---
_id: '8547'
abstract:
- lang: eng
  text: The cerebral cortex contains multiple hierarchically organized areas with
    distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying
    the emergence of this diversity remain unclear. Here, we have quantitatively investigated
    the neuronal output of individual progenitor cells in the ventricular zone of
    the developing mouse neocortex using a combination of methods that together circumvent
    the biases and limitations of individual approaches. We found that individual
    cortical progenitor cells show a high degree of stochasticity and generate pyramidal
    cell lineages that adopt a wide range of laminar configurations. Mathematical
    modelling these lineage data suggests that a small number of progenitor cell populations,
    each generating pyramidal cells following different stochastic developmental programs,
    suffice to generate the heterogenous complement of pyramidal cell lineages that
    collectively build the complex cytoarchitecture of the neocortex.
acknowledgement: We thank I. Andrew and S.E. Bae for excellent technical assistance,
  F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members
  of the Marín and Rico laboratories for stimulating discussions and ideas. Our research
  on this topic is supported by grants from the European Research Council (ERC-2017-AdG
  787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M.
  L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received
  support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO
  postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the
  European Commission under the H2020 Programme.
article_processing_charge: No
author:
- first_name: Alfredo
  full_name: Llorca, Alfredo
  last_name: Llorca
- first_name: Gabriele
  full_name: Ciceri, Gabriele
  last_name: Ciceri
- first_name: Robert J
  full_name: Beattie, Robert J
  id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
  last_name: Beattie
  orcid: 0000-0002-8483-8753
- first_name: Fong K.
  full_name: Wong, Fong K.
  last_name: Wong
- first_name: Giovanni
  full_name: Diana, Giovanni
  last_name: Diana
- first_name: Eleni
  full_name: Serafeimidou, Eleni
  last_name: Serafeimidou
- first_name: Marian
  full_name: Fernández-Otero, Marian
  last_name: Fernández-Otero
- first_name: Carmen
  full_name: Streicher, Carmen
  id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
  last_name: Streicher
- first_name: Sebastian J.
  full_name: Arnold, Sebastian J.
  last_name: Arnold
- first_name: Martin
  full_name: Meyer, Martin
  last_name: Meyer
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
- first_name: Miguel
  full_name: Maravall, Miguel
  last_name: Maravall
- first_name: Oscar
  full_name: Marín, Oscar
  last_name: Marín
citation:
  ama: Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors
    underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a
    href="https://doi.org/10.1101/494088">10.1101/494088</a>
  apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou,
    E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly
    of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory.
    <a href="https://doi.org/10.1101/494088">https://doi.org/10.1101/494088</a>
  chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni
    Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor
    Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>.
    Cold Spring Harbor Laboratory, n.d. <a href="https://doi.org/10.1101/494088">https://doi.org/10.1101/494088</a>.
  ieee: A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie
    the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor
    Laboratory.
  ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero
    M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous
    progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture.
    bioRxiv, <a href="https://doi.org/10.1101/494088">10.1101/494088</a>.
  mla: Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the
    Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor
    Laboratory, doi:<a href="https://doi.org/10.1101/494088">10.1101/494088</a>.
  short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou,
    M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
    O. Marín, BioRxiv (n.d.).
date_created: 2020-09-21T12:01:50Z
date_published: 2018-12-13T00:00:00Z
date_updated: 2021-01-12T08:20:00Z
day: '13'
department:
- _id: SiHi
doi: 10.1101/494088
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/494088
month: '12'
oa: 1
oa_version: Preprint
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
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02416
  name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Heterogeneous progenitor cell behaviors underlie the assembly of neocortical
  cytoarchitecture
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '86'
abstract:
- lang: eng
  text: Responsiveness—the requirement that every request to a system be eventually
    handled—is one of the fundamental liveness properties of a reactive system. Average
    response time is a quantitative measure for the responsiveness requirement used
    commonly in performance evaluation. We show how average response time can be computed
    on state-transition graphs, on Markov chains, and on game graphs. In all three
    cases, we give polynomial-time algorithms.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
  (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein
  Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
  (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland
  under grant 2014/15/D/ST6/04543.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Jan
  full_name: Otop, Jan
  id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
  last_name: Otop
citation:
  ama: 'Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh
    M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer;
    2018:143-161. doi:<a href="https://doi.org/10.1007/978-3-319-95246-8_9">10.1007/978-3-319-95246-8_9</a>'
  apa: Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average
    response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles
    of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href="https://doi.org/10.1007/978-3-319-95246-8_9">https://doi.org/10.1007/978-3-319-95246-8_9</a>
  chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average
    Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia
    Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href="https://doi.org/10.1007/978-3-319-95246-8_9">https://doi.org/10.1007/978-3-319-95246-8_9</a>.
  ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,”
    in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani,
    Eds. Springer, 2018, pp. 143–161.
  ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time.
    In: Principles of Modeling. LNCS, vol. 10760, 143–161.'
  mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles
    of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018,
    pp. 143–61, doi:<a href="https://doi.org/10.1007/978-3-319-95246-8_9">10.1007/978-3-319-95246-8_9</a>.
  short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani
    (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-95246-8_9
ec_funded: 1
editor:
- first_name: Marten
  full_name: Lohstroh, Marten
  last_name: Lohstroh
- first_name: Patricia
  full_name: Derler, Patricia
  last_name: Derler
- first_name: Marjan
  full_name: Sirjani, Marjan
  last_name: Sirjani
file:
- access_level: open_access
  checksum: 9995c6ce6957333baf616fc4f20be597
  content_type: application/pdf
  creator: dernst
  date_created: 2019-11-19T08:22:18Z
  date_updated: 2020-07-14T12:48:14Z
  file_id: '7053'
  file_name: 2018_PrinciplesModeling_Chatterjee.pdf
  file_size: 516307
  relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: '     10760'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 143 - 161
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11407
  name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
  grant_number: ICT15-003
  name: Efficient Algorithms for Computer Aided Verification
publication: Principles of Modeling
publication_status: published
publisher: Springer
publist_id: '7968'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing average response time
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10760
year: '2018'
...
---
_id: '8618'
abstract:
- lang: eng
  text: The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT
    nanoscopy have been developed from fluorescent proteins of the GFP superfamily.
    These proteins are bright, but exhibit several drawbacks such as relatively large
    size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore,
    RSFPs from other origins with improved properties need to be explored. Here, we
    report the development of two RSFPs based on the LOV domain of the photoreceptor
    protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by
    association with the abundant cellular cofactor flavin mononucleotide (FMN). Under
    illumination with blue and ultraviolet light, they undergo a photocycle, making
    these proteins inherently photoswitchable. Our first improved variant, rsLOV1,
    can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy
    of living cells with a resolution of down to 50 nm. In addition to their smaller
    size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability
    at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and
    off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date.
    Therefore, LOV-domain-based RSFPs have potential for applications where the switching
    speed of GFP-based proteins is limiting.
article_number: '2724'
article_processing_charge: No
article_type: original
author:
- first_name: Carola
  full_name: Gregor, Carola
  last_name: Gregor
- first_name: Sven C.
  full_name: Sidenstein, Sven C.
  last_name: Sidenstein
- first_name: Martin
  full_name: Andresen, Martin
  last_name: Andresen
- first_name: Steffen J.
  full_name: Sahl, Steffen J.
  last_name: Sahl
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Stefan W.
  full_name: Hell, Stefan W.
  last_name: Hell
citation:
  ama: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly
    switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from
    the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href="https://doi.org/10.1038/s41598-018-19947-1">10.1038/s41598-018-19947-1</a>
  apa: Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38;
    Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT
    and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific
    Reports</i>. Springer Nature. <a href="https://doi.org/10.1038/s41598-018-19947-1">https://doi.org/10.1038/s41598-018-19947-1</a>
  chicago: Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann
    G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins
    for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
    <i>Scientific Reports</i>. Springer Nature, 2018. <a href="https://doi.org/10.1038/s41598-018-19947-1">https://doi.org/10.1038/s41598-018-19947-1</a>.
  ieee: C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S.
    W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED
    nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>,
    vol. 8. Springer Nature, 2018.
  ista: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel
    reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered
    from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.
  mla: Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for
    RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
    <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href="https://doi.org/10.1038/s41598-018-19947-1">10.1038/s41598-018-19947-1</a>.
  short: C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell,
    Scientific Reports 8 (2018).
date_created: 2020-10-06T16:33:37Z
date_published: 2018-02-09T00:00:00Z
date_updated: 2023-09-19T15:04:49Z
day: '09'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41598-018-19947-1
external_id:
  isi:
  - '000424630400037'
  pmid:
  - '29426833'
file:
- access_level: open_access
  checksum: e642080fcbde9584c63544f587c74f03
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-06T16:35:16Z
  date_updated: 2020-10-06T16:35:16Z
  file_id: '8619'
  file_name: 2018_ScientificReports_Gregor.pdf
  file_size: 2818077
  relation: main_file
  success: 1
file_date_updated: 2020-10-06T16:35:16Z
has_accepted_license: '1'
intvolume: '         8'
isi: 1
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
  issn:
  - 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy
  engineered from the bacterial photoreceptor YtvA
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '87'
abstract:
- lang: eng
  text: Using the geodesic distance on the n-dimensional sphere, we study the expected
    radius function of the Delaunay mosaic of a random set of points. Specifically,
    we consider the partition of the mosaic into intervals of the radius function
    and determine the expected number of intervals whose radii are less than or equal
    to a given threshold. We find that the expectations are essentially the same as
    for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the
    points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to
    the boundary complex of the convex hull in Rn+1, so we also get the expected number
    of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in
    Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric
    to the standard n-simplex equipped with the Fisher information metric. It follows
    that the latter space has similar stochastic properties as the n-dimensional Euclidean
    space. Our results are therefore relevant in information geometry and in population
    genetics.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Anton
  full_name: Nikitenko, Anton
  id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
  last_name: Nikitenko
  orcid: 0000-0002-0659-3201
citation:
  ama: Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius
    functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. 2018;28(5):3215-3238.
    doi:<a href="https://doi.org/10.1214/18-AAP1389">10.1214/18-AAP1389</a>
  apa: Edelsbrunner, H., &#38; Nikitenko, A. (2018). Random inscribed polytopes have
    similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>.
    Institute of Mathematical Statistics. <a href="https://doi.org/10.1214/18-AAP1389">https://doi.org/10.1214/18-AAP1389</a>
  chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes
    Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied
    Probability</i>. Institute of Mathematical Statistics, 2018. <a href="https://doi.org/10.1214/18-AAP1389">https://doi.org/10.1214/18-AAP1389</a>.
  ieee: H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar
    radius functions as Poisson-Delaunay mosaics,” <i>Annals of Applied Probability</i>,
    vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.
  ista: Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar
    radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5),
    3215–3238.
  mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have
    Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>,
    vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:<a
    href="https://doi.org/10.1214/18-AAP1389">10.1214/18-AAP1389</a>.
  short: H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-15T12:10:35Z
day: '01'
department:
- _id: HeEd
doi: 10.1214/18-AAP1389
external_id:
  arxiv:
  - '1705.02870'
  isi:
  - '000442893500018'
intvolume: '        28'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1705.02870
month: '10'
oa: 1
oa_version: Preprint
page: 3215 - 3238
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I02979-N35
  name: Persistence and stability of geometric complexes
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7967'
quality_controlled: '1'
related_material:
  record:
  - id: '6287'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Random inscribed polytopes have similar radius functions as Poisson-Delaunay
  mosaics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '9'
abstract:
- lang: eng
  text: 'Immune cells migrating to the sites of infection navigate through diverse
    tissue architectures and switch their migratory mechanisms upon demand. However,
    little is known about systemic regulators that could allow the acquisition of
    these mechanisms. We performed a genetic screen in Drosophila melanogaster to
    identify regulators of germband invasion by embryonic macrophages into the confined
    space between the ectoderm and mesoderm. We have found that bZIP circadian transcription
    factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage
    germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are
    enriched in the macrophages during migration and genetically interact to control
    it. Kayak sets a less coordinated mode of migration of the macrophage group and
    increases the probability and length of Levy walks. Intriguingly, the motility
    of kayak mutant macrophages was also strongly affected during initial germband
    invasion but not along another less confined route. Inhibiting Rho1 signaling
    within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly
    suggesting that migrating macrophages have to overcome a barrier imposed by the
    stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance
    of the round cell shape and the rear edge translocation of the macrophages invading
    the germband. Complementary to this, the cortical actin cytoskeleton of Kayak-
    deficient macrophages was strongly affected. RNA sequencing revealed the filamin
    Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation
    and immunostaining revealed that the formin Diaphanous is another downstream target
    of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream
    target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages
    for germband invasion, and expression of constitutively active Diaphanous in macrophages
    was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are
    also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak,
    through its targets, increases actin polymerization and cortical tension in macrophages
    and thus allows extra force generation necessary for macrophage dissemination
    and migration through confined stiff tissues, while Vrille counterbalances it.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vera
  full_name: Belyaeva, Vera
  id: 47F080FE-F248-11E8-B48F-1D18A9856A87
  last_name: Belyaeva
citation:
  ama: Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila
    melanogaster embryo . 2018. doi:<a href="https://doi.org/10.15479/AT:ISTA:th1064">10.15479/AT:ISTA:th1064</a>
  apa: Belyaeva, V. (2018). <i>Transcriptional regulation of macrophage migration
    in the Drosophila melanogaster embryo </i>. Institute of Science and Technology
    Austria. <a href="https://doi.org/10.15479/AT:ISTA:th1064">https://doi.org/10.15479/AT:ISTA:th1064</a>
  chicago: Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in
    the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria,
    2018. <a href="https://doi.org/10.15479/AT:ISTA:th1064">https://doi.org/10.15479/AT:ISTA:th1064</a>.
  ieee: V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila
    melanogaster embryo ,” Institute of Science and Technology Austria, 2018.
  ista: Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the
    Drosophila melanogaster embryo . Institute of Science and Technology Austria.
  mla: Belyaeva, Vera. <i>Transcriptional Regulation of Macrophage Migration in the
    Drosophila Melanogaster Embryo </i>. Institute of Science and Technology Austria,
    2018, doi:<a href="https://doi.org/10.15479/AT:ISTA:th1064">10.15479/AT:ISTA:th1064</a>.
  short: V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila
    Melanogaster Embryo , Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:08Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-07T12:43:10Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
doi: 10.15479/AT:ISTA:th1064
file:
- access_level: closed
  checksum: d27b2465cb70d0c9678a0381b9b6ced1
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: dernst
  date_created: 2019-04-08T14:13:12Z
  date_updated: 2020-07-14T12:48:14Z
  embargo_to: open_access
  file_id: '6243'
  file_name: 2018_Thesis_Belyaeva_source.docx
  file_size: 102737483
  relation: source_file
- access_level: open_access
  checksum: a2939b61bde2de7b8ced77bbae0eaaed
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-08T14:14:08Z
  date_updated: 2021-02-11T11:17:16Z
  embargo: 2019-11-19
  file_id: '6244'
  file_name: 2018_Thesis_Belyaeva.pdf
  file_size: 88077843
  relation: main_file
file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '96'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8047'
pubrep_id: '1064'
status: public
supervisor:
- first_name: Daria E
  full_name: Siekhaus, Daria E
  id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
  last_name: Siekhaus
  orcid: 0000-0001-8323-8353
title: 'Transcriptional regulation of macrophage migration in the Drosophila melanogaster
  embryo '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '913'
abstract:
- lang: eng
  text: Coordinated cell polarization in developing tissues is a recurrent theme in
    multicellular organisms. In plants, a directional distribution of the plant hormone
    auxin is at the core of many developmental programs. A feedback regulation of
    auxin on the polarized localization of PIN auxin transporters in individual cells
    has been proposed as a self-organizing mechanism for coordinated tissue polarization,
    but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport
    remain unknown. We performed a microarray-based approach to find regulators of
    the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified
    a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs
    (PATL). Here, we show that PATLs are expressed in partially overlapping cells
    types in different tissues going through mitosis or initiating differentiation
    programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis
    embryos, primary roots, lateral root primordia, and developing stomata. Higher
    order patl mutants display reduced PIN1 repolarization in response to auxin, shorter
    root apical meristem, and drastic defects in embryo and seedling development.
    This suggests PATLs redundantly play a crucial role in polarity and patterning
    in Arabidopsis.
article_number: jcs.204198
article_processing_charge: No
author:
- first_name: Ricardo
  full_name: Tejos, Ricardo
  last_name: Tejos
- first_name: Cecilia
  full_name: Rodríguez Furlán, Cecilia
  last_name: Rodríguez Furlán
- first_name: Maciek
  full_name: Adamowski, Maciek
  id: 45F536D2-F248-11E8-B48F-1D18A9856A87
  last_name: Adamowski
  orcid: 0000-0001-6463-5257
- first_name: Michael
  full_name: Sauer, Michael
  last_name: Sauer
- first_name: Lorena
  full_name: Norambuena, Lorena
  last_name: Norambuena
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS
    are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis
    thaliana. <i>Journal of Cell Science</i>. 2018;131(2). doi:<a href="https://doi.org/10.1242/jcs.204198">10.1242/jcs.204198</a>
  apa: Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L.,
    &#38; Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation
    and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>.
    Company of Biologists. <a href="https://doi.org/10.1242/jcs.204198">https://doi.org/10.1242/jcs.204198</a>
  chicago: Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer,
    Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated
    PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of
    Cell Science</i>. Company of Biologists, 2018. <a href="https://doi.org/10.1242/jcs.204198">https://doi.org/10.1242/jcs.204198</a>.
  ieee: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and
    J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant
    development in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 131,
    no. 2. Company of Biologists, 2018.
  ista: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J.
    2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
    in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.
  mla: Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation
    and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>,
    vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:<a href="https://doi.org/10.1242/jcs.204198">10.1242/jcs.204198</a>.
  short: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J.
    Friml, Journal of Cell Science 131 (2018).
date_created: 2018-12-11T11:49:10Z
date_published: 2018-01-29T00:00:00Z
date_updated: 2025-05-07T11:12:29Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1242/jcs.204198
ec_funded: 1
external_id:
  isi:
  - '000424842400019'
file:
- access_level: open_access
  checksum: bf156c20a4f117b4b932370d54cbac8c
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-12T08:46:32Z
  date_updated: 2020-07-14T12:48:15Z
  file_id: '6299'
  file_name: 2017_adamowski_PATELLINS_are.pdf
  file_size: 14925985
  relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: '       131'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '282300'
  name: Polarity and subcellular dynamics in plants
publication: Journal of Cell Science
publication_identifier:
  issn:
  - '00219533'
publication_status: published
publisher: Company of Biologists
publist_id: '6530'
pubrep_id: '988'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
  in Arabidopsis thaliana
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 131
year: '2018'
...
---
_id: '9229'
alternative_title:
- Molecular and cellular neuroscience
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera
    Medica et Physiologica</i>. 2018;4(S1):11. doi:<a href="https://doi.org/10.20388/omp2018.00s1.001">10.20388/omp2018.00s1.001</a>
  apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology.
    <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod.
    <a href="https://doi.org/10.20388/omp2018.00s1.001">https://doi.org/10.20388/omp2018.00s1.001</a>
  chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
    <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod,
    2018. <a href="https://doi.org/10.20388/omp2018.00s1.001">https://doi.org/10.20388/omp2018.00s1.001</a>.
  ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,”
    <i>Opera Medica et Physiologica</i>, vol. 4, no. S1. Lobachevsky State University
    of Nizhny Novgorod, p. 11, 2018.
  ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology.
    Opera Medica et Physiologica. 4(S1), 11.
  mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
    <i>Opera Medica et Physiologica</i>, vol. 4, no. S1, Lobachevsky State University
    of Nizhny Novgorod, 2018, p. 11, doi:<a href="https://doi.org/10.20388/omp2018.00s1.001">10.20388/omp2018.00s1.001</a>.
  short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.
date_created: 2021-03-07T23:01:25Z
date_published: 2018-06-30T00:00:00Z
date_updated: 2021-12-03T07:31:05Z
day: '30'
department:
- _id: JoDa
doi: 10.20388/omp2018.00s1.001
intvolume: '         4'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://operamedphys.org/content/molecular-and-cellular-neuroscience
month: '06'
oa: 1
oa_version: Published Version
page: '11'
publication: Opera Medica et Physiologica
publication_identifier:
  eissn:
  - 2500-2295
  issn:
  - 2500-2287
publication_status: published
publisher: Lobachevsky State University of Nizhny Novgorod
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diffraction-unlimited optical imaging for synaptic physiology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 4
year: '2018'
...
---
_id: '691'
abstract:
- lang: eng
  text: "Background: Transport protein particle (TRAPP) is a multisubunit complex
    that regulates membrane trafficking through the Golgi apparatus. The clinical
    phenotype associated with mutations in various TRAPP subunits has allowed elucidation
    of their functions in specific tissues. The role of some subunits in human disease,
    however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective:
    We aimed to expand the range of neurodevelopmental disorders associated with mutations
    in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods:
    Linkage and homozygosity mapping and candidate gene analysis were used to identify
    homozygous mutations in families. Patient fibroblasts were used to study splicing
    defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals
    from three unrelated families with a founder homozygous splice mutation in TRAPPC6B,
    encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental
    disorder characterised by microcephaly, epilepsy and autistic features, and showed
    splicing defect. Zebrafish trappc6b morphants replicated the human phenotype,
    displaying decreased head size and neuronal hyperexcitability, leading to a lower
    seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional
    evidence of the role of TRAPPC6B in brain development and function."
article_processing_charge: No
article_type: original
author:
- first_name: Isaac
  full_name: Marin Valencia, Isaac
  last_name: Marin Valencia
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Anide
  full_name: Johansen, Anide
  last_name: Johansen
- first_name: Başak
  full_name: Rosti, Başak
  last_name: Rosti
- first_name: Mahmoud
  full_name: Issa, Mahmoud
  last_name: Issa
- first_name: Damir
  full_name: Musaev, Damir
  last_name: Musaev
- first_name: Gifty
  full_name: Bhat, Gifty
  last_name: Bhat
- first_name: Eric
  full_name: Scott, Eric
  last_name: Scott
- first_name: Jennifer
  full_name: Silhavy, Jennifer
  last_name: Silhavy
- first_name: Valentina
  full_name: Stanley, Valentina
  last_name: Stanley
- first_name: Rasim
  full_name: Rosti, Rasim
  last_name: Rosti
- first_name: Jeremy
  full_name: Gleeson, Jeremy
  last_name: Gleeson
- first_name: Farhad
  full_name: Imam, Farhad
  last_name: Imam
- first_name: Maha
  full_name: Zaki, Maha
  last_name: Zaki
- first_name: Joseph
  full_name: Gleeson, Joseph
  last_name: Gleeson
citation:
  ama: Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation
    in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly
    epilepsy and autistic features. <i>Journal of Medical Genetics</i>. 2018;55(1):48-54.
    doi:<a href="https://doi.org/10.1136/jmedgenet-2017-104627">10.1136/jmedgenet-2017-104627</a>
  apa: Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev,
    D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates
    with a neurodevelopmental disorder characterised by microcephaly epilepsy and
    autistic features. <i>Journal of Medical Genetics</i>. BMJ Publishing Group. <a
    href="https://doi.org/10.1136/jmedgenet-2017-104627">https://doi.org/10.1136/jmedgenet-2017-104627</a>
  chicago: Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud
    Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B
    Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy
    and Autistic Features.” <i>Journal of Medical Genetics</i>. BMJ Publishing Group,
    2018. <a href="https://doi.org/10.1136/jmedgenet-2017-104627">https://doi.org/10.1136/jmedgenet-2017-104627</a>.
  ieee: I. Marin Valencia <i>et al.</i>, “A homozygous founder mutation in TRAPPC6B
    associates with a neurodevelopmental disorder characterised by microcephaly epilepsy
    and autistic features,” <i>Journal of Medical Genetics</i>, vol. 55, no. 1. BMJ
    Publishing Group, pp. 48–54, 2018.
  ista: Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat
    G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson
    J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
    disorder characterised by microcephaly epilepsy and autistic features. Journal
    of Medical Genetics. 55(1), 48–54.
  mla: Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates
    with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and
    Autistic Features.” <i>Journal of Medical Genetics</i>, vol. 55, no. 1, BMJ Publishing
    Group, 2018, pp. 48–54, doi:<a href="https://doi.org/10.1136/jmedgenet-2017-104627">10.1136/jmedgenet-2017-104627</a>.
  short: I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev,
    G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki,
    J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-10-16T09:55:43Z
day: '01'
department:
- _id: GaNo
doi: 10.1136/jmedgenet-2017-104627
external_id:
  isi:
  - '000418199800007'
  pmid:
  - '28626029'
intvolume: '        55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/
month: '01'
oa: 1
oa_version: Submitted Version
page: 48 - 54
pmid: 1
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
  grant_number: '401299'
  name: Probing development and reversibility of autism spectrum disorders
publication: Journal of Medical Genetics
publication_identifier:
  issn:
  - 0022-2593
publication_status: published
publisher: BMJ Publishing Group
publist_id: '7016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
  disorder characterised by microcephaly epilepsy and autistic features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2018'
...
---
_id: '692'
abstract:
- lang: eng
  text: We consider families of confocal conics and two pencils of Apollonian circles
    having the same foci. We will show that these families of curves generate trivial
    3-webs and find the exact formulas describing them.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
  full_name: Akopyan, Arseniy
  id: 430D2C90-F248-11E8-B48F-1D18A9856A87
  last_name: Akopyan
  orcid: 0000-0002-2548-617X
citation:
  ama: Akopyan A. 3-Webs generated by confocal conics and circles. <i>Geometriae Dedicata</i>.
    2018;194(1):55-64. doi:<a href="https://doi.org/10.1007/s10711-017-0265-6">10.1007/s10711-017-0265-6</a>
  apa: Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. <i>Geometriae
    Dedicata</i>. Springer. <a href="https://doi.org/10.1007/s10711-017-0265-6">https://doi.org/10.1007/s10711-017-0265-6</a>
  chicago: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” <i>Geometriae
    Dedicata</i>. Springer, 2018. <a href="https://doi.org/10.1007/s10711-017-0265-6">https://doi.org/10.1007/s10711-017-0265-6</a>.
  ieee: A. Akopyan, “3-Webs generated by confocal conics and circles,” <i>Geometriae
    Dedicata</i>, vol. 194, no. 1. Springer, pp. 55–64, 2018.
  ista: Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae
    Dedicata. 194(1), 55–64.
  mla: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” <i>Geometriae
    Dedicata</i>, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:<a href="https://doi.org/10.1007/s10711-017-0265-6">10.1007/s10711-017-0265-6</a>.
  short: A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-08T11:40:29Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s10711-017-0265-6
ec_funded: 1
external_id:
  isi:
  - '000431418800004'
file:
- access_level: open_access
  checksum: 1febcfc1266486053a069e3425ea3713
  content_type: application/pdf
  creator: kschuh
  date_created: 2020-01-03T11:35:08Z
  date_updated: 2020-07-14T12:47:44Z
  file_id: '7222'
  file_name: 2018_Springer_Akopyan.pdf
  file_size: 1140860
  relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: '       194'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 55 - 64
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '7014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3-Webs generated by confocal conics and circles
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 194
year: '2018'
...
---
_id: '6941'
abstract:
- lang: eng
  text: "Bitcoin has become the most successful cryptocurrency ever deployed, and
    its most distinctive feature is that it is decentralized. Its underlying protocol
    (Nakamoto consensus) achieves this by using proof of work, which has the drawback
    that it causes the consumption of vast amounts of energy to maintain the ledger.
    Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards
    addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs
    of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather
    than computation. We argue that SpaceMint’s design solves or alleviates several
    of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also
    rewards smaller miners fairly according to their contribution to the network,
    thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof
    of space to enable its use in cryptocurrency, studies the attacks that can arise
    against a Bitcoin-like blockchain that uses proof of space, and proposes a new
    blockchain format and transaction types to address these attacks. Our prototype
    shows that initializing 1 TB for mining takes about a day (a one-off setup cost),
    and miners spend on average just a fraction of a second per block mined. Finally,
    we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the
    canonical game-theoretic notion for games that take place over time) and show
    that this stylized game satisfies a strong equilibrium notion, thereby arguing
    for SpaceMint ’s stability and consensus."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sunoo
  full_name: Park, Sunoo
  last_name: Park
- first_name: Albert
  full_name: Kwon, Albert
  last_name: Kwon
- first_name: Georg
  full_name: Fuchsbauer, Georg
  id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
  last_name: Fuchsbauer
- first_name: Peter
  full_name: Gazi, Peter
  id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
  last_name: Gazi
- first_name: Joel F
  full_name: Alwen, Joel F
  id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
  last_name: Alwen
- first_name: Krzysztof Z
  full_name: Pietrzak, Krzysztof Z
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A
    cryptocurrency based on proofs of space. In: <i>22nd International Conference
    on Financial Cryptography and Data Security</i>. Vol 10957. Springer Nature; 2018:480-499.
    doi:<a href="https://doi.org/10.1007/978-3-662-58387-6_26">10.1007/978-3-662-58387-6_26</a>'
  apa: 'Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., &#38; Pietrzak,
    K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In <i>22nd
    International Conference on Financial Cryptography and Data Security</i> (Vol.
    10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. <a href="https://doi.org/10.1007/978-3-662-58387-6_26">https://doi.org/10.1007/978-3-662-58387-6_26</a>'
  chicago: 'Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen,
    and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.”
    In <i>22nd International Conference on Financial Cryptography and Data Security</i>,
    10957:480–99. Springer Nature, 2018. <a href="https://doi.org/10.1007/978-3-662-58387-6_26">https://doi.org/10.1007/978-3-662-58387-6_26</a>.'
  ieee: 'S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak,
    “SpaceMint: A cryptocurrency based on proofs of space,” in <i>22nd International
    Conference on Financial Cryptography and Data Security</i>, Nieuwpoort, Curacao,
    2018, vol. 10957, pp. 480–499.'
  ista: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint:
    A cryptocurrency based on proofs of space. 22nd International Conference on Financial
    Cryptography and Data Security. FC: Financial Cryptography and Data Security,
    LNCS, vol. 10957, 480–499.'
  mla: 'Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.”
    <i>22nd International Conference on Financial Cryptography and Data Security</i>,
    vol. 10957, Springer Nature, 2018, pp. 480–99, doi:<a href="https://doi.org/10.1007/978-3-662-58387-6_26">10.1007/978-3-662-58387-6_26</a>.'
  short: S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:,
    22nd International Conference on Financial Cryptography and Data Security, Springer
    Nature, 2018, pp. 480–499.
conference:
  end_date: 2018-03-02
  location: Nieuwpoort, Curacao
  name: 'FC: Financial Cryptography and Data Security'
  start_date: 2018-02-26
date_created: 2019-10-14T06:35:38Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2023-09-19T15:02:13Z
day: '07'
department:
- _id: KrPi
doi: 10.1007/978-3-662-58387-6_26
ec_funded: 1
external_id:
  isi:
  - '000540656400026'
intvolume: '     10957'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2015/528
month: '12'
oa: 1
oa_version: Submitted Version
page: 480-499
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
publication: 22nd International Conference on Financial Cryptography and Data Security
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9783662583869'
  - '9783662583876'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SpaceMint: A cryptocurrency based on proofs of space'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10957
year: '2018'
...
---
_id: '7'
abstract:
- lang: eng
  text: Animal social networks are shaped by multiple selection pressures, including
    the need to ensure efficient communication and functioning while simultaneously
    limiting disease transmission. Social animals could potentially further reduce
    epidemic risk by altering their social networks in the presence of pathogens,
    yet there is currently no evidence for such pathogen-triggered responses. We tested
    this hypothesis experimentally in the ant Lasius niger using a combination of
    automated tracking, controlled pathogen exposure, transmission quantification,
    and temporally explicit simulations. Pathogen exposure induced behavioral changes
    in both exposed ants and their nestmates, which helped contain the disease by
    reinforcing key transmission-inhibitory properties of the colony's contact network.
    This suggests that social network plasticity in response to pathogens is an effective
    strategy for mitigating the effects of disease in social groups.
acknowledgement: This project was funded by two European Research Council Advanced
  Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science
  Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research
  Council Starting Grant (SocialVaccines, 243071) to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Nathalie
  full_name: Stroeymeyt, Nathalie
  last_name: Stroeymeyt
- first_name: Anna V
  full_name: Grasse, Anna V
  id: 406F989C-F248-11E8-B48F-1D18A9856A87
  last_name: Grasse
- first_name: Alessandro
  full_name: Crespi, Alessandro
  last_name: Crespi
- first_name: Danielle
  full_name: Mersch, Danielle
  last_name: Mersch
- first_name: Sylvia
  full_name: Cremer, Sylvia
  id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
  last_name: Cremer
  orcid: 0000-0002-2193-3868
- first_name: Laurent
  full_name: Keller, Laurent
  last_name: Keller
citation:
  ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
    plasticity decreases disease transmission in a eusocial insect. <i>Science</i>.
    2018;362(6417):941-945. doi:<a href="https://doi.org/10.1126/science.aat4793">10.1126/science.aat4793</a>
  apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller,
    L. (2018). Social network plasticity decreases disease transmission in a eusocial
    insect. <i>Science</i>. AAAS. <a href="https://doi.org/10.1126/science.aat4793">https://doi.org/10.1126/science.aat4793</a>
  chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
    Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
    Transmission in a Eusocial Insect.” <i>Science</i>. AAAS, 2018. <a href="https://doi.org/10.1126/science.aat4793">https://doi.org/10.1126/science.aat4793</a>.
  ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
    “Social network plasticity decreases disease transmission in a eusocial insect,”
    <i>Science</i>, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.
  ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
    network plasticity decreases disease transmission in a eusocial insect. Science.
    362(6417), 941–945.
  mla: Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission
    in a Eusocial Insect.” <i>Science</i>, vol. 362, no. 6417, AAAS, 2018, pp. 941–45,
    doi:<a href="https://doi.org/10.1126/science.aat4793">10.1126/science.aat4793</a>.
  short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science
    362 (2018) 941–945.
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-23T00:00:00Z
date_updated: 2023-10-17T11:50:05Z
day: '23'
department:
- _id: SyCr
doi: 10.1126/science.aat4793
ec_funded: 1
external_id:
  isi:
  - '000451124500041'
intvolume: '       362'
isi: 1
issue: '6417'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 941 - 945
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '243071'
  name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
    Effects'
publication: Science
publication_identifier:
  issn:
  - 1095-9203
publication_status: published
publisher: AAAS
publist_id: '8049'
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/
  record:
  - id: '13055'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 362
year: '2018'
...
---
_id: '70'
abstract:
- lang: eng
  text: We consider the totally asymmetric simple exclusion process in a critical
    scaling parametrized by a≥0, which creates a shock in the particle density of
    order aT−1/3, T the observation time. When starting from step initial data, we
    provide bounds on the limiting law which in particular imply that in the double
    limit lima→∞limT→∞ one recovers the product limit law and the degeneration of
    the correlation length observed at shocks of order 1. This result is shown to
    apply to a general last-passage percolation model. We also obtain bounds on the
    two-point functions of several airy processes.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
  full_name: Nejjar, Peter
  id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
  last_name: Nejjar
citation:
  ama: Nejjar P. Transition to shocks in TASEP and decoupling of last passage times.
    <i>Latin American Journal of Probability and Mathematical Statistics</i>. 2018;15(2):1311-1334.
    doi:<a href="https://doi.org/10.30757/ALEA.v15-49">10.30757/ALEA.v15-49</a>
  apa: Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage
    times. <i>Latin American Journal of Probability and Mathematical Statistics</i>.
    Instituto Nacional de Matematica Pura e Aplicada. <a href="https://doi.org/10.30757/ALEA.v15-49">https://doi.org/10.30757/ALEA.v15-49</a>
  chicago: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
    Times.” <i>Latin American Journal of Probability and Mathematical Statistics</i>.
    Instituto Nacional de Matematica Pura e Aplicada, 2018. <a href="https://doi.org/10.30757/ALEA.v15-49">https://doi.org/10.30757/ALEA.v15-49</a>.
  ieee: P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,”
    <i>Latin American Journal of Probability and Mathematical Statistics</i>, vol.
    15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.
  ista: Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage
    times. Latin American Journal of Probability and Mathematical Statistics. 15(2),
    1311–1334.
  mla: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
    Times.” <i>Latin American Journal of Probability and Mathematical Statistics</i>,
    vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34,
    doi:<a href="https://doi.org/10.30757/ALEA.v15-49">10.30757/ALEA.v15-49</a>.
  short: P. Nejjar, Latin American Journal of Probability and Mathematical Statistics
    15 (2018) 1311–1334.
date_created: 2018-12-11T11:44:28Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-10-10T13:11:29Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
- _id: JaMa
doi: 10.30757/ALEA.v15-49
ec_funded: 1
external_id:
  arxiv:
  - '1705.08836'
  isi:
  - '000460475800022'
file:
- access_level: open_access
  checksum: 2ded46aa284a836a8cbb34133a64f1cb
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-02-14T09:44:10Z
  date_updated: 2020-07-14T12:47:46Z
  file_id: '5981'
  file_name: 2018_ALEA_Nejjar.pdf
  file_size: 394851
  relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: '        15'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1311-1334
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '338804'
  name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '716117'
  name: Optimal Transport and Stochastic Dynamics
publication: Latin American Journal of Probability and Mathematical Statistics
publication_identifier:
  issn:
  - 1980-0436
publication_status: published
publisher: Instituto Nacional de Matematica Pura e Aplicada
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to shocks in TASEP and decoupling of last passage times
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '703'
abstract:
- lang: eng
  text: We consider the NP-hard problem of MAP-inference for undirected discrete graphical
    models. We propose a polynomial time and practically efficient algorithm for finding
    a part of its optimal solution. Specifically, our algorithm marks some labels
    of the considered graphical model either as (i) optimal, meaning that they belong
    to all optimal solutions of the inference problem; (ii) non-optimal if they provably
    do not belong to any solution. With access to an exact solver of a linear programming
    relaxation to the MAP-inference problem, our algorithm marks the maximal possible
    (in a specified sense) number of labels. We also present a version of the algorithm,
    which has access to a suboptimal dual solver only and still can ensure the (non-)optimality
    for the marked labels, although the overall number of the marked labels may decrease.
    We propose an efficient implementation, which runs in time comparable to a single
    run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art
    results on computational benchmarks from machine learning and computer vision.
arxiv: 1
author:
- first_name: Alexander
  full_name: Shekhovtsov, Alexander
  last_name: Shekhovtsov
- first_name: Paul
  full_name: Swoboda, Paul
  id: 446560C6-F248-11E8-B48F-1D18A9856A87
  last_name: Swoboda
- first_name: Bogdan
  full_name: Savchynskyy, Bogdan
  last_name: Savchynskyy
citation:
  ama: Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative
    relaxed inference with graphical models. <i>IEEE Transactions on Pattern Analysis
    and Machine Intelligence</i>. 2018;40(7):1668-1682. doi:<a href="https://doi.org/10.1109/TPAMI.2017.2730884">10.1109/TPAMI.2017.2730884</a>
  apa: Shekhovtsov, A., Swoboda, P., &#38; Savchynskyy, B. (2018). Maximum persistency
    via iterative relaxed inference with graphical models. <i>IEEE Transactions on
    Pattern Analysis and Machine Intelligence</i>. IEEE. <a href="https://doi.org/10.1109/TPAMI.2017.2730884">https://doi.org/10.1109/TPAMI.2017.2730884</a>
  chicago: Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum
    Persistency via Iterative Relaxed Inference with Graphical Models.” <i>IEEE Transactions
    on Pattern Analysis and Machine Intelligence</i>. IEEE, 2018. <a href="https://doi.org/10.1109/TPAMI.2017.2730884">https://doi.org/10.1109/TPAMI.2017.2730884</a>.
  ieee: A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative
    relaxed inference with graphical models,” <i>IEEE Transactions on Pattern Analysis
    and Machine Intelligence</i>, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.
  ista: Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative
    relaxed inference with graphical models. IEEE Transactions on Pattern Analysis
    and Machine Intelligence. 40(7), 1668–1682.
  mla: Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference
    with Graphical Models.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>,
    vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:<a href="https://doi.org/10.1109/TPAMI.2017.2730884">10.1109/TPAMI.2017.2730884</a>.
  short: A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern
    Analysis and Machine Intelligence 40 (2018) 1668–1682.
date_created: 2018-12-11T11:48:01Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2021-01-12T08:11:32Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/TPAMI.2017.2730884
external_id:
  arxiv:
  - '1508.07902'
intvolume: '        40'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1508.07902
month: '07'
oa: 1
oa_version: Preprint
page: 1668-1682
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_identifier:
  issn:
  - '01628828'
publication_status: published
publisher: IEEE
publist_id: '6992'
quality_controlled: '1'
scopus_import: 1
status: public
title: Maximum persistency via iterative relaxed inference with graphical models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2018'
...
---
_id: '705'
abstract:
- lang: eng
  text: Although dopamine receptors D1 and D2 play key roles in hippocampal function,
    their synaptic localization within the hippocampus has not been fully elucidated.
    In order to understand precise functions of pre- or postsynaptic dopamine receptors
    (DRs), the development of protocols to differentiate pre- and postsynaptic DRs
    is essential. So far, most studies on determination and quantification of DRs
    did not discriminate between subsynaptic localization. Therefore, the aim of the
    study was to generate a robust workflow for the localization of DRs. This work
    provides the basis for future work on hippocampal DRs, in light that DRs may have
    different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi
    isolated by a sucrose gradient protocol were prepared for super-resolution direct
    stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic
    zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated
    antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594
    enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites.
    D1R immunoreactivity clusters were observed within the presynaptic active zone
    as well as at perisynaptic sites at the edge of the presynaptic active zone. The
    results may be useful for the interpretation of previous studies and the design
    of future work on DRs in the hippocampus. Moreover, the reduction of the complexity
    of brain tissue by the use of synaptosomal preparations and dSTORM technology
    may represent a useful tool for synaptic localization of brain proteins.
article_processing_charge: No
author:
- first_name: Andras
  full_name: Miklosi, Andras
  last_name: Miklosi
- first_name: Giorgia
  full_name: Del Favero, Giorgia
  last_name: Del Favero
- first_name: Tanja
  full_name: Bulat, Tanja
  last_name: Bulat
- first_name: Harald
  full_name: Höger, Harald
  last_name: Höger
- first_name: Ryuichi
  full_name: Shigemoto, Ryuichi
  id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
  last_name: Shigemoto
  orcid: 0000-0001-8761-9444
- first_name: Doris
  full_name: Marko, Doris
  last_name: Marko
- first_name: Gert
  full_name: Lubec, Gert
  last_name: Lubec
citation:
  ama: Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization
    of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. <i>Molecular Neurobiology</i>.
    2018;55(6):4857 – 4869. doi:<a href="https://doi.org/10.1007/s12035-017-0688-y">10.1007/s12035-017-0688-y</a>
  apa: Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D.,
    &#38; Lubec, G. (2018). Super resolution microscopical localization of dopamine
    receptors 1 and 2 in rat hippocampal synaptosomes. <i>Molecular Neurobiology</i>.
    Springer. <a href="https://doi.org/10.1007/s12035-017-0688-y">https://doi.org/10.1007/s12035-017-0688-y</a>
  chicago: Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi
    Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization
    of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” <i>Molecular Neurobiology</i>.
    Springer, 2018. <a href="https://doi.org/10.1007/s12035-017-0688-y">https://doi.org/10.1007/s12035-017-0688-y</a>.
  ieee: A. Miklosi <i>et al.</i>, “Super resolution microscopical localization of
    dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” <i>Molecular Neurobiology</i>,
    vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.
  ista: Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G.
    2018. Super resolution microscopical localization of dopamine receptors 1 and
    2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.
  mla: Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine
    Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” <i>Molecular Neurobiology</i>,
    vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:<a href="https://doi.org/10.1007/s12035-017-0688-y">10.1007/s12035-017-0688-y</a>.
  short: A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G.
    Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.
date_created: 2018-12-11T11:48:02Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T09:58:11Z
day: '01'
department:
- _id: RySh
doi: 10.1007/s12035-017-0688-y
external_id:
  isi:
  - '000431991500025'
intvolume: '        55'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 4857 – 4869
publication: Molecular Neurobiology
publication_status: published
publisher: Springer
publist_id: '6991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Super resolution microscopical localization of dopamine receptors 1 and 2 in
  rat hippocampal synaptosomes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 55
year: '2018'
...
---
_id: '7116'
abstract:
- lang: eng
  text: 'Training deep learning models has received tremendous research interest recently.
    In particular, there has been intensive research on reducing the communication
    cost of training when using multiple computational devices, through reducing the
    precision of the underlying data representation. Naturally, such methods induce
    system trade-offs—lowering communication precision could de-crease communication
    overheads and improve scalability; but, on the other hand, it can also reduce
    the accuracy of training. In this paper, we study this trade-off space, and ask:Can
    low-precision communication consistently improve the end-to-end performance of
    training modern neural networks, with no accuracy loss?From the performance point
    of view, the answer to this question may appear deceptively easy: compressing
    communication through low precision should help when the ratio between communication
    and computation is high. However, this answer is less straightforward when we
    try to generalize this principle across various neural network architectures (e.g.,
    AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g.,
    EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL),
    and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is
    not clear how a realistic realization of all these factors maps to the speed up
    provided by low-precision communication. In this paper, we conduct an empirical
    study to answer this question and report the insights.'
article_processing_charge: No
author:
- first_name: Demjan
  full_name: Grubic, Demjan
  last_name: Grubic
- first_name: Leo
  full_name: Tam, Leo
  last_name: Tam
- 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: Ce
  full_name: Zhang, Ce
  last_name: Zhang
citation:
  ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for
    deep learning with low-precision communications: An empirical study. In: <i>Proceedings
    of the 21st International Conference on Extending Database Technology</i>. OpenProceedings;
    2018:145-156. doi:<a href="https://doi.org/10.5441/002/EDBT.2018.14">10.5441/002/EDBT.2018.14</a>'
  apa: 'Grubic, D., Tam, L., Alistarh, D.-A., &#38; Zhang, C. (2018). Synchronous
    multi-GPU training for deep learning with low-precision communications: An empirical
    study. In <i>Proceedings of the 21st International Conference on Extending Database
    Technology</i> (pp. 145–156). Vienna, Austria: OpenProceedings. <a href="https://doi.org/10.5441/002/EDBT.2018.14">https://doi.org/10.5441/002/EDBT.2018.14</a>'
  chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous
    Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical
    Study.” In <i>Proceedings of the 21st International Conference on Extending Database
    Technology</i>, 145–56. OpenProceedings, 2018. <a href="https://doi.org/10.5441/002/EDBT.2018.14">https://doi.org/10.5441/002/EDBT.2018.14</a>.'
  ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training
    for deep learning with low-precision communications: An empirical study,” in <i>Proceedings
    of the 21st International Conference on Extending Database Technology</i>, Vienna,
    Austria, 2018, pp. 145–156.'
  ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training
    for deep learning with low-precision communications: An empirical study. Proceedings
    of the 21st International Conference on Extending Database Technology. EDBT: Conference
    on Extending Database Technology, 145–156.'
  mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with
    Low-Precision Communications: An Empirical Study.” <i>Proceedings of the 21st
    International Conference on Extending Database Technology</i>, OpenProceedings,
    2018, pp. 145–56, doi:<a href="https://doi.org/10.5441/002/EDBT.2018.14">10.5441/002/EDBT.2018.14</a>.'
  short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st
    International Conference on Extending Database Technology, OpenProceedings, 2018,
    pp. 145–156.
conference:
  end_date: 2018-03-29
  location: Vienna, Austria
  name: 'EDBT: Conference on Extending Database Technology'
  start_date: 2018-03-26
date_created: 2019-11-26T14:19:11Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2023-02-23T12:59:17Z
day: '26'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.5441/002/EDBT.2018.14
file:
- access_level: open_access
  checksum: ec979b56abc71016d6e6adfdadbb4afe
  content_type: application/pdf
  creator: dernst
  date_created: 2019-11-26T14:23:04Z
  date_updated: 2020-07-14T12:47:49Z
  file_id: '7118'
  file_name: 2018_OpenProceedings_Grubic.pdf
  file_size: 1603204
  relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 145-156
publication: Proceedings of the 21st International Conference on Extending Database
  Technology
publication_identifier:
  isbn:
  - '9783893180783'
  issn:
  - 2367-2005
publication_status: published
publisher: OpenProceedings
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Synchronous multi-GPU training for deep learning with low-precision communications:
  An empirical study'
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7123'
abstract:
- lang: eng
  text: "Population protocols are a popular model of distributed computing, in which
    n agents with limited local state interact randomly, and cooperate to collectively
    compute global predicates. Inspired by recent developments in DNA programming,
    an extensive series of papers, across different communities, has examined the
    computability and complexity characteristics of this model. Majority, or consensus,
    is a central task in this model, in which agents need to collectively reach a
    decision as to which one of two states A or B had a higher initial count. Two
    metrics are important: the time that a protocol requires to stabilize to an output
    decision, and the state space size that each agent requires to do so. It is known
    that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic
    time) stabilization, and that O(log2 n) states are sufficient. Thus, there is
    an exponential gap between the space upper and lower bounds for this problem.
    This paper addresses this question.\r\n\r\nOn the negative side, we provide a
    new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c)
    expected time, for any constant c > 0. This result is conditional on monotonicity
    and output assumptions, satisfied by all known protocols. Technically, it represents
    a departure from previous lower bounds, in that it does not rely on the existence
    of dense configurations. Instead, we introduce a new generalized surgery technique
    to prove the existence of incorrect executions for any algorithm which would contradict
    the lower bound. Subsequently, our lower bound also applies to general initial
    configurations, including ones with a leader. On the positive side, we give a
    new algorithm for majority which uses O(log n) states, and stabilizes in O(log2
    n) expected time. Central to the algorithm is a new leaderless phase clock technique,
    which allows agents to synchronize in phases of Θ(n log n) consecutive interactions
    using O(log n) states per agent, exploiting a new connection between population
    protocols and power-of-two-choices load balancing mechanisms. We also employ our
    phase clock to build a leader election algorithm with a state space of size O(log
    n), which stabilizes in O(log2 n) expected time."
article_processing_charge: No
arxiv: 1
author:
- 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: James
  full_name: Aspnes, James
  last_name: Aspnes
- first_name: Rati
  full_name: Gelashvili, Rati
  last_name: Gelashvili
citation:
  ama: 'Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population
    protocols. In: <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
    Algorithms</i>. ACM; 2018:2221-2239. doi:<a href="https://doi.org/10.1137/1.9781611975031.144">10.1137/1.9781611975031.144</a>'
  apa: 'Alistarh, D.-A., Aspnes, J., &#38; Gelashvili, R. (2018). Space-optimal majority
    in population protocols. In <i>Proceedings of the 29th Annual ACM-SIAM Symposium
    on Discrete Algorithms</i> (pp. 2221–2239). New Orleans, LA, United States: ACM.
    <a href="https://doi.org/10.1137/1.9781611975031.144">https://doi.org/10.1137/1.9781611975031.144</a>'
  chicago: Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal
    Majority in Population Protocols.” In <i>Proceedings of the 29th Annual ACM-SIAM
    Symposium on Discrete Algorithms</i>, 2221–39. ACM, 2018. <a href="https://doi.org/10.1137/1.9781611975031.144">https://doi.org/10.1137/1.9781611975031.144</a>.
  ieee: D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population
    protocols,” in <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
    Algorithms</i>, New Orleans, LA, United States, 2018, pp. 2221–2239.
  ista: 'Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population
    protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms.
    SODA: Symposium on Discrete Algorithms, 2221–2239.'
  mla: Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.”
    <i>Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>,
    ACM, 2018, pp. 2221–39, doi:<a href="https://doi.org/10.1137/1.9781611975031.144">10.1137/1.9781611975031.144</a>.
  short: D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual
    ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.
conference:
  end_date: 2018-01-10
  location: New Orleans, LA, United States
  name: 'SODA: Symposium on Discrete Algorithms'
  start_date: 2018-01-07
date_created: 2019-11-26T15:10:55Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2023-09-19T15:03:16Z
day: '30'
department:
- _id: DaAl
doi: 10.1137/1.9781611975031.144
external_id:
  arxiv:
  - '1704.04947'
  isi:
  - '000483921200145'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1704.04947
month: '01'
oa: 1
oa_version: Preprint
page: 2221-2239
publication: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
  isbn:
  - '9781611975031'
publication_status: published
publisher: ACM
quality_controlled: '1'
status: public
title: Space-optimal majority in population protocols
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '723'
abstract:
- lang: eng
  text: Escaping local optima is one of the major obstacles to function optimisation.
    Using the metaphor of a fitness landscape, local optima correspond to hills separated
    by fitness valleys that have to be overcome. We define a class of fitness valleys
    of tunable difficulty by considering their length, representing the Hamming path
    between the two optima and their depth, the drop in fitness. For this function
    class we present a runtime comparison between stochastic search algorithms using
    different search strategies. The (1+1) EA is a simple and well-studied evolutionary
    algorithm that has to jump across the valley to a point of higher fitness because
    it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm
    and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population
    genetics, are both able to cross the fitness valley by accepting worsening moves.
    We show that the runtime of the (1+1) EA depends critically on the length of the
    valley while the runtimes of the non-elitist algorithms depend crucially on the
    depth of the valley. Moreover, we show that both SSWM and Metropolis can also
    efficiently optimise a rugged function consisting of consecutive valleys.
article_processing_charge: No
author:
- first_name: Pietro
  full_name: Oliveto, Pietro
  last_name: Oliveto
- first_name: Tiago
  full_name: Paixao, Tiago
  id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
  last_name: Paixao
  orcid: 0000-0003-2361-3953
- first_name: Jorge
  full_name: Pérez Heredia, Jorge
  last_name: Pérez Heredia
- first_name: Dirk
  full_name: Sudholt, Dirk
  last_name: Sudholt
- first_name: Barbora
  full_name: Trubenova, Barbora
  id: 42302D54-F248-11E8-B48F-1D18A9856A87
  last_name: Trubenova
  orcid: 0000-0002-6873-2967
citation:
  ama: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape
    local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>.
    2018;80(5):1604-1633. doi:<a href="https://doi.org/10.1007/s00453-017-0369-2">10.1007/s00453-017-0369-2</a>
  apa: Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B.
    (2018). How to escape local optima in black box optimisation when non elitism
    outperforms elitism. <i>Algorithmica</i>. Springer. <a href="https://doi.org/10.1007/s00453-017-0369-2">https://doi.org/10.1007/s00453-017-0369-2</a>
  chicago: Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora
    Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism
    Outperforms Elitism.” <i>Algorithmica</i>. Springer, 2018. <a href="https://doi.org/10.1007/s00453-017-0369-2">https://doi.org/10.1007/s00453-017-0369-2</a>.
  ieee: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How
    to escape local optima in black box optimisation when non elitism outperforms
    elitism,” <i>Algorithmica</i>, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.
  ista: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to
    escape local optima in black box optimisation when non elitism outperforms elitism.
    Algorithmica. 80(5), 1604–1633.
  mla: Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation
    When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>, vol. 80, no. 5, Springer,
    2018, pp. 1604–33, doi:<a href="https://doi.org/10.1007/s00453-017-0369-2">10.1007/s00453-017-0369-2</a>.
  short: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica
    80 (2018) 1604–1633.
date_created: 2018-12-11T11:48:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:11:35Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-017-0369-2
ec_funded: 1
external_id:
  isi:
  - '000428239300010'
file:
- access_level: open_access
  checksum: 7d92f5d7be81e387edeec4f06442791c
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:14Z
  date_updated: 2020-07-14T12:47:54Z
  file_id: '4674'
  file_name: IST-2018-1014-v1+1_2018_Paixao_Escape.pdf
  file_size: 691245
  relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: '        80'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1604 - 1633
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '618091'
  name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6957'
pubrep_id: '1014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to escape local optima in black box optimisation when non elitism outperforms
  elitism
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 80
year: '2018'
...
---
_id: '738'
abstract:
- lang: eng
  text: 'This paper is devoted to automatic competitive analysis of real-time scheduling
    algorithms for firm-deadline tasksets, where only completed tasks con- tribute
    some utility to the system. Given such a taskset T , the competitive ratio of
    an on-line scheduling algorithm A for T is the worst-case utility ratio of A over
    the utility achieved by a clairvoyant algorithm. We leverage the theory of quantitative
    graph games to address the competitive analysis and competitive synthesis problems.
    For the competitive analysis case, given any taskset T and any finite-memory on-
    line scheduling algorithm A , we show that the competitive ratio of A in T can
    be computed in polynomial time in the size of the state space of A . Our approach
    is flexible as it also provides ways to model meaningful constraints on the released
    task sequences that determine the competitive ratio. We provide an experimental
    study of many well-known on-line scheduling algorithms, which demonstrates the
    feasibility of our competitive analysis approach that effectively replaces human
    ingenuity (required Preliminary versions of this paper have appeared in Chatterjee
    et al. ( 2013 , 2014 ). B Andreas Pavlogiannis pavlogiannis@ist.ac.at Krishnendu
    Chatterjee krish.chat@ist.ac.at Alexander Kößler koe@ecs.tuwien.ac.at Ulrich Schmid
    s@ecs.tuwien.ac.at 1 IST Austria (Institute of Science and Technology Austria),
    Am Campus 1, 3400 Klosterneuburg, Austria 2 Embedded Computing Systems Group,
    Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria 123 Real-Time
    Syst for finding worst-case scenarios) by computing power. For the competitive
    synthesis case, we are just given a taskset T , and the goal is to automatically
    synthesize an opti- mal on-line scheduling algorithm A , i.e., one that guarantees
    the largest competitive ratio possible for T . We show how the competitive synthesis
    problem can be reduced to a two-player graph game with partial information, and
    establish that the compu- tational complexity of solving this game is Np -complete.
    The competitive synthesis problem is hence in Np in the size of the state space
    of the non-deterministic labeled transition system encoding the taskset. Overall,
    the proposed framework assists in the selection of suitable scheduling algorithms
    for a given taskset, which is in fact the most common situation in real-time systems
    design. '
article_processing_charge: No
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Andreas
  full_name: Pavlogiannis, Andreas
  id: 49704004-F248-11E8-B48F-1D18A9856A87
  last_name: Pavlogiannis
  orcid: 0000-0002-8943-0722
- first_name: Alexander
  full_name: Kößler, Alexander
  last_name: Kößler
- first_name: Ulrich
  full_name: Schmid, Ulrich
  last_name: Schmid
citation:
  ama: Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. Automated competitive analysis
    of real time scheduling with graph games. <i>Real-Time Systems</i>. 2018;54(1):166-207.
    doi:<a href="https://doi.org/10.1007/s11241-017-9293-4">10.1007/s11241-017-9293-4</a>
  apa: Chatterjee, K., Pavlogiannis, A., Kößler, A., &#38; Schmid, U. (2018). Automated
    competitive analysis of real time scheduling with graph games. <i>Real-Time Systems</i>.
    Springer. <a href="https://doi.org/10.1007/s11241-017-9293-4">https://doi.org/10.1007/s11241-017-9293-4</a>
  chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich
    Schmid. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.”
    <i>Real-Time Systems</i>. Springer, 2018. <a href="https://doi.org/10.1007/s11241-017-9293-4">https://doi.org/10.1007/s11241-017-9293-4</a>.
  ieee: K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “Automated competitive
    analysis of real time scheduling with graph games,” <i>Real-Time Systems</i>,
    vol. 54, no. 1. Springer, pp. 166–207, 2018.
  ista: Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2018. Automated competitive
    analysis of real time scheduling with graph games. Real-Time Systems. 54(1), 166–207.
  mla: Chatterjee, Krishnendu, et al. “Automated Competitive Analysis of Real Time
    Scheduling with Graph Games.” <i>Real-Time Systems</i>, vol. 54, no. 1, Springer,
    2018, pp. 166–207, doi:<a href="https://doi.org/10.1007/s11241-017-9293-4">10.1007/s11241-017-9293-4</a>.
  short: K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, Real-Time Systems 54
    (2018) 166–207.
date_created: 2018-12-11T11:48:14Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-27T12:52:38Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/s11241-017-9293-4
ec_funded: 1
external_id:
  isi:
  - '000419955500006'
file:
- access_level: open_access
  checksum: c2590ef160709d8054cf29ee173f1454
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:17:14Z
  date_updated: 2020-07-14T12:47:56Z
  file_id: '5267'
  file_name: IST-2018-960-v1+1_2017_Chatterjee_Automated_competetive.pdf
  file_size: 1163507
  relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: '        54'
isi: 1
issue: '1'
language:
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month: '01'
oa: 1
oa_version: Published Version
page: 166 - 207
project:
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  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11407
  name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P 23499-N23
  name: Modern Graph Algorithmic Techniques in Formal Verification
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  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
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  name: Microsoft Research Faculty Fellowship
publication: Real-Time Systems
publication_status: published
publisher: Springer
publist_id: '6929'
pubrep_id: '960'
quality_controlled: '1'
related_material:
  record:
  - id: '2820'
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scopus_import: '1'
status: public
title: Automated competitive analysis of real time scheduling with graph games
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  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2018'
...
---
_id: '7407'
abstract:
- lang: eng
  text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems
    where a prover can convince a verifier that he "wastes" disk space. PoS were introduced
    as a more ecological and economical replacement for proofs of work which are currently
    used to secure blockchains like Bitcoin. In this work we investigate extensions
    of PoS which allow the prover to embed useful data into the dedicated space, which
    later can be recovered. Our first contribution is a security proof for the original
    PoS from CRYPTO''15 in the random oracle model (the original proof only applied
    to a restricted class of adversaries which can store a subset of the data an honest
    prover would store). When this PoS is instantiated with recent constructions of
    maximally depth robust graphs, our proof implies basically optimal security. As
    a second contribution we show three different extensions of this PoS where useful
    data can be embedded into the space required by the prover. Our security proof
    for the PoS extends (non-trivially) to these constructions. We discuss how some
    of these variants can be used as proofs of catalytic space (PoCS), a notion we
    put forward in this work, and which basically is a PoS where most of the space
    required by the prover can be used to backup useful data. Finally we discuss how
    one of the extensions is a candidate construction for a proof of replication (PoR),
    a proof system recently suggested in the Filecoin whitepaper. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Krzysztof Z
  full_name: Pietrzak, Krzysztof Z
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Pietrzak KZ. Proofs of catalytic space. In: <i>10th Innovations in Theoretical
    Computer Science  Conference (ITCS 2019)</i>. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum
    für Informatik; 2018:59:1-59:25. doi:<a href="https://doi.org/10.4230/LIPICS.ITCS.2019.59">10.4230/LIPICS.ITCS.2019.59</a>'
  apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In <i>10th Innovations
    in Theoretical Computer Science  Conference (ITCS 2019)</i> (Vol. 124, p. 59:1-59:25).
    San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
    <a href="https://doi.org/10.4230/LIPICS.ITCS.2019.59">https://doi.org/10.4230/LIPICS.ITCS.2019.59</a>'
  chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In <i>10th Innovations
    in Theoretical Computer Science  Conference (ITCS 2019)</i>, 124:59:1-59:25. Schloss
    Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href="https://doi.org/10.4230/LIPICS.ITCS.2019.59">https://doi.org/10.4230/LIPICS.ITCS.2019.59</a>.
  ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in <i>10th Innovations in Theoretical
    Computer Science  Conference (ITCS 2019)</i>, San Diego, CA, United States, 2018,
    vol. 124, p. 59:1-59:25.
  ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical
    Computer Science  Conference (ITCS 2019). ITCS: Innovations in theoretical Computer
    Science Conference, LIPIcs, vol. 124, 59:1-59:25.'
  mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” <i>10th Innovations in
    Theoretical Computer Science  Conference (ITCS 2019)</i>, vol. 124, Schloss Dagstuhl
    - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:<a href="https://doi.org/10.4230/LIPICS.ITCS.2019.59">10.4230/LIPICS.ITCS.2019.59</a>.
  short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science  Conference
    (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.
conference:
  end_date: 2019-01-12
  location: San Diego, CA, United States
  name: 'ITCS: Innovations in theoretical Computer Science Conference'
  start_date: 2019-01-10
date_created: 2020-01-30T09:16:05Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2021-01-12T08:13:26Z
day: '31'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.4230/LIPICS.ITCS.2019.59
ec_funded: 1
file:
- access_level: open_access
  checksum: 5cebb7f7849a3beda898f697d755dd96
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  creator: dernst
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  date_updated: 2020-07-14T12:47:57Z
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  file_name: 2018_LIPIcs_Pietrzak.pdf
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file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: '       124'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2018/194
month: '12'
oa: 1
oa_version: Published Version
page: 59:1-59:25
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
publication: 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019)
publication_identifier:
  isbn:
  - 978-3-95977-095-8
  issn:
  - 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Proofs of catalytic space
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  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2018'
...
---
_id: '742'
abstract:
- lang: eng
  text: 'We give a detailed and easily accessible proof of Gromov’s Topological Overlap
    Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral
    cell complex of dimension d. Informally, the theorem states that if X has sufficiently
    strong higher-dimensional expansion properties (which generalize edge expansion
    of graphs and are defined in terms of cellular cochains of X) then X has the following
    topological overlap property: for every continuous map (Formula presented.) there
    exists a point (Formula presented.) that is contained in the images of a positive
    fraction (Formula presented.) of the d-cells of X. More generally, the conclusion
    holds if (Formula presented.) is replaced by any d-dimensional piecewise-linear
    manifold M, with a constant (Formula presented.) that depends only on d and on
    the expansion properties of X, but not on M.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Dominic
  full_name: Dotterrer, Dominic
  last_name: Dotterrer
- first_name: Tali
  full_name: Kaufman, Tali
  last_name: Kaufman
- first_name: Uli
  full_name: Wagner, Uli
  id: 36690CA2-F248-11E8-B48F-1D18A9856A87
  last_name: Wagner
  orcid: 0000-0002-1494-0568
citation:
  ama: Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. <i>Geometriae
    Dedicata</i>. 2018;195(1):307–317. doi:<a href="https://doi.org/10.1007/s10711-017-0291-4">10.1007/s10711-017-0291-4</a>
  apa: Dotterrer, D., Kaufman, T., &#38; Wagner, U. (2018). On expansion and topological
    overlap. <i>Geometriae Dedicata</i>. Springer. <a href="https://doi.org/10.1007/s10711-017-0291-4">https://doi.org/10.1007/s10711-017-0291-4</a>
  chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological
    Overlap.” <i>Geometriae Dedicata</i>. Springer, 2018. <a href="https://doi.org/10.1007/s10711-017-0291-4">https://doi.org/10.1007/s10711-017-0291-4</a>.
  ieee: D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,”
    <i>Geometriae Dedicata</i>, vol. 195, no. 1. Springer, pp. 307–317, 2018.
  ista: Dotterrer D, Kaufman T, Wagner U. 2018. On expansion and topological overlap.
    Geometriae Dedicata. 195(1), 307–317.
  mla: Dotterrer, Dominic, et al. “On Expansion and Topological Overlap.” <i>Geometriae
    Dedicata</i>, vol. 195, no. 1, Springer, 2018, pp. 307–317, doi:<a href="https://doi.org/10.1007/s10711-017-0291-4">10.1007/s10711-017-0291-4</a>.
  short: D. Dotterrer, T. Kaufman, U. Wagner, Geometriae Dedicata 195 (2018) 307–317.
date_created: 2018-12-11T11:48:16Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-27T12:29:57Z
day: '01'
ddc:
- '514'
- '516'
department:
- _id: UlWa
doi: 10.1007/s10711-017-0291-4
external_id:
  isi:
  - '000437122700017'
file:
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  checksum: d2f70fc132156504aa4c626aa378a7ab
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-01-15T13:44:05Z
  date_updated: 2020-07-14T12:47:58Z
  file_id: '5835'
  file_name: s10711-017-0291-4.pdf
  file_size: 412486
  relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: '       195'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 307–317
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
  grant_number: PP00P2_138948
  name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '6925'
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quality_controlled: '1'
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    status: public
scopus_import: '1'
status: public
title: On expansion and topological overlap
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  image: /images/cc_by.png
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  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 195
year: '2018'
...
