external_id:
  isi:
  - '000464412700050'
  pmid:
  - '30944466'
file:
- access_level: open_access
  checksum: 6b84ab602a34382cf0340a37a1378c75
  content_type: application/pdf
  creator: dernst
  date_created: 2020-11-13T07:37:41Z
  date_updated: 2020-11-13T07:37:41Z
  file_id: '8751'
  file_name: 2019_Nature _Cao_accepted.pdf
  file_size: 4321328
  relation: main_file
  success: 1
file_date_updated: 2020-11-13T07:37:41Z
has_accepted_license: '1'
intvolume: '       568'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 240-243
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature
publication_identifier:
  eissn:
  - 1476-4687
  issn:
  - 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/
scopus_import: '1'
status: public
title: TMK1-mediated auxin signalling regulates differential growth of the apical
  hook
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 568
year: '2019'
...
---
_id: '6262'
abstract:
- lang: eng
  text: "Gravitropism is an adaptive response that orients plant growth parallel to
    the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a
    necessary prerequisite to the tropic bending both in roots and\r\nshoots. During
    hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells
    to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization
    to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower
    side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization
    restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed
    a forward genetic screen to identify regulators of both PIN3 polarization events
    during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations
    based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced
    hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb)
    and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated
    typically with defective gravity-induced PIN3 relocation whereas all analyzed
    hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation
    sequencing-aided mutation map-\r\nping identified several candidate genes, including
    SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin
    cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe
    hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms
    underlying cell\r\npolarity and plant adaptive development."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hana
  full_name: Rakusová, Hana
  last_name: Rakusová
- first_name: Huibin
  full_name: Han, Huibin
  id: 31435098-F248-11E8-B48F-1D18A9856A87
  last_name: Han
- first_name: Petr
  full_name: Valošek, Petr
  id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87
  last_name: Valošek
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating
    PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant
    Journal</i>. 2019;98(6):1048-1059. doi:<a href="https://doi.org/10.1111/tpj.14301">10.1111/tpj.14301</a>
  apa: Rakusová, H., Han, H., Valošek, P., &#38; Friml, J. (2019). Genetic screen
    for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana
    hypocotyls. <i>The Plant Journal</i>. Wiley. <a href="https://doi.org/10.1111/tpj.14301">https://doi.org/10.1111/tpj.14301</a>
  chicago: Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen
    for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana
    Hypocotyls.” <i>The Plant Journal</i>. Wiley, 2019. <a href="https://doi.org/10.1111/tpj.14301">https://doi.org/10.1111/tpj.14301</a>.
  ieee: H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors
    mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,”
    <i>The Plant Journal</i>, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.
  ista: Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating
    PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
    Journal. 98(6), 1048–1059.
  mla: Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization
    in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>,
    vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:<a href="https://doi.org/10.1111/tpj.14301">10.1111/tpj.14301</a>.
  short: H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.
date_created: 2019-04-09T08:46:44Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-04-15T07:48:04Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/tpj.14301
ec_funded: 1
external_id:
  isi:
  - '000473644100008'
  pmid:
  - '30821050'
file:
- access_level: open_access
  checksum: ad3b5e270b67ba2a45f894ce3be27920
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-15T09:38:43Z
  date_updated: 2020-07-14T12:47:25Z
  file_id: '6304'
  file_name: 2019_PlantJournal_Rakusov.pdf
  file_size: 1383100
  relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: '        98'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1048-1059
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '282300'
  name: Polarity and subcellular dynamics in plants
publication: The Plant Journal
publication_identifier:
  eissn:
  - 1365-313x
  issn:
  - 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis
  thaliana hypocotyls
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 98
year: '2019'
...
---
_id: '6297'
abstract:
- lang: eng
  text: Cell-cell and cell-glycocalyx interactions under flow are important for the
    behaviour of circulating cells in blood and lymphatic vessels. However, such interactions
    are not well understood due in part to a lack of tools to study them in defined
    environments. Here, we develop a versatile in vitro platform for the study of
    cell-glycocalyx interactions in well-defined physical and chemical settings under
    flow. Our approach is demonstrated with the interaction between hyaluronan (HA,
    a key component of the endothelial glycocalyx) and its cell receptor CD44. We
    generate HA brushes in situ within a microfluidic device, and demonstrate the
    tuning of their physical (thickness and softness) and chemical (density of CD44
    binding sites) properties using characterisation with reflection interference
    contrast microscopy (RICM) and application of polymer theory. We highlight the
    interactions of HA brushes with CD44-displaying beads and cells under flow. Observations
    of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories
    to be generated, and revealed interactions in the form of stop and go phases with
    reduced rolling velocity and reduced distance between the bead and the HA brush,
    compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+
    AKR1 T-lymphocytes revealed complementary information about the dynamics of cell
    rolling and cell morphology, and highlighted the formation of tethers and slings,
    as they interacted with a HA brush under flow. This platform can readily incorporate
    more complex models of the glycocalyx, and should permit the study of how mechanical
    and biochemical factors are orchestrated to enable highly selective blood cell-vessel
    wall interactions under flow.
article_processing_charge: No
article_type: original
author:
- first_name: Heather S.
  full_name: Davies, Heather S.
  last_name: Davies
- first_name: Natalia S.
  full_name: Baranova, Natalia S.
  id: 38661662-F248-11E8-B48F-1D18A9856A87
  last_name: Baranova
  orcid: 0000-0002-3086-9124
- first_name: Nouha
  full_name: El Amri, Nouha
  last_name: El Amri
- first_name: Liliane
  full_name: Coche-Guérente, Liliane
  last_name: Coche-Guérente
- first_name: Claude
  full_name: Verdier, Claude
  last_name: Verdier
- first_name: Lionel
  full_name: Bureau, Lionel
  last_name: Bureau
- first_name: Ralf P.
  full_name: Richter, Ralf P.
  last_name: Richter
- first_name: Delphine
  full_name: Débarre, Delphine
  last_name: Débarre
citation:
  ama: Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial
    glycocalyx-blood cell interactions under flow in mechanically and biochemically
    well-defined environments. <i>Matrix Biology</i>. 2019;78-79:47-59. doi:<a href="https://doi.org/10.1016/j.matbio.2018.12.002">10.1016/j.matbio.2018.12.002</a>
  apa: Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C.,
    Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood
    cell interactions under flow in mechanically and biochemically well-defined environments.
    <i>Matrix Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.matbio.2018.12.002">https://doi.org/10.1016/j.matbio.2018.12.002</a>
  chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
    Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated
    Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically
    and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>. Elsevier,
    2019. <a href="https://doi.org/10.1016/j.matbio.2018.12.002">https://doi.org/10.1016/j.matbio.2018.12.002</a>.
  ieee: H. S. Davies <i>et al.</i>, “An integrated assay to probe endothelial glycocalyx-blood
    cell interactions under flow in mechanically and biochemically well-defined environments,”
    <i>Matrix Biology</i>, vol. 78–79. Elsevier, pp. 47–59, 2019.
  ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
    Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood
    cell interactions under flow in mechanically and biochemically well-defined environments.
    Matrix Biology. 78–79, 47–59.
  mla: Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood
    Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.”
    <i>Matrix Biology</i>, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:<a href="https://doi.org/10.1016/j.matbio.2018.12.002">10.1016/j.matbio.2018.12.002</a>.
  short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
    Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.
date_created: 2019-04-11T20:55:01Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:11:28Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.matbio.2018.12.002
external_id:
  isi:
  - '000468707600005'
file:
- access_level: open_access
  checksum: 790878cd78bfc54a147ddcc7c8f286a0
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-14T09:02:07Z
  date_updated: 2020-07-14T12:47:27Z
  file_id: '7825'
  file_name: 2018_MatrixBiology_Davies.pdf
  file_size: 4444339
  relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 47-59
publication: Matrix Biology
publication_identifier:
  issn:
  - 0945-053X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: An integrated assay to probe endothelial glycocalyx-blood cell interactions
  under flow in mechanically and biochemically well-defined environments
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 78-79
year: '2019'
...
---
_id: '6310'
abstract:
- lang: eng
  text: An asymptotic formula is established for the number of rational points of
    bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary
    smooth biquadratic hypersurface in sufficiently many variables. The proof uses
    the Hardy–Littlewood circle method.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
  full_name: Browning, Timothy D
  id: 35827D50-F248-11E8-B48F-1D18A9856A87
  last_name: Browning
  orcid: 0000-0002-8314-0177
- first_name: L.Q.
  full_name: Hu, L.Q.
  last_name: Hu
citation:
  ama: Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces.
    <i>Advances in Mathematics</i>. 2019;349:920-940. doi:<a href="https://doi.org/10.1016/j.aim.2019.04.031">10.1016/j.aim.2019.04.031</a>
  apa: Browning, T. D., &#38; Hu, L. Q. (2019). Counting rational points on biquadratic
    hypersurfaces. <i>Advances in Mathematics</i>. Elsevier. <a href="https://doi.org/10.1016/j.aim.2019.04.031">https://doi.org/10.1016/j.aim.2019.04.031</a>
  chicago: Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic
    Hypersurfaces.” <i>Advances in Mathematics</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.aim.2019.04.031">https://doi.org/10.1016/j.aim.2019.04.031</a>.
  ieee: T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,”
    <i>Advances in Mathematics</i>, vol. 349. Elsevier, pp. 920–940, 2019.
  ista: Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces.
    Advances in Mathematics. 349, 920–940.
  mla: Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic
    Hypersurfaces.” <i>Advances in Mathematics</i>, vol. 349, Elsevier, 2019, pp.
    920–40, doi:<a href="https://doi.org/10.1016/j.aim.2019.04.031">10.1016/j.aim.2019.04.031</a>.
  short: T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.
date_created: 2019-04-16T09:13:25Z
date_published: 2019-06-20T00:00:00Z
date_updated: 2025-07-10T11:53:19Z
day: '20'
ddc:
- '512'
department:
- _id: TiBr
doi: 10.1016/j.aim.2019.04.031
external_id:
  arxiv:
  - '1810.08426'
  isi:
  - '000468857300025'
file:
- access_level: open_access
  checksum: a63594a3a91b4ba6e2a1b78b0720b3d0
  content_type: application/pdf
  creator: tbrownin
  date_created: 2019-04-16T09:12:20Z
  date_updated: 2020-07-14T12:47:27Z
  file_id: '6311'
  file_name: wliqun.pdf
  file_size: 379158
  relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: '       349'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 920-940
publication: Advances in Mathematics
publication_identifier:
  eissn:
  - 1090-2082
  issn:
  - 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting rational points on biquadratic hypersurfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 349
year: '2019'
...
---
_id: '6343'
abstract:
- lang: eng
  text: Cryo-electron tomography (cryo-ET) provides unprecedented insights into the
    molecular constituents of biological environments. In combination with an image
    processing method called subtomogram averaging (STA), detailed 3D structures of
    biological molecules can be obtained in large, irregular macromolecular assemblies
    or in situ, without the need for purification. The contextual meta-information
    these methods also provide, such as a protein’s location within its native environment,
    can then be combined with functional data. This allows the derivation of a detailed
    view on the physiological or pathological roles of proteins from the molecular
    to cellular level. Despite their tremendous potential in in situ structural biology,
    cryo-ET and STA have been restricted by methodological limitations, such as the
    low obtainable resolution. Exciting progress now allows one to reach unprecedented
    resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here,
    I review current frontiers and future challenges in routinely determining high-resolution
    structures in in situ environments using cryo-ET and STA.
acknowledgement: The author acknowledges support from IST Austria and the Austrian
  Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Florian KM
  full_name: Schur, Florian KM
  id: 48AD8942-F248-11E8-B48F-1D18A9856A87
  last_name: Schur
  orcid: 0000-0003-4790-8078
citation:
  ama: Schur FK. Toward high-resolution in situ structural biology with cryo-electron
    tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>.
    2019;58(10):1-9. doi:<a href="https://doi.org/10.1016/j.sbi.2019.03.018">10.1016/j.sbi.2019.03.018</a>
  apa: Schur, F. K. (2019). Toward high-resolution in situ structural biology with
    cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural
    Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.sbi.2019.03.018">https://doi.org/10.1016/j.sbi.2019.03.018</a>
  chicago: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
    Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural
    Biology</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.sbi.2019.03.018">https://doi.org/10.1016/j.sbi.2019.03.018</a>.
  ieee: F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron
    tomography and subtomogram averaging,” <i>Current Opinion in Structural Biology</i>,
    vol. 58, no. 10. Elsevier, pp. 1–9, 2019.
  ista: Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron
    tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10),
    1–9.
  mla: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
    Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural
    Biology</i>, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:<a href="https://doi.org/10.1016/j.sbi.2019.03.018">10.1016/j.sbi.2019.03.018</a>.
  short: F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.
date_created: 2019-04-19T11:19:13Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-25T10:13:31Z
day: '01'
department:
- _id: FlSc
doi: 10.1016/j.sbi.2019.03.018
external_id:
  isi:
  - '000494891800004'
intvolume: '        58'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1-9
publication: Current Opinion in Structural Biology
publication_identifier:
  issn:
  - 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward high-resolution in situ structural biology with cryo-electron tomography
  and subtomogram averaging
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 58
year: '2019'
...
---
_id: '6348'
abstract:
- lang: eng
  text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing,
    whereby hundreds of individually stabilized lasers encode information within a
    single-mode optical fibre. Higher bandwidths require higher total optical power,
    but the power sent into the fibre is limited by optical nonlinearities within
    the fibre, and energy consumption by the light sources starts to become a substantial
    cost factor1. Optical frequency combs have been suggested to remedy this problem
    by generating numerous discrete, equidistant laser lines within a monolithic device;
    however, at present their stability and coherence allow them to operate only within
    small parameter ranges2,3,4. Here we show that a broadband frequency comb realized
    through the electro-optic effect within a high-quality whispering-gallery-mode
    resonator can operate at low microwave and optical powers. Unlike the usual third-order
    Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear
    effect, which is much more efficient. Our result uses a fixed microwave signal
    that is mixed with an optical-pump signal to generate a coherent frequency comb
    with a precisely determined carrier separation. The resonant enhancement enables
    us to work with microwave powers that are three orders of magnitude lower than
    those in commercially available devices. We emphasize the practical relevance
    of our results to high rates of data communication. To circumvent the limitations
    imposed by nonlinear effects in optical communication fibres, one has to solve
    two problems: to provide a compact and fully integrated, yet high-quality and
    coherent, frequency comb generator; and to calculate nonlinear signal propagation
    in real time5. We report a solution to the first problem.'
article_processing_charge: No
arxiv: 1
author:
- 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: Florian
  full_name: Sedlmeir, Florian
  last_name: Sedlmeir
- first_name: Madhuri
  full_name: Kumari, Madhuri
  last_name: Kumari
- first_name: Gerd
  full_name: Leuchs, Gerd
  last_name: Leuchs
- first_name: Harald G.L.
  full_name: Schwefel, Harald G.L.
  last_name: Schwefel
citation:
  ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic
    frequency comb. <i>Nature</i>. 2019;568(7752):378-381. doi:<a href="https://doi.org/10.1038/s41586-019-1110-x">10.1038/s41586-019-1110-x</a>
  apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., &#38; Schwefel,
    H. G. L. (2019). Resonant electro-optic frequency comb. <i>Nature</i>. Springer
    Nature. <a href="https://doi.org/10.1038/s41586-019-1110-x">https://doi.org/10.1038/s41586-019-1110-x</a>
  chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs,
    and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>.
    Springer Nature, 2019. <a href="https://doi.org/10.1038/s41586-019-1110-x">https://doi.org/10.1038/s41586-019-1110-x</a>.
  ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel,
    “Resonant electro-optic frequency comb,” <i>Nature</i>, vol. 568, no. 7752. Springer
    Nature, pp. 378–381, 2019.
  ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant
    electro-optic frequency comb. Nature. 568(7752), 378–381.
  mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.”
    <i>Nature</i>, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:<a href="https://doi.org/10.1038/s41586-019-1110-x">10.1038/s41586-019-1110-x</a>.
  short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature
    568 (2019) 378–381.
date_created: 2019-04-28T21:59:13Z
date_published: 2019-04-18T00:00:00Z
date_updated: 2025-07-10T11:53:19Z
day: '18'
department:
- _id: JoFi
doi: 10.1038/s41586-019-1110-x
external_id:
  arxiv:
  - '1808.10608'
  isi:
  - '000464950700053'
intvolume: '       568'
isi: 1
issue: '7752'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1808.10608
month: '04'
oa: 1
oa_version: Preprint
page: 378-381
publication: Nature
publication_identifier:
  eissn:
  - 1476-4687
  issn:
  - 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1038/s41586-019-1220-5
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 568
year: '2019'
...
---
_id: '6415'
abstract:
- lang: eng
  text: Ant invasions are often harmful to native species communities. Their pathogens
    and host disease defense mechanisms may be one component of their devastating
    success. First, they can introduce harmful diseases to their competitors in the
    introduced range, to which they themselves are tolerant. Second, their supercolonial
    social structure of huge multi-queen nest networks means that they will harbor
    a broad pathogen spectrum and high pathogen load while remaining resilient, unlike
    the smaller, territorial colonies of the native species. Thus, it is likely that
    invasive ants act as a disease reservoir, promoting their competitive advantage
    and invasive success.
article_processing_charge: No
author:
- first_name: Sylvia
  full_name: Cremer, Sylvia
  id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
  last_name: Cremer
  orcid: 0000-0002-2193-3868
citation:
  ama: Cremer S. Pathogens and disease defense of invasive ants. <i>Current Opinion
    in Insect Science</i>. 2019;33:63-68. doi:<a href="https://doi.org/10.1016/j.cois.2019.03.011">10.1016/j.cois.2019.03.011</a>
  apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. <i>Current
    Opinion in Insect Science</i>. Elsevier. <a href="https://doi.org/10.1016/j.cois.2019.03.011">https://doi.org/10.1016/j.cois.2019.03.011</a>
  chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current
    Opinion in Insect Science</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.cois.2019.03.011">https://doi.org/10.1016/j.cois.2019.03.011</a>.
  ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” <i>Current Opinion
    in Insect Science</i>, vol. 33. Elsevier, pp. 63–68, 2019.
  ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion
    in Insect Science. 33, 63–68.
  mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current
    Opinion in Insect Science</i>, vol. 33, Elsevier, 2019, pp. 63–68, doi:<a href="https://doi.org/10.1016/j.cois.2019.03.011">10.1016/j.cois.2019.03.011</a>.
  short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.
date_created: 2019-05-13T07:58:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-07-10T11:53:22Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2019.03.011
external_id:
  isi:
  - '000477666000012'
intvolume: '        33'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 63-68
publication: Current Opinion in Insect Science
publication_identifier:
  eissn:
  - 2214-5753
  issn:
  - 2214-5745
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathogens and disease defense of invasive ants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2019'
...
---
_id: '6418'
abstract:
- lang: eng
  text: Males and females of Artemia franciscana, a crustacean commonly used in the
    aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes,
    but the nature and extent of differentiation of these chromosomes is unknown.
    Here, we characterize the Z chromosome by detecting genomic regions that show
    lower genomic coverage in female than in male samples, and regions that harbor
    an excess of female-specific SNPs. We detect many Z-specific genes, which no longer
    have homologs on the W, but also Z-linked genes that appear to have diverged very
    recently from their existing W-linked homolog. We assess patterns of male and
    female expression in two tissues with extensive morphological dimorphism, gonads,
    and heads. In agreement with their morphology, sex-biased expression is common
    in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased
    genes, and seems to in fact have a mechanism of dosage compensation that leads
    to equal expression in males and in females. Both of these patterns are contrary
    to most ZW systems studied so far, making A. franciscana an excellent model for
    investigating the interplay between the evolution of sexual dimorphism and dosage
    compensation, as well as Z chromosome evolution in general.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Ann K
  full_name: Huylmans, Ann K
  id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
  last_name: Huylmans
  orcid: 0000-0001-8871-4961
- first_name: Melissa A
  full_name: Toups, Melissa A
  id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
  last_name: Toups
  orcid: 0000-0002-9752-7380
- first_name: Ariana
  full_name: Macon, Ariana
  id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
  last_name: Macon
- first_name: William J
  full_name: Gammerdinger, William J
  id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
  last_name: Gammerdinger
  orcid: 0000-0001-9638-1220
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
citation:
  ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene
    expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome
    biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href="https://doi.org/10.1093/gbe/evz053">10.1093/gbe/evz053</a>
  apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso,
    B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana
    Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a
    href="https://doi.org/10.1093/gbe/evz053">https://doi.org/10.1093/gbe/evz053</a>
  chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger,
    and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the
    Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford
    University Press, 2019. <a href="https://doi.org/10.1093/gbe/evz053">https://doi.org/10.1093/gbe/evz053</a>.
  ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso,
    “Sex-biased gene expression and dosage compensation on the Artemia franciscana
    Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University
    Press, pp. 1033–1044, 2019.
  ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased
    gene expression and dosage compensation on the Artemia franciscana Z-chromosome.
    Genome biology and evolution. 11(4), 1033–1044.
  mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation
    on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>,
    vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href="https://doi.org/10.1093/gbe/evz053">10.1093/gbe/evz053</a>.
  short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome
    Biology and Evolution 11 (2019) 1033–1044.
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2025-04-14T07:41:21Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evz053
ec_funded: 1
external_id:
  isi:
  - '000476569800003'
file:
- access_level: open_access
  checksum: 7d0ede297b6741f3dc89cd59017c7642
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-14T08:29:38Z
  date_updated: 2020-07-14T12:47:29Z
  file_id: '6446'
  file_name: 2019_GBE_Huylmans.pdf
  file_size: 1256303
  relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: '        11'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1033-1044
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715257'
  name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genome biology and evolution
publication_identifier:
  eissn:
  - 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  record:
  - id: '6060'
    relation: popular_science
    status: public
scopus_import: '1'
status: public
title: Sex-biased gene expression and dosage compensation on the Artemia franciscana
  Z-chromosome
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2019'
...
---
_id: '6428'
abstract:
- lang: eng
  text: 'Safety and security are major concerns in the development of Cyber-Physical
    Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify
    and monitor the correctness of CPS relativeto formalized requirements. Incorporating
    STL into a developmentprocess enables designers to automatically monitor and diagnosetraces,
    compute robustness estimates based on requirements, andperform requirement falsification,
    leading to productivity gains inverification and validation activities; however,
    in its current formSTL is agnostic to the input/output classification of signals,
    andthis negatively impacts the relevance of the analysis results.In this paper
    we propose to make the interface explicit in theSTL language by introducing input/output
    signal declarations. Wethen define new measures of input vacuity and output robustnessthat
    better reflect the nature of the system and the specification in-tent. The resulting
    framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification
    and validation activities.We demonstrate the benefits of IA-STL on several CPS
    analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand
    (3) fault localization. We describe an implementation of our en-hancement to STL
    and associated notions of robustness and vacuityin a prototype extension of Breach,
    a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these
    methodologi-cal improvements and evaluate our results on two examples fromthe
    automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell
    system.'
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
- first_name: Dejan
  full_name: Nickovic, Dejan
  id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
  last_name: Nickovic
- first_name: Alexandre
  full_name: Donzé, Alexandre
  last_name: Donzé
- first_name: Hisahiro
  full_name: Ito, Hisahiro
  last_name: Ito
- first_name: James
  full_name: Kapinski, James
  last_name: Kapinski
citation:
  ama: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal
    temporal logic. In: <i>Proceedings of the 2019 22nd ACM International Conference
    on Hybrid Systems: Computation and Control</i>. ACM; 2019:57-66. doi:<a href="https://doi.org/10.1145/3302504.3311800">10.1145/3302504.3311800</a>'
  apa: 'Ferrere, T., Nickovic, D., Donzé, A., Ito, H., &#38; Kapinski, J. (2019).
    Interface-aware signal temporal logic. In <i>Proceedings of the 2019 22nd ACM
    International Conference on Hybrid Systems: Computation and Control</i> (pp. 57–66).
    Montreal, Canada: ACM. <a href="https://doi.org/10.1145/3302504.3311800">https://doi.org/10.1145/3302504.3311800</a>'
  chicago: 'Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James
    Kapinski. “Interface-Aware Signal Temporal Logic.” In <i>Proceedings of the 2019
    22nd ACM International Conference on Hybrid Systems: Computation and Control</i>,
    57–66. ACM, 2019. <a href="https://doi.org/10.1145/3302504.3311800">https://doi.org/10.1145/3302504.3311800</a>.'
  ieee: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware
    signal temporal logic,” in <i>Proceedings of the 2019 22nd ACM International Conference
    on Hybrid Systems: Computation and Control</i>, Montreal, Canada, 2019, pp. 57–66.'
  ista: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware
    signal temporal logic. Proceedings of the 2019 22nd ACM International Conference
    on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation
    and Control, 57–66.'
  mla: 'Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” <i>Proceedings
    of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and
    Control</i>, ACM, 2019, pp. 57–66, doi:<a href="https://doi.org/10.1145/3302504.3311800">10.1145/3302504.3311800</a>.'
  short: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings
    of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and
    Control, ACM, 2019, pp. 57–66.'
conference:
  end_date: 2019-04-18
  location: Montreal, Canada
  name: 'HSCC: Hybrid Systems - Computation and Control'
  start_date: 2019-04-16
date_created: 2019-05-13T08:13:46Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2025-07-10T11:53:22Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3302504.3311800
external_id:
  isi:
  - '000516713900007'
file:
- access_level: open_access
  checksum: b8e967081e051d1c55ca5d18fb187890
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-08T17:25:45Z
  date_updated: 2020-10-08T17:25:45Z
  file_id: '8633'
  file_name: 2019_ACM_Ferrere.pdf
  file_size: 1055421
  relation: main_file
  success: 1
file_date_updated: 2020-10-08T17:25:45Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 57-66
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: Formal methods for the design and analysis of complex systems
publication: 'Proceedings of the 2019 22nd ACM International Conference on Hybrid
  Systems: Computation and Control'
publication_identifier:
  isbn:
  - '9781450362825'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interface-aware signal temporal logic
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6442'
abstract:
- lang: eng
  text: This paper investigates the use of fundamental solutions for animating detailed
    linear water surface waves. We first propose an analytical solution for efficiently
    animating circular ripples in closed form. We then show how to adapt the method
    of fundamental solutions (MFS) to create ambient waves interacting with complex
    obstacles. Subsequently, we present a novel wavelet-based discretization which
    outperforms the state of the art MFS approach for simulating time-varying water
    surface waves with moving obstacles. Our results feature high-resolution spatial
    details, interactions with complex boundaries, and large open ocean domains. Our
    method compares favorably with previous work as well as known analytical solutions.
    We also present comparisons between our method and real world examples.
acknowledged_ssus:
- _id: ScienComp
article_number: '130'
article_processing_charge: No
author:
- first_name: Camille
  full_name: Schreck, Camille
  id: 2B14B676-F248-11E8-B48F-1D18A9856A87
  last_name: Schreck
- first_name: Christian
  full_name: Hafner, Christian
  id: 400429CC-F248-11E8-B48F-1D18A9856A87
  last_name: Hafner
- first_name: Christopher J
  full_name: Wojtan, Christopher J
  id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
  last_name: Wojtan
  orcid: 0000-0001-6646-5546
citation:
  ama: Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation.
    <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href="https://doi.org/10.1145/3306346.3323002">10.1145/3306346.3323002</a>
  apa: Schreck, C., Hafner, C., &#38; Wojtan, C. (2019). Fundamental solutions for
    water wave animation. <i>ACM Transactions on Graphics</i>. ACM. <a href="https://doi.org/10.1145/3306346.3323002">https://doi.org/10.1145/3306346.3323002</a>
  chicago: Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions
    for Water Wave Animation.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a
    href="https://doi.org/10.1145/3306346.3323002">https://doi.org/10.1145/3306346.3323002</a>.
  ieee: C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave
    animation,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.
  ista: Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave
    animation. ACM Transactions on Graphics. 38(4), 130.
  mla: Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.”
    <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 130, ACM, 2019, doi:<a href="https://doi.org/10.1145/3306346.3323002">10.1145/3306346.3323002</a>.
  short: C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).
date_created: 2019-05-14T07:04:06Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2024-10-22T09:58:22Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ChWo
doi: 10.1145/3306346.3323002
ec_funded: 1
external_id:
  isi:
  - '000475740600104'
file:
- access_level: open_access
  checksum: 1b737dfe3e051aba8f3f4ab1dceda673
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-14T07:03:55Z
  date_updated: 2020-07-14T12:47:30Z
  file_id: '6443'
  file_name: 2019_ACM_Schreck.pdf
  file_size: 44328918
  relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: '        38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '638176'
  name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
    Scales'
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715767'
  name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
    Modeling'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/
scopus_import: '1'
status: public
title: Fundamental solutions for water wave animation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6451'
abstract:
- lang: eng
  text: Epidermal growth factor receptor (EGFR) signaling controls skin development
    and homeostasis inmice and humans, and its deficiency causes severe skin inflammation,
    which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent
    effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle
    stem cells. Expression and alternative splicing analysisof RNA sequencing data
    from interfollicular epidermis and outer root sheath indicate that EGFR con-trols
    genes involved in epidermal differentiation and also in centrosome function, DNA
    damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in
    EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions
    in proliferative epidermal compartments, aswell asp53-independent functions in
    differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1
    protein specifically in the innermost epithelial hair layers, resulting in disorganizationof
    medulla cells. Thus, our results uncover important spatial and temporal features
    of cell-autonomousEGFR functions in the epidermis.
article_processing_charge: No
author:
- first_name: Nicole
  full_name: Amberg, Nicole
  id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
  last_name: Amberg
  orcid: 0000-0002-3183-8207
- first_name: Panagiota A.
  full_name: Sotiropoulou, Panagiota A.
  last_name: Sotiropoulou
- first_name: Gerwin
  full_name: Heller, Gerwin
  last_name: Heller
- first_name: Beate M.
  full_name: Lichtenberger, Beate M.
  last_name: Lichtenberger
- first_name: Martin
  full_name: Holcmann, Martin
  last_name: Holcmann
- first_name: Bahar
  full_name: Camurdanoglu, Bahar
  last_name: Camurdanoglu
- first_name: Temenuschka
  full_name: Baykuscheva-Gentscheva, Temenuschka
  last_name: Baykuscheva-Gentscheva
- first_name: Cedric
  full_name: Blanpain, Cedric
  last_name: Blanpain
- first_name: Maria
  full_name: Sibilia, Maria
  last_name: Sibilia
citation:
  ama: Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation
    in a p53-independent manner. <i>iScience</i>. 2019;15:243-256. doi:<a href="https://doi.org/10.1016/j.isci.2019.04.018">10.1016/j.isci.2019.04.018</a>
  apa: Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann,
    M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation
    in a p53-independent manner. <i>IScience</i>. Elsevier. <a href="https://doi.org/10.1016/j.isci.2019.04.018">https://doi.org/10.1016/j.isci.2019.04.018</a>
  chicago: Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger,
    Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric
    Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent
    Manner.” <i>IScience</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.isci.2019.04.018">https://doi.org/10.1016/j.isci.2019.04.018</a>.
  ieee: N. Amberg <i>et al.</i>, “EGFR controls hair shaft differentiation in a p53-independent
    manner,” <i>iScience</i>, vol. 15. Elsevier, pp. 243–256, 2019.
  ista: Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu
    B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft
    differentiation in a p53-independent manner. iScience. 15, 243–256.
  mla: Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent
    Manner.” <i>IScience</i>, vol. 15, Elsevier, 2019, pp. 243–56, doi:<a href="https://doi.org/10.1016/j.isci.2019.04.018">10.1016/j.isci.2019.04.018</a>.
  short: N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann,
    B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience
    15 (2019) 243–256.
date_created: 2019-05-14T11:47:40Z
date_published: 2019-05-31T00:00:00Z
date_updated: 2023-09-08T11:38:04Z
day: '31'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.isci.2019.04.018
external_id:
  isi:
  - '000470104600022'
file:
- access_level: open_access
  checksum: a9ad2296726c9474ad5860c9c2f53622
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-14T11:51:51Z
  date_updated: 2020-07-14T12:47:30Z
  file_id: '6452'
  file_name: 2019_iScience_Amberg.pdf
  file_size: 8365970
  relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: '        15'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 243-256
publication: iScience
publication_identifier:
  issn:
  - 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: EGFR controls hair shaft differentiation in a p53-independent manner
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2019'
...
---
_id: '6454'
abstract:
- lang: eng
  text: 'Adult neural stem cells and multiciliated ependymalcells are glial cells
    essential for neurological func-tions. Together, they make up the adult neurogenicniche.
    Using both high-throughput clonal analysisand single-cell resolution of progenitor
    division pat-terns and fate, we show that these two componentsof the neurogenic
    niche are lineally related: adult neu-ral stem cells are sister cells to ependymal
    cells,whereas most ependymal cells arise from the termi-nal symmetric divisions
    of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation,
    GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells.
    Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and
    identify the Geminin familymembers as key regulators of the initial pool of adultneural
    stem cells.'
article_processing_charge: No
author:
- first_name: G
  full_name: Ortiz-Álvarez, G
  last_name: Ortiz-Álvarez
- first_name: M
  full_name: Daclin, M
  last_name: Daclin
- first_name: A
  full_name: Shihavuddin, A
  last_name: Shihavuddin
- first_name: P
  full_name: Lansade, P
  last_name: Lansade
- first_name: A
  full_name: Fortoul, A
  last_name: Fortoul
- first_name: M
  full_name: Faucourt, M
  last_name: Faucourt
- first_name: S
  full_name: Clavreul, S
  last_name: Clavreul
- first_name: ME
  full_name: Lalioti, ME
  last_name: Lalioti
- first_name: S
  full_name: Taraviras, S
  last_name: Taraviras
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
- first_name: J
  full_name: Livet, J
  last_name: Livet
- first_name: A
  full_name: Meunier, A
  last_name: Meunier
- first_name: A
  full_name: Genovesio, A
  last_name: Genovesio
- first_name: N
  full_name: Spassky, N
  last_name: Spassky
citation:
  ama: Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and
    multiciliated ependymal cells share a common lineage regulated by the Geminin
    family members. <i>Neuron</i>. 2019;102(1):159-172.e7. doi:<a href="https://doi.org/10.1016/j.neuron.2019.01.051">10.1016/j.neuron.2019.01.051</a>
  apa: Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt,
    M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal
    cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.neuron.2019.01.051">https://doi.org/10.1016/j.neuron.2019.01.051</a>
  chicago: Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt,
    S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells
    Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>.
    Elsevier, 2019. <a href="https://doi.org/10.1016/j.neuron.2019.01.051">https://doi.org/10.1016/j.neuron.2019.01.051</a>.
  ieee: G. Ortiz-Álvarez <i>et al.</i>, “Adult neural stem cells and multiciliated
    ependymal cells share a common lineage regulated by the Geminin family members,”
    <i>Neuron</i>, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.
  ista: Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M,
    Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio
    A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells
    share a common lineage regulated by the Geminin family members. Neuron. 102(1),
    159–172.e7.
  mla: Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal
    Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>,
    vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:<a href="https://doi.org/10.1016/j.neuron.2019.01.051">10.1016/j.neuron.2019.01.051</a>.
  short: G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt,
    S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A.
    Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7.
date_created: 2019-05-14T13:06:30Z
date_published: 2019-04-03T00:00:00Z
date_updated: 2025-04-14T07:43:05Z
day: '03'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2019.01.051
ec_funded: 1
external_id:
  isi:
  - '000463337900018'
  pmid:
  - '30824354'
file:
- access_level: open_access
  checksum: 1fb6e195c583eb0c5cabf26f69ff6675
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-15T09:28:41Z
  date_updated: 2020-07-14T12:47:30Z
  file_id: '6457'
  file_name: 2019_Neuron_Ortiz.pdf
  file_size: 7288572
  relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: '       102'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 159-172.e7
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '725780'
  name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Neuron
publication_identifier:
  eissn:
  - 1097-4199
  issn:
  - 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adult neural stem cells and multiciliated ependymal cells share a common lineage
  regulated by the Geminin family members
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 102
year: '2019'
...
---
_id: '6462'
abstract:
- lang: eng
  text: A controller is a device that interacts with a plant. At each time point,it
    reads the plant’s state and issues commands with the goal that the plant oper-ates
    optimally. Constructing optimal controllers is a fundamental and challengingproblem.
    Machine learning techniques have recently been successfully applied totrain controllers,
    yet they have limitations. Learned controllers are monolithic andhard to reason
    about. In particular, it is difficult to add features without retraining,to guarantee
    any level of performance, and to achieve acceptable performancewhen encountering
    untrained scenarios. These limitations can be addressed bydeploying quantitative
    run-timeshieldsthat serve as a proxy for the controller.At each time point, the
    shield reads the command issued by the controller andmay choose to alter it before
    passing it on to the plant. We show how optimalshields that interfere as little
    as possible while guaranteeing a desired level ofcontroller performance, can be
    generated systematically and automatically usingreactive  synthesis.  First,  we  abstract  the  plant  by  building  a  stochastic  model.Second,
    we consider the learned controller to be a black box. Third, we mea-surecontroller
    performanceandshield interferenceby two quantitative run-timemeasures that are
    formally defined using weighted automata. Then, the problemof constructing a shield
    that guarantees maximal performance with minimal inter-ference is the problem
    of finding an optimal strategy in a stochastic2-player game“controller versus
    shield” played on the abstract state space of the plant with aquantitative objective
    obtained from combining the performance and interferencemeasures. We illustrate
    the effectiveness of our approach by automatically con-structing lightweight shields
    for learned traffic-light controllers in various roadnetworks. The shields we
    generate avoid liveness bugs, improve controller per-formance in untrained and
    changing traffic situations, and add features to learnedcontrollers, such as giving
    priority to emergency vehicles.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
  full_name: Avni, Guy
  id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
  last_name: Avni
  orcid: 0000-0001-5588-8287
- first_name: Roderick
  full_name: Bloem, Roderick
  last_name: Bloem
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Bettina
  full_name: Konighofer, Bettina
  last_name: Konighofer
- first_name: Stefan
  full_name: Pranger, Stefan
  last_name: Pranger
citation:
  ama: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time
    optimization for learned controllers through quantitative games. In: <i>31st International
    Conference on Computer-Aided Verification</i>. Vol 11561. Springer; 2019:630-649.
    doi:<a href="https://doi.org/10.1007/978-3-030-25540-4_36">10.1007/978-3-030-25540-4_36</a>'
  apa: 'Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., &#38;
    Pranger, S. (2019). Run-time optimization for learned controllers through quantitative
    games. In <i>31st International Conference on Computer-Aided Verification</i>
    (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. <a href="https://doi.org/10.1007/978-3-030-25540-4_36">https://doi.org/10.1007/978-3-030-25540-4_36</a>'
  chicago: Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina
    Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers
    through Quantitative Games.” In <i>31st International Conference on Computer-Aided
    Verification</i>, 11561:630–49. Springer, 2019. <a href="https://doi.org/10.1007/978-3-030-25540-4_36">https://doi.org/10.1007/978-3-030-25540-4_36</a>.
  ieee: G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger,
    “Run-time optimization for learned controllers through quantitative games,” in
    <i>31st International Conference on Computer-Aided Verification</i>, New York,
    NY, United States, 2019, vol. 11561, pp. 630–649.
  ista: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019.
    Run-time optimization for learned controllers through quantitative games. 31st
    International Conference on Computer-Aided Verification. CAV: Computer Aided Verification,
    LNCS, vol. 11561, 630–649.'
  mla: Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative
    Games.” <i>31st International Conference on Computer-Aided Verification</i>, vol.
    11561, Springer, 2019, pp. 630–49, doi:<a href="https://doi.org/10.1007/978-3-030-25540-4_36">10.1007/978-3-030-25540-4_36</a>.
  short: G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger,
    in:, 31st International Conference on Computer-Aided Verification, Springer, 2019,
    pp. 630–649.
conference:
  end_date: 2019-07-18
  location: New York, NY, United States
  name: 'CAV: Computer Aided Verification'
  start_date: 2019-07-13
corr_author: '1'
date_created: 2019-05-16T11:22:30Z
date_published: 2019-07-12T00:00:00Z
date_updated: 2025-04-15T06:26:05Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-030-25540-4_36
external_id:
  isi:
  - '000491468000036'
file:
- access_level: open_access
  checksum: c231579f2485c6fd4df17c9443a4d80b
  content_type: application/pdf
  creator: dernst
  date_created: 2019-08-14T09:35:24Z
  date_updated: 2020-07-14T12:47:31Z
  file_id: '6816'
  file_name: 2019_CAV_Avni.pdf
  file_size: 659766
  relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: '     11561'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 630-649
project:
- _id: 264B3912-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02369
  name: Formal Methods meets Algorithmic Game Theory
- _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: 31st International Conference on Computer-Aided Verification
publication_identifier:
  isbn:
  - '9783030255398'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Run-time optimization for learned controllers through quantitative games
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11561
year: '2019'
...
---
_id: '6477'
abstract:
- lang: eng
  text: 'Thermalizing quantum systems are conventionallydescribed by statistical mechanics
    at equilib-rium. However, not all systems fall into this category, with many-body
    localization providinga generic mechanism for thermalization to fail in strongly
    disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators
    at nonzero temperature, which do notthermalize and therefore cannot be describedusing
    statistical mechanics. This Colloquiumreviews recent theoretical and experimental
    advances in studies of MBL systems, focusing onthe new perspective provided by
    entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically,
    MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal
    integrals of motion emerges, which provides an intuitive explanationof the breakdown
    of thermalization. A description based on quasilocal integrals of motion isused
    to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement,
    the behavior of local observables, and the response to external dissipativeprocesses.
    Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden
    in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing
    of the quantum-to-classical transitionbetween many-body localized and ergodic
    phasesand anomalous transport in the vicinity of that transition. Experimentally,
    synthetic quantumsystems, which are well isolated from an external thermal reservoir,
    provide natural platforms forrealizing the MBL phase. Recent experiments with
    ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in
    which different signatures of many-body localization have beenobserved, are reviewed.
    This Colloquium concludes by listing outstanding challenges andpromising future
    research directions.'
article_number: '021001'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dmitry A.
  full_name: Abanin, Dmitry A.
  last_name: Abanin
- first_name: Ehud
  full_name: Altman, Ehud
  last_name: Altman
- first_name: Immanuel
  full_name: Bloch, Immanuel
  last_name: Bloch
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
citation:
  ama: 'Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization,
    thermalization, and entanglement. <i>Reviews of Modern Physics</i>. 2019;91(2).
    doi:<a href="https://doi.org/10.1103/revmodphys.91.021001">10.1103/revmodphys.91.021001</a>'
  apa: 'Abanin, D. A., Altman, E., Bloch, I., &#38; Serbyn, M. (2019). Colloquium:
    Many-body localization, thermalization, and entanglement. <i>Reviews of Modern
    Physics</i>. American Physical Society. <a href="https://doi.org/10.1103/revmodphys.91.021001">https://doi.org/10.1103/revmodphys.91.021001</a>'
  chicago: 'Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium:
    Many-Body Localization, Thermalization, and Entanglement.” <i>Reviews of Modern
    Physics</i>. American Physical Society, 2019. <a href="https://doi.org/10.1103/revmodphys.91.021001">https://doi.org/10.1103/revmodphys.91.021001</a>.'
  ieee: 'D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body
    localization, thermalization, and entanglement,” <i>Reviews of Modern Physics</i>,
    vol. 91, no. 2. American Physical Society, 2019.'
  ista: 'Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization,
    thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.'
  mla: 'Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization,
    and Entanglement.” <i>Reviews of Modern Physics</i>, vol. 91, no. 2, 021001, American
    Physical Society, 2019, doi:<a href="https://doi.org/10.1103/revmodphys.91.021001">10.1103/revmodphys.91.021001</a>.'
  short: D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91
    (2019).
date_created: 2019-05-23T07:38:43Z
date_published: 2019-05-22T00:00:00Z
date_updated: 2023-08-25T10:37:56Z
day: '22'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/revmodphys.91.021001
external_id:
  arxiv:
  - '1804.11065'
  isi:
  - '000469046900001'
file:
- access_level: open_access
  checksum: 4aec0e6662b09f6e0f828cd30ff2c3a6
  content_type: application/pdf
  creator: mserbyn
  date_created: 2019-05-23T07:39:05Z
  date_updated: 2020-07-14T12:47:31Z
  file_id: '6478'
  file_name: RevModPhys.91.021001.pdf
  file_size: 1695677
  relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: '        91'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Reviews of Modern Physics
publication_identifier:
  eissn:
  - 0034-6861
  issn:
  - 1539-0756
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Colloquium: Many-body localization, thermalization, and entanglement'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 91
year: '2019'
...
---
_id: '6482'
abstract:
- lang: eng
  text: 'Computer vision systems for automatic image categorization have become accurate
    and reliable enough that they can run continuously for days or even years as components
    of real-world commercial applications. A major open problem in this context, however,
    is quality control. Good classification performance can only be expected if systems
    run under the specific conditions, in particular data distributions, that they
    were trained for. Surprisingly, none of the currently used deep network architectures
    have a built-in functionality that could detect if a network operates on data
    from a distribution it was not trained for, such that potentially a warning to
    the human users could be triggered. In this work, we describe KS(conf), a procedure
    for detecting such outside of specifications (out-of-specs) operation, based on
    statistical testing of the network outputs. We show by extensive experiments using
    the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that
    KS(conf) reliably detects out-of-specs situations. It furthermore has a number
    of properties that make it a promising candidate for practical deployment: it
    is easy to implement, adds almost no overhead to the system, works with all networks,
    including pretrained ones, and requires no a priori knowledge of how the data
    distribution could change. '
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Rémy
  full_name: Sun, Rémy
  last_name: Sun
- first_name: Christoph
  full_name: Lampert, Christoph
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
citation:
  ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside
    of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:<a href="https://doi.org/10.1007/978-3-030-12939-2_18">10.1007/978-3-030-12939-2_18</a>'
  apa: 'Sun, R., &#38; Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet
    operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at
    the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature.
    <a href="https://doi.org/10.1007/978-3-030-12939-2_18">https://doi.org/10.1007/978-3-030-12939-2_18</a>'
  chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a
    ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature,
    2019. <a href="https://doi.org/10.1007/978-3-030-12939-2_18">https://doi.org/10.1007/978-3-030-12939-2_18</a>.'
  ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates
    outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition,
    Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.'
  ista: 'Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates
    outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS,
    vol. 11269, 244–259.'
  mla: 'Sun, Rémy, and Christoph Lampert. <i>KS(Conf): A Light-Weight Test If a ConvNet
    Operates Outside of Its Specifications</i>. Vol. 11269, Springer Nature, 2019,
    pp. 244–59, doi:<a href="https://doi.org/10.1007/978-3-030-12939-2_18">10.1007/978-3-030-12939-2_18</a>.'
  short: R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.
conference:
  end_date: 2018-10-12
  location: Stuttgart, Germany
  name: 'GCPR: Conference on Pattern Recognition'
  start_date: 2018-10-09
date_created: 2019-05-24T09:48:36Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2025-04-15T07:10:25Z
day: '14'
department:
- _id: ChLa
doi: 10.1007/978-3-030-12939-2_18
ec_funded: 1
external_id:
  arxiv:
  - '1804.04171'
intvolume: '     11269'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1804.04171
month: '02'
oa: 1
oa_version: Preprint
page: 244-259
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '308036'
  name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9783030129385'
  - '9783030129392'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '6944'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: 'KS(conf): A light-weight test if a ConvNet operates outside of Its specifications'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11269
year: '2019'
...
---
_id: '6485'
abstract:
- lang: eng
  text: Traditional concurrent programming involves manipulating shared mutable state.
    Alternatives to this programming style are communicating sequential processes
    (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous
    channelis the common abstraction for communication between several processes,
    where senders and receivers perform a rendezvous handshake as a part of their
    protocol (senders wait for receivers and vice versa). Additionally to this, channels
    support the select expression. In this work, we present the first efficient lock-free
    channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.
article_processing_charge: No
author:
- first_name: Nikita
  full_name: Koval, Nikita
  id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
  last_name: Koval
- first_name: Dan-Adrian
  full_name: Alistarh, Dan-Adrian
  id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
  last_name: Alistarh
  orcid: 0000-0003-3650-940X
- first_name: Roman
  full_name: Elizarov, Roman
  last_name: Elizarov
citation:
  ama: Koval N, Alistarh D-A, Elizarov R. <i>Lock-Free Channels for Programming via
    Communicating Sequential Processes</i>. ACM; 2019:417-418. doi:<a href="https://doi.org/10.1145/3293883.3297000">10.1145/3293883.3297000</a>
  apa: 'Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2019). <i>Lock-free channels
    for programming via communicating sequential processes</i>. <i>Proceedings of
    the 24th Symposium on Principles and Practice of Parallel Programming</i> (pp.
    417–418). Washington, NY, United States: ACM. <a href="https://doi.org/10.1145/3293883.3297000">https://doi.org/10.1145/3293883.3297000</a>'
  chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. <i>Lock-Free Channels
    for Programming via Communicating Sequential Processes</i>. <i>Proceedings of
    the 24th Symposium on Principles and Practice of Parallel Programming</i>. ACM,
    2019. <a href="https://doi.org/10.1145/3293883.3297000">https://doi.org/10.1145/3293883.3297000</a>.
  ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, <i>Lock-free channels for programming
    via communicating sequential processes</i>. ACM, 2019, pp. 417–418.
  ista: Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming
    via communicating sequential processes, ACM,p.
  mla: Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating
    Sequential Processes.” <i>Proceedings of the 24th Symposium on Principles and
    Practice of Parallel Programming</i>, ACM, 2019, pp. 417–18, doi:<a href="https://doi.org/10.1145/3293883.3297000">10.1145/3293883.3297000</a>.
  short: N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming
    via Communicating Sequential Processes, ACM, 2019.
conference:
  end_date: 2019-02-20
  location: Washington, NY, United States
  name: 'PPoPP: Principles and Practice of Parallel Programming'
  start_date: 2019-02-16
date_created: 2019-05-24T10:09:12Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2024-12-11T11:42:22Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3293883.3297000
external_id:
  isi:
  - '000587604600044'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 417-418
publication: Proceedings of the 24th Symposium on Principles and Practice of Parallel
  Programming
publication_identifier:
  isbn:
  - '9781450362252'
publication_status: published
publisher: ACM
quality_controlled: '1'
status: public
title: Lock-free channels for programming via communicating sequential processes
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6493'
abstract:
- lang: eng
  text: We present two algorithmic approaches for synthesizing linear hybrid automata
    from experimental data. Unlike previous approaches, our algorithms work without
    a template and generate an automaton with nondeterministic guards and invariants,
    and with an arbitrary number and topology of modes. They thus construct a succinct
    model from the data and provide formal guarantees. In particular, (1) the generated
    automaton can reproduce the data up to a specified tolerance and (2) the automaton
    is tight, given the first guarantee. Our first approach encodes the synthesis
    problem as a logical formula in the theory of linear arithmetic, which can then
    be solved by an SMT solver. This approach minimizes the number of modes in the
    resulting model but is only feasible for limited data sets. To address scalability,
    we propose a second approach that does not enforce to find a minimal model. The
    algorithm constructs an initial automaton and then iteratively extends the automaton
    based on processing new data. Therefore the algorithm is well-suited for online
    and synthesis-in-the-loop applications. The core of the algorithm is a membership
    query that checks whether, within the specified tolerance, a given data set can
    result from the execution of a given automaton. We solve this membership problem
    for linear hybrid automata by repeated reachability computations. We demonstrate
    the effectiveness of the algorithm on synthetic data sets and on cardiac-cell
    measurements.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Miriam
  full_name: Garcia Soto, Miriam
  id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
  last_name: Garcia Soto
  orcid: 0000−0003−2936−5719
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Christian
  full_name: Schilling, Christian
  id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
  last_name: Schilling
  orcid: 0000-0003-3658-1065
- first_name: Luka
  full_name: Zeleznik, Luka
  id: 3ADCA2E4-F248-11E8-B48F-1D18A9856A87
  last_name: Zeleznik
citation:
  ama: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis
    of linear hybrid automata. In: <i>31st International Conference on Computer-Aided
    Verification</i>. Vol 11561. Springer; 2019:297-314. doi:<a href="https://doi.org/10.1007/978-3-030-25540-4_16">10.1007/978-3-030-25540-4_16</a>'
  apa: 'Garcia Soto, M., Henzinger, T. A., Schilling, C., &#38; Zeleznik, L. (2019).
    Membership-based synthesis of linear hybrid automata. In <i>31st International
    Conference on Computer-Aided Verification</i> (Vol. 11561, pp. 297–314). New York
    City, NY, USA: Springer. <a href="https://doi.org/10.1007/978-3-030-25540-4_16">https://doi.org/10.1007/978-3-030-25540-4_16</a>'
  chicago: Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka
    Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In <i>31st International
    Conference on Computer-Aided Verification</i>, 11561:297–314. Springer, 2019.
    <a href="https://doi.org/10.1007/978-3-030-25540-4_16">https://doi.org/10.1007/978-3-030-25540-4_16</a>.
  ieee: M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based
    synthesis of linear hybrid automata,” in <i>31st International Conference on Computer-Aided
    Verification</i>, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.
  ista: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based
    synthesis of linear hybrid automata. 31st International Conference on Computer-Aided
    Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.'
  mla: Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.”
    <i>31st International Conference on Computer-Aided Verification</i>, vol. 11561,
    Springer, 2019, pp. 297–314, doi:<a href="https://doi.org/10.1007/978-3-030-25540-4_16">10.1007/978-3-030-25540-4_16</a>.
  short: M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International
    Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.
conference:
  end_date: 2019-07-18
  location: New York City, NY, USA
  name: 'CAV: Computer-Aided Verification'
  start_date: 2019-07-15
corr_author: '1'
date_created: 2019-05-27T07:09:53Z
date_published: 2019-07-12T00:00:00Z
date_updated: 2025-04-15T06:26:13Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-25540-4_16
ec_funded: 1
external_id:
  isi:
  - '000491468000016'
file:
- access_level: open_access
  checksum: 1f1d61b83a151031745ef70a501da3d6
  content_type: application/pdf
  creator: dernst
  date_created: 2019-08-14T11:05:30Z
  date_updated: 2020-07-14T12:47:32Z
  file_id: '6817'
  file_name: 2019_CAV_GarciaSoto.pdf
  file_size: 674795
  relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: '     11561'
isi: 1
keyword:
- Synthesis
- Linear hybrid automaton
- Membership
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 297-314
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: Formal methods for the design and analysis of complex systems
publication: 31st International Conference on Computer-Aided Verification
publication_identifier:
  isbn:
  - '9783030255398'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Membership-based synthesis of linear hybrid automata
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  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11561
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...
