---
_id: '6650'
abstract:
- lang: eng
  text: We propose a novel technique for the automatic design of molds to cast highly
    complex shapes. The technique generates composite, two-piece molds. Each mold
    piece is made up of a hard plastic shell and a flexible silicone part. Thanks
    to the thin, soft, and smartly shaped silicone part, which is kept in place by
    a hard plastic shell, we can cast objects of unprecedented complexity. An innovative
    algorithm based on a volumetric analysis defines the layout of the internal cuts
    in the silicone mold part. Our approach can robustly handle thin protruding features
    and intertwined topologies that have caused previous methods to fail. We compare
    our results with state of the art techniques, and we demonstrate the casting of
    shapes with extremely complex geometry.
article_number: '110'
article_processing_charge: No
author:
- first_name: Thomas
  full_name: Alderighi, Thomas
  last_name: Alderighi
- first_name: Luigi
  full_name: Malomo, Luigi
  last_name: Malomo
- first_name: Daniela
  full_name: Giorgi, Daniela
  last_name: Giorgi
- first_name: Bernd
  full_name: Bickel, Bernd
  id: 49876194-F248-11E8-B48F-1D18A9856A87
  last_name: Bickel
  orcid: 0000-0001-6511-9385
- first_name: Paolo
  full_name: Cignoni, Paolo
  last_name: Cignoni
- first_name: Nico
  full_name: Pietroni, Nico
  last_name: Pietroni
citation:
  ama: Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware
    design of composite molds. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a
    href="https://doi.org/10.1145/3306346.3322981">10.1145/3306346.3322981</a>
  apa: Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., &#38; Pietroni,
    N. (2019). Volume-aware design of composite molds. <i>ACM Transactions on Graphics</i>.
    ACM. <a href="https://doi.org/10.1145/3306346.3322981">https://doi.org/10.1145/3306346.3322981</a>
  chicago: Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni,
    and Nico Pietroni. “Volume-Aware Design of Composite Molds.” <i>ACM Transactions
    on Graphics</i>. ACM, 2019. <a href="https://doi.org/10.1145/3306346.3322981">https://doi.org/10.1145/3306346.3322981</a>.
  ieee: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni,
    “Volume-aware design of composite molds,” <i>ACM Transactions on Graphics</i>,
    vol. 38, no. 4. ACM, 2019.
  ista: Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware
    design of composite molds. ACM Transactions on Graphics. 38(4), 110.
  mla: Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” <i>ACM
    Transactions on Graphics</i>, vol. 38, no. 4, 110, ACM, 2019, doi:<a href="https://doi.org/10.1145/3306346.3322981">10.1145/3306346.3322981</a>.
  short: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM
    Transactions on Graphics 38 (2019).
date_created: 2019-07-19T06:18:15Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:35:52Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3306346.3322981
ec_funded: 1
external_id:
  isi:
  - '000475740600084'
file:
- access_level: open_access
  checksum: b4562af94672b44d2a501046427412af
  content_type: application/pdf
  creator: dernst
  date_created: 2019-07-19T06:18:53Z
  date_updated: 2020-07-14T12:47:35Z
  file_id: '6651'
  file_name: 2019_ACM_Alderighi_AuthorVersion.pdf
  file_size: 74316182
  relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: '        38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715767'
  name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
    Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
  issn:
  - 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
  link:
  - description: YouTube Video
    relation: supplementary_material
    url: https://youtu.be/SO349S8-x_w
scopus_import: '1'
status: public
title: Volume-aware design of composite molds
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6657'
abstract:
- lang: eng
  text: 'In this article a model is described how Open Access definitions can be formed
    on the basis of objective criteria. The common Open Access definitions such as
    "gold" and "green" are not exactly defined. This becomes a problem as soon as
    one begins to measure Open Access, for example if the development of the Open
    Access share should be monitored. This was discussed in the working group on Open
    Access Monitoring  of  the  AT2OA  project  and  the  present  model  was  developed,
    which is based on 5 critics with 4 characteristics: location, licence, version,
    embargo and conditions of the Open Access publication are taken into account.
    In the meantime, the model has also been tested in practice using R scripts, and
    the initial results are quite promising.'
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
  full_name: Danowski, Patrick
  id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
  last_name: Danowski
  orcid: 0000-0002-6026-4409
citation:
  ama: Danowski P. An Austrian proposal for the classification of Open Access Tuples
    (COAT) - distinguish different open access types beyond colors. <i>Mitteilungen
    der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2019;72(1):59-65.
    doi:<a href="https://doi.org/10.31263/voebm.v72i1.2276">10.31263/voebm.v72i1.2276</a>
  apa: Danowski, P. (2019). An Austrian proposal for the classification of Open Access
    Tuples (COAT) - distinguish different open access types beyond colors. <i>Mitteilungen
    Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. Vereinigung
    Österreichischer Bibliothekarinnen und Bibliothekare. <a href="https://doi.org/10.31263/voebm.v72i1.2276">https://doi.org/10.31263/voebm.v72i1.2276</a>
  chicago: Danowski, Patrick. “An Austrian Proposal for the Classification of Open
    Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.”
    <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>.
    Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. <a href="https://doi.org/10.31263/voebm.v72i1.2276">https://doi.org/10.31263/voebm.v72i1.2276</a>.
  ieee: P. Danowski, “An Austrian proposal for the classification of Open Access Tuples
    (COAT) - distinguish different open access types beyond colors,” <i>Mitteilungen
    der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol.
    72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp.
    59–65, 2019.
  ista: Danowski P. 2019. An Austrian proposal for the classification of Open Access
    Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen
    der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65.
  mla: Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access
    Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” <i>Mitteilungen
    Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>, vol.
    72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019,
    pp. 59–65, doi:<a href="https://doi.org/10.31263/voebm.v72i1.2276">10.31263/voebm.v72i1.2276</a>.
  short: P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
    Und Bibliothekare 72 (2019) 59–65.
date_created: 2019-07-21T21:59:15Z
date_published: 2019-05-17T00:00:00Z
date_updated: 2023-10-17T11:33:58Z
day: '17'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v72i1.2276
file:
- access_level: open_access
  checksum: c0d2695d6d0d34e62ba06fb3f0ebaaed
  content_type: application/pdf
  creator: apreinsp
  date_created: 2019-07-22T08:45:03Z
  date_updated: 2020-07-14T12:47:35Z
  file_id: '6661'
  file_name: 2019_MitteilungenDerVOEB_Danowski.pdf
  file_size: 468558
  relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: '        72'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 59-65
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
  eissn:
  - 1022-2588
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
quality_controlled: '1'
related_material:
  record:
  - id: '5686'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: An Austrian proposal for the classification of Open Access Tuples (COAT) -
  distinguish different open access types beyond colors
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2019'
...
---
_id: '6658'
abstract:
- lang: eng
  text: 'New genes are a major source of novelties, and a disproportionate amount
    of them are known to show testis expression in later phases of male gametogenesis
    in different groups such as mammals and plants. Here, we propose that this enhanced
    expression is a consequence of haploid selection during the latter stages of male
    gametogenesis. Because emerging adaptive mutations will be fixed faster if their
    phenotypes are expressed by haploid rather than diploid genotypes, new genes with
    advantageous functions arising during this unique stage of development have a
    better chance to become fixed. To test this hypothesis, expression levels of genes
    of differing evolutionary age were examined at various stages of Drosophila spermatogenesis.
    We found, consistent with a model based on haploid selection, that new Drosophila
    genes are both expressed in later haploid phases of spermatogenesis and harbor
    a significant enrichment of adaptive mutations. Additionally, the observed overexpression
    of new genes in the latter phases of spermatogenesis was limited to the autosomes.
    Because all male cells exhibit hemizygous expression for X-linked genes (and therefore
    effectively haploid), there is no expectation that selection acting on late spermatogenesis
    will have a different effect on X-linked genes in comparison to initial diploid
    phases. Together, our proposed hypothesis and the analyzed data suggest that natural
    selection in haploid cells elucidates several aspects of the origin of new genes
    by explaining the general prevalence of their testis expression, and a parsimonious
    solution for new alleles to avoid being lost by genetic drift or pseudogenization. '
article_processing_charge: No
author:
- first_name: Julia
  full_name: Raices, Julia
  id: 3EE67F22-F248-11E8-B48F-1D18A9856A87
  last_name: Raices
- first_name: Paulo
  full_name: Otto, Paulo
  last_name: Otto
- first_name: Maria
  full_name: Vibranovski, Maria
  last_name: Vibranovski
citation:
  ama: Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline
    expression. <i>Genome Research</i>. 2019;29(7):1115-1122. doi:<a href="https://doi.org/10.1101/gr.238824.118">10.1101/gr.238824.118</a>
  apa: Raices, J., Otto, P., &#38; Vibranovski, M. (2019). Haploid selection drives
    new gene male germline expression. <i>Genome Research</i>. CSH Press. <a href="https://doi.org/10.1101/gr.238824.118">https://doi.org/10.1101/gr.238824.118</a>
  chicago: Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives
    New Gene Male Germline Expression.” <i>Genome Research</i>. CSH Press, 2019. <a
    href="https://doi.org/10.1101/gr.238824.118">https://doi.org/10.1101/gr.238824.118</a>.
  ieee: J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene
    male germline expression,” <i>Genome Research</i>, vol. 29, no. 7. CSH Press,
    pp. 1115–1122, 2019.
  ista: Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male
    germline expression. Genome Research. 29(7), 1115–1122.
  mla: Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.”
    <i>Genome Research</i>, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:<a href="https://doi.org/10.1101/gr.238824.118">10.1101/gr.238824.118</a>.
  short: J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.
date_created: 2019-07-21T21:59:15Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:35:05Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1101/gr.238824.118
external_id:
  isi:
  - '000473730600007'
file:
- access_level: open_access
  checksum: 4636f03a6750f90b88bf2bc3eb9d71ae
  content_type: application/pdf
  creator: apreinsp
  date_created: 2019-07-24T08:05:56Z
  date_updated: 2020-07-14T12:47:35Z
  file_id: '6670'
  file_name: 2019_GenomeResearch_Raices.pdf
  file_size: 2319022
  relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: '        29'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1115-1122
publication: Genome Research
publication_status: published
publisher: CSH Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Haploid selection drives new gene male germline expression
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
_id: '6659'
abstract:
- lang: eng
  text: Chemical labeling of proteins with synthetic molecular probes offers the possibility
    to probe the functions of proteins of interest in living cells. However, the methods
    for covalently labeling targeted proteins using complementary peptide tag-probe
    pairs are still limited, irrespective of the versatility of such pairs in biological
    research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific
    covalent labeling of proteins. A broad-range evaluation of the reactivity profiles
    of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized
    and high labeling selectivity and reactivity. In particular, the labeling specificity
    of this pair was notably improved compared to the previously reported one. This
    pair was successfully utilized for the fluorescence imaging of membrane proteins
    on the surfaces of living cells, demonstrating its potential utility in biological
    research.
acknowledgement: his work was supported by the Grant-in-Aid for Scientific Research
  B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative
  Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no.
  JP17H06349 to A. O.); and the European Union (European Research Council Advanced
  grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges
  the financial support of the Takeda Science Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Naoki
  full_name: Zenmyo, Naoki
  last_name: Zenmyo
- first_name: Hiroki
  full_name: Tokumaru, Hiroki
  last_name: Tokumaru
- first_name: Shohei
  full_name: Uchinomiya, Shohei
  last_name: Uchinomiya
- first_name: Hirokazu
  full_name: Fuchida, Hirokazu
  last_name: Fuchida
- first_name: Shigekazu
  full_name: Tabata, Shigekazu
  id: 4427179E-F248-11E8-B48F-1D18A9856A87
  last_name: Tabata
- first_name: Itaru
  full_name: Hamachi, Itaru
  last_name: Hamachi
- first_name: Ryuichi
  full_name: Shigemoto, Ryuichi
  id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
  last_name: Shigemoto
  orcid: 0000-0001-8761-9444
- first_name: Akio
  full_name: Ojida, Akio
  last_name: Ojida
citation:
  ama: Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis
    tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins.
    <i>Bulletin of the Chemical Society of Japan</i>. 2019;92(5):995-1000. doi:<a
    href="https://doi.org/10.1246/bcsj.20190034">10.1246/bcsj.20190034</a>
  apa: Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi,
    I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA
    probe for highly selective chemical labeling of membrane proteins. <i>Bulletin
    of the Chemical Society of Japan</i>. Bulletin of the Chemical Society of Japan.
    <a href="https://doi.org/10.1246/bcsj.20190034">https://doi.org/10.1246/bcsj.20190034</a>
  chicago: Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu
    Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction
    Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling
    of Membrane Proteins.” <i>Bulletin of the Chemical Society of Japan</i>. Bulletin
    of the Chemical Society of Japan, 2019. <a href="https://doi.org/10.1246/bcsj.20190034">https://doi.org/10.1246/bcsj.20190034</a>.
  ieee: N. Zenmyo <i>et al.</i>, “Optimized reaction pair of the CysHis tag and Ni(II)-NTA
    probe for highly selective chemical labeling of membrane proteins,” <i>Bulletin
    of the Chemical Society of Japan</i>, vol. 92, no. 5. Bulletin of the Chemical
    Society of Japan, pp. 995–1000, 2019.
  ista: Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto
    R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe
    for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical
    Society of Japan. 92(5), 995–1000.
  mla: Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA
    Probe for Highly Selective Chemical Labeling of Membrane Proteins.” <i>Bulletin
    of the Chemical Society of Japan</i>, vol. 92, no. 5, Bulletin of the Chemical
    Society of Japan, 2019, pp. 995–1000, doi:<a href="https://doi.org/10.1246/bcsj.20190034">10.1246/bcsj.20190034</a>.
  short: N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi,
    R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000.
date_created: 2019-07-21T21:59:16Z
date_published: 2019-05-15T00:00:00Z
date_updated: 2021-01-12T08:08:26Z
day: '15'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1246/bcsj.20190034
ec_funded: 1
file:
- access_level: open_access
  checksum: 186de511d6e0ca93f5d981e2443eb8cd
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-02T08:49:58Z
  date_updated: 2020-10-02T08:49:58Z
  file_id: '8594'
  file_name: 2019_BCSJ_Zenmyo.pdf
  file_size: 2464903
  relation: main_file
  success: 1
file_date_updated: 2020-10-02T08:49:58Z
has_accepted_license: '1'
intvolume: '        92'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 995-1000
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '694539'
  name: 'In situ analysis of single channel subunit composition in neurons: physiological
    implication in synaptic plasticity and behaviour'
publication: Bulletin of the Chemical Society of Japan
publication_identifier:
  issn:
  - '00092673'
publication_status: published
publisher: Bulletin of the Chemical Society of Japan
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective
  chemical labeling of membrane proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2019'
...
---
_id: '6660'
abstract:
- lang: eng
  text: "Commercially available full-color 3D printing allows for detailed control
    of material deposition in a volume, but an exact reproduction of a target surface
    appearance is hampered by the strong subsurface scattering that causes nontrivial
    volumetric cross-talk at the print surface. Previous work showed how an iterative
    optimization scheme based on accumulating absorptive materials at the surface
    can be used to find a volumetric distribution of print materials that closely
    approximates a given target appearance.\r\n\r\nIn this work, we first revisit
    the assumption that pushing the absorptive materials to the surface results in
    minimal volumetric cross-talk. We design a full-fledged optimization on a small
    domain for this task and confirm this previously reported heuristic. Then, we
    extend the above approach that is critically limited to color reproduction on
    planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color
    texture reproduction on 3D prints by effectively compensating for internal light
    scattering within arbitrarily shaped objects. In addition, we propose a content-aware
    gamut mapping that significantly improves color reproduction for the pathological
    case of thin geometric features. Using a wide range of sample objects with complex
    textures and geometries, we demonstrate color reproduction whose fidelity is superior
    to state-of-the-art drivers for color 3D printers."
article_number: '111'
article_processing_charge: No
author:
- first_name: Denis
  full_name: Sumin, Denis
  last_name: Sumin
- first_name: Tim
  full_name: Weyrich, Tim
  last_name: Weyrich
- first_name: Tobias
  full_name: Rittig, Tobias
  last_name: Rittig
- first_name: Vahid
  full_name: Babaei, Vahid
  last_name: Babaei
- first_name: Thomas
  full_name: Nindel, Thomas
  last_name: Nindel
- first_name: Alexander
  full_name: Wilkie, Alexander
  last_name: Wilkie
- first_name: Piotr
  full_name: Didyk, Piotr
  last_name: Didyk
- first_name: Bernd
  full_name: Bickel, Bernd
  id: 49876194-F248-11E8-B48F-1D18A9856A87
  last_name: Bickel
  orcid: 0000-0001-6511-9385
- first_name: Jaroslav
  full_name: Křivánek, Jaroslav
  last_name: Křivánek
- first_name: Karol
  full_name: Myszkowski, Karol
  last_name: Myszkowski
citation:
  ama: Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation
    for 3D printing. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href="https://doi.org/10.1145/3306346.3322992">10.1145/3306346.3322992</a>
  apa: Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski,
    K. (2019). Geometry-aware scattering compensation for 3D printing. <i>ACM Transactions
    on Graphics</i>. ACM. <a href="https://doi.org/10.1145/3306346.3322992">https://doi.org/10.1145/3306346.3322992</a>
  chicago: Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel,
    Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski.
    “Geometry-Aware Scattering Compensation for 3D Printing.” <i>ACM Transactions
    on Graphics</i>. ACM, 2019. <a href="https://doi.org/10.1145/3306346.3322992">https://doi.org/10.1145/3306346.3322992</a>.
  ieee: D. Sumin <i>et al.</i>, “Geometry-aware scattering compensation for 3D printing,”
    <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.
  ista: Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel
    B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for
    3D printing. ACM Transactions on Graphics. 38(4), 111.
  mla: Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.”
    <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 111, ACM, 2019, doi:<a href="https://doi.org/10.1145/3306346.3322992">10.1145/3306346.3322992</a>.
  short: D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk,
    B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).
date_created: 2019-07-22T07:22:28Z
date_published: 2019-07-04T00:00:00Z
date_updated: 2023-08-29T06:40:49Z
day: '04'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3306346.3322992
ec_funded: 1
external_id:
  isi:
  - '000475740600085'
file:
- access_level: open_access
  checksum: 43c2019d6b48ed9c56e31686c4c2d1f5
  content_type: application/pdf
  creator: dernst
  date_created: 2019-07-24T07:36:08Z
  date_updated: 2020-07-14T12:47:36Z
  file_id: '6669'
  file_name: 2019_ACM_Sumin_AuthorVersion.pdf
  file_size: 10109800
  relation: main_file
- access_level: open_access
  checksum: f80f365a04e35855fa467ea7ab26b16c
  content_type: application/zip
  creator: dernst
  date_created: 2019-10-11T06:51:07Z
  date_updated: 2020-07-14T12:47:36Z
  file_id: '6938'
  file_name: sumin19geometry-aware-suppl.zip
  file_size: 11051245
  relation: supplementary_material
file_date_updated: 2020-07-14T12:47:36Z
has_accepted_license: '1'
intvolume: '        38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '642841'
  name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715767'
  name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
    Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
  issn:
  - 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry-aware scattering compensation for 3D printing
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6671'
abstract:
- lang: eng
  text: 'In this paper we discuss three results. The first two concern general sets
    of positive reach: we first characterize the reach of a closed set by means of
    a bound on the metric distortion between the distance measured in the ambient
    Euclidean space and the shortest path distance measured in the set. Secondly,
    we prove that the intersection of a ball with radius less than the reach with
    the set is geodesically convex, meaning that the shortest path between any two
    points in the intersection lies itself in the intersection. For our third result
    we focus on manifolds with positive reach and give a bound on the angle between
    tangent spaces at two different points in terms of the reach and the distance
    between the two points.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jean-Daniel
  full_name: Boissonnat, Jean-Daniel
  last_name: Boissonnat
- first_name: André
  full_name: Lieutier, André
  last_name: Lieutier
- first_name: Mathijs
  full_name: Wintraecken, Mathijs
  id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
  last_name: Wintraecken
  orcid: 0000-0002-7472-2220
citation:
  ama: Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic
    convexity and the variation of tangent spaces. <i>Journal of Applied and Computational
    Topology</i>. 2019;3(1-2):29–58. doi:<a href="https://doi.org/10.1007/s41468-019-00029-8">10.1007/s41468-019-00029-8</a>
  apa: Boissonnat, J.-D., Lieutier, A., &#38; Wintraecken, M. (2019). The reach, metric
    distortion, geodesic convexity and the variation of tangent spaces. <i>Journal
    of Applied and Computational Topology</i>. Springer Nature. <a href="https://doi.org/10.1007/s41468-019-00029-8">https://doi.org/10.1007/s41468-019-00029-8</a>
  chicago: Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The
    Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.”
    <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2019. <a
    href="https://doi.org/10.1007/s41468-019-00029-8">https://doi.org/10.1007/s41468-019-00029-8</a>.
  ieee: J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion,
    geodesic convexity and the variation of tangent spaces,” <i>Journal of Applied
    and Computational Topology</i>, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.
  ista: Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion,
    geodesic convexity and the variation of tangent spaces. Journal of Applied and
    Computational Topology. 3(1–2), 29–58.
  mla: Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity
    and the Variation of Tangent Spaces.” <i>Journal of Applied and Computational
    Topology</i>, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:<a href="https://doi.org/10.1007/s41468-019-00029-8">10.1007/s41468-019-00029-8</a>.
  short: J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational
    Topology 3 (2019) 29–58.
date_created: 2019-07-24T08:37:29Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-22T12:37:47Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s41468-019-00029-8
ec_funded: 1
file:
- access_level: open_access
  checksum: a5b244db9f751221409cf09c97ee0935
  content_type: application/pdf
  creator: dernst
  date_created: 2019-07-31T08:09:56Z
  date_updated: 2020-07-14T12:47:36Z
  file_id: '6741'
  file_name: 2019_JournAppliedComputTopol_Boissonnat.pdf
  file_size: 2215157
  relation: main_file
file_date_updated: 2020-07-14T12:47:36Z
has_accepted_license: '1'
intvolume: '         3'
issue: 1-2
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 29–58
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
  name: IST Austria Open Access Fund
publication: Journal of Applied and Computational Topology
publication_identifier:
  eissn:
  - 2367-1734
  issn:
  - 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The reach, metric distortion, geodesic convexity and the variation of tangent
  spaces
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2019'
...
---
_id: '6673'
abstract:
- lang: eng
  text: Several classic problems in graph processing and computational geometry are
    solved via incremental algorithms, which split computation into a series of small
    tasks acting on shared state, which gets updated progressively. While the sequential
    variant of such algorithms usually specifies a fixed (but sometimes random) order
    in which the tasks should be performed, a standard approach to parallelizing such
    algorithms is to relax this constraint to allow for out-of-order parallel execution.
    This is the case for parallel implementations of Dijkstra's single-source shortest-paths
    (SSSP) algorithm, and for parallel Delaunay mesh triangulation. While many software
    frameworks parallelize incremental computation in this way, it is still not well
    understood whether this relaxed ordering approach can still provide any complexity
    guarantees. In this paper, we address this problem, and analyze the efficiency
    guarantees provided by a range of incremental algorithms when parallelized via
    relaxed schedulers. We show that, for algorithms such as Delaunay mesh triangulation
    and sorting by insertion, schedulers with a maximum relaxation factor of k in
    terms of the maximum priority inversion allowed will introduce a maximum amount
    of wasted work of O(łog n poly(k)), where n is the number of tasks to be executed.
    For SSSP, we show that the additional work is O(poly(k), dmax / wmin), where dmax
    is the maximum distance between two nodes, and wmin is the minimum such distance.
    In practical settings where n >> k, this suggests that the overheads of relaxation
    will be outweighed by the improved scalability of the relaxed scheduler. On the
    negative side, we provide lower bounds showing that certain algorithms will inherently
    incur a non-trivial amount of wasted work due to scheduler relaxation, even for
    relatively benign relaxed schedulers.
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: Giorgi
  full_name: Nadiradze, Giorgi
  id: 3279A00C-F248-11E8-B48F-1D18A9856A87
  last_name: Nadiradze
  orcid: 0000-0001-5634-0731
- first_name: Nikita
  full_name: Koval, Nikita
  id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
  last_name: Koval
citation:
  ama: 'Alistarh D-A, Nadiradze G, Koval N. Efficiency guarantees for parallel incremental
    algorithms under relaxed schedulers. In: <i>31st ACM Symposium on Parallelism
    in Algorithms and Architectures</i>. ACM Press; 2019:145-154. doi:<a href="https://doi.org/10.1145/3323165.3323201">10.1145/3323165.3323201</a>'
  apa: 'Alistarh, D.-A., Nadiradze, G., &#38; Koval, N. (2019). Efficiency guarantees
    for parallel incremental algorithms under relaxed schedulers. In <i>31st ACM Symposium
    on Parallelism in Algorithms and Architectures</i> (pp. 145–154). Phoenix, AZ,
    United States: ACM Press. <a href="https://doi.org/10.1145/3323165.3323201">https://doi.org/10.1145/3323165.3323201</a>'
  chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Nikita Koval. “Efficiency Guarantees
    for Parallel Incremental Algorithms under Relaxed Schedulers.” In <i>31st ACM
    Symposium on Parallelism in Algorithms and Architectures</i>, 145–54. ACM Press,
    2019. <a href="https://doi.org/10.1145/3323165.3323201">https://doi.org/10.1145/3323165.3323201</a>.
  ieee: D.-A. Alistarh, G. Nadiradze, and N. Koval, “Efficiency guarantees for parallel
    incremental algorithms under relaxed schedulers,” in <i>31st ACM Symposium on
    Parallelism in Algorithms and Architectures</i>, Phoenix, AZ, United States, 2019,
    pp. 145–154.
  ista: 'Alistarh D-A, Nadiradze G, Koval N. 2019. Efficiency guarantees for parallel
    incremental algorithms under relaxed schedulers. 31st ACM Symposium on Parallelism
    in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms
    and Architectures, 145–154.'
  mla: Alistarh, Dan-Adrian, et al. “Efficiency Guarantees for Parallel Incremental
    Algorithms under Relaxed Schedulers.” <i>31st ACM Symposium on Parallelism in
    Algorithms and Architectures</i>, ACM Press, 2019, pp. 145–54, doi:<a href="https://doi.org/10.1145/3323165.3323201">10.1145/3323165.3323201</a>.
  short: D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism
    in Algorithms and Architectures, ACM Press, 2019, pp. 145–154.
conference:
  end_date: 2019-06-24
  location: Phoenix, AZ, United States
  name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
  start_date: 2019-06-22
date_created: 2019-07-24T08:59:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T13:31:39Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3323165.3323201
ec_funded: 1
external_id:
  arxiv:
  - '2003.09363'
  isi:
  - '000507618500018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2003.09363
month: '06'
oa: 1
oa_version: Preprint
page: 145-154
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '805223'
  name: Elastic Coordination for Scalable Machine Learning
publication: 31st ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
  isbn:
  - '9781450361842'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
  record:
  - id: '10429'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Efficiency guarantees for parallel incremental algorithms under relaxed schedulers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6676'
abstract:
- lang: eng
  text: "It is impossible to deterministically solve wait-free consensus in an asynchronous
    system. The classic proof uses a valency argument, which constructs an infinite
    execution by repeatedly extending a finite execution. We introduce extension-based
    proofs, a class of impossibility proofs that are modelled as an interaction between
    a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs
    based on combinatorial topology, it has been shown that it is impossible to deterministically
    solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However,
    it was unknown whether proofs based on simpler techniques were possible. We show
    that this impossibility result cannot be obtained by an extension-based proof
    and, hence, extension-based proofs are limited in power."
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: Faith
  full_name: Ellen, Faith
  last_name: Ellen
- first_name: Rati
  full_name: Gelashvili, Rati
  last_name: Gelashvili
- first_name: Leqi
  full_name: Zhu, Leqi
  last_name: Zhu
citation:
  ama: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based
    proofs fail. In: <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
    of Computing</i>. ACM Press; 2019:986-996. doi:<a href="https://doi.org/10.1145/3313276.3316407">10.1145/3313276.3316407</a>'
  apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2019).
    Why extension-based proofs fail. In <i>Proceedings of the 51st Annual ACM SIGACT
    Symposium on Theory of Computing</i> (pp. 986–996). Phoenix, AZ, United States:
    ACM Press. <a href="https://doi.org/10.1145/3313276.3316407">https://doi.org/10.1145/3313276.3316407</a>'
  chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi
    Zhu. “Why Extension-Based Proofs Fail.” In <i>Proceedings of the 51st Annual ACM
    SIGACT Symposium on Theory of Computing</i>, 986–96. ACM Press, 2019. <a href="https://doi.org/10.1145/3313276.3316407">https://doi.org/10.1145/3313276.3316407</a>.
  ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based
    proofs fail,” in <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
    of Computing</i>, Phoenix, AZ, United States, 2019, pp. 986–996.
  ista: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based
    proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of
    Computing. STOC: Symposium on Theory of Computing, 986–996.'
  mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” <i>Proceedings
    of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i>, ACM Press,
    2019, pp. 986–96, doi:<a href="https://doi.org/10.1145/3313276.3316407">10.1145/3313276.3316407</a>.
  short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings
    of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019,
    pp. 986–996.
conference:
  end_date: 2019-06-26
  location: Phoenix, AZ, United States
  name: 'STOC: Symposium on Theory of Computing'
  start_date: 2019-06-23
date_created: 2019-07-24T09:13:05Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-12-13T12:28:28Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3313276.3316407
external_id:
  arxiv:
  - '1811.01421'
  isi:
  - '000523199100089'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1811.01421
month: '06'
oa: 1
oa_version: Preprint
page: 986-996
publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
  isbn:
  - '9781450367059'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
  record:
  - id: '14364'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Why extension-based proofs fail
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6677'
abstract:
- lang: eng
  text: "The Fiat-Shamir heuristic transforms a public-coin interactive proof into
    a non-interactive argument, by replacing the verifier with a cryptographic hash
    function that is applied to the protocol’s transcript. Constructing hash functions
    for which this transformation is sound is a central and long-standing open question
    in cryptography.\r\n\r\nWe show that solving the END−OF−METERED−LINE problem is
    no easier than breaking the soundness of the Fiat-Shamir transformation when applied
    to the sumcheck protocol. In particular, if the transformed protocol is sound,
    then any hard problem in #P gives rise to a hard distribution in the class CLS,
    which is contained in PPAD. Our result opens up the possibility of sampling moderately-sized
    games for which it is hard to find a Nash equilibrium, by reducing the inversion
    of appropriately chosen one-way functions to #SAT.\r\n\r\nOur main technical contribution
    is a stateful incrementally verifiable procedure that, given a SAT instance over
    n variables, counts the number of satisfying assignments. This is accomplished
    via an exponential sequence of small steps, each computable in time poly(n). Incremental
    verifiability means that each intermediate state includes a sumcheck-based proof
    of its correctness, and the proof can be updated and verified in time poly(n)."
article_processing_charge: No
author:
- first_name: Arka Rai
  full_name: Choudhuri, Arka Rai
  last_name: Choudhuri
- first_name: Pavel
  full_name: Hubáček, Pavel
  last_name: Hubáček
- first_name: Chethan
  full_name: Kamath Hosdurg, Chethan
  id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
  last_name: Kamath Hosdurg
- first_name: Krzysztof Z
  full_name: Pietrzak, Krzysztof Z
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
- first_name: Alon
  full_name: Rosen, Alon
  last_name: Rosen
- first_name: Guy N.
  full_name: Rothblum, Guy N.
  last_name: Rothblum
citation:
  ama: 'Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum
    GN. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In: <i>Proceedings
    of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019</i>.
    ACM Press; 2019:1103-1114. doi:<a href="https://doi.org/10.1145/3313276.3316400">10.1145/3313276.3316400</a>'
  apa: 'Choudhuri, A. R., Hubáček, P., Kamath Hosdurg, C., Pietrzak, K. Z., Rosen,
    A., &#38; Rothblum, G. N. (2019). Finding a Nash equilibrium is no easier than
    breaking Fiat-Shamir. In <i>Proceedings of the 51st Annual ACM SIGACT Symposium
    on Theory of Computing  - STOC 2019</i> (pp. 1103–1114). Phoenix, AZ, United States:
    ACM Press. <a href="https://doi.org/10.1145/3313276.3316400">https://doi.org/10.1145/3313276.3316400</a>'
  chicago: Choudhuri, Arka Rai, Pavel Hubáček, Chethan Kamath Hosdurg, Krzysztof Z
    Pietrzak, Alon Rosen, and Guy N. Rothblum. “Finding a Nash Equilibrium Is No Easier
    than Breaking Fiat-Shamir.” In <i>Proceedings of the 51st Annual ACM SIGACT Symposium
    on Theory of Computing  - STOC 2019</i>, 1103–14. ACM Press, 2019. <a href="https://doi.org/10.1145/3313276.3316400">https://doi.org/10.1145/3313276.3316400</a>.
  ieee: A. R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K. Z. Pietrzak, A. Rosen,
    and G. N. Rothblum, “Finding a Nash equilibrium is no easier than breaking Fiat-Shamir,”
    in <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing 
    - STOC 2019</i>, Phoenix, AZ, United States, 2019, pp. 1103–1114.
  ista: 'Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum
    GN. 2019. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. Proceedings
    of the 51st Annual ACM SIGACT Symposium on Theory of Computing  - STOC 2019. STOC:
    Symposium on Theory of Computing, 1103–1114.'
  mla: Choudhuri, Arka Rai, et al. “Finding a Nash Equilibrium Is No Easier than Breaking
    Fiat-Shamir.” <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
    of Computing  - STOC 2019</i>, ACM Press, 2019, pp. 1103–14, doi:<a href="https://doi.org/10.1145/3313276.3316400">10.1145/3313276.3316400</a>.
  short: A.R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K.Z. Pietrzak, A. Rosen, G.N.
    Rothblum, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of
    Computing  - STOC 2019, ACM Press, 2019, pp. 1103–1114.
conference:
  end_date: 2019-06-26
  location: Phoenix, AZ, United States
  name: 'STOC: Symposium on Theory of Computing'
  start_date: 2019-06-23
date_created: 2019-07-24T09:20:53Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T13:15:55Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3313276.3316400
ec_funded: 1
external_id:
  isi:
  - '000523199100100'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2019/549
month: '06'
oa: 1
oa_version: Preprint
page: 1103-1114
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing  -
  STOC 2019
publication_identifier:
  isbn:
  - '9781450367059'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
  record:
  - id: '7896'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Finding a Nash equilibrium is no easier than breaking Fiat-Shamir
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6680'
abstract:
- lang: eng
  text: This paper analyzes how partial selfing in a large source population influences
    its ability to colonize a new habitat via the introduction of a few founder individuals.
    Founders experience inbreeding depression due to partially recessive deleterious
    alleles as well as maladaptation to the new environment due to selection on a
    large number of additive loci. I first introduce a simplified version of the Inbreeding
    History Model (Kelly, 2007) in order to characterize mutation‐selection balance
    in a large, partially selfing source population under selection involving multiple
    non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary
    dynamics of founders establishing in the new habitat under a model of hard selection.
    The study explores how selfing rate shapes establishment probabilities of founders
    via effects on both inbreeding depression and adaptability to the new environment,
    and also distinguishes the effects of selfing on the initial fitness of founders
    from its effects on the long‐term adaptive response of the populations they found.
    A high rate of (but not complete) selfing is found to aid establishment over a
    wide range of parameters, even in the absence of mate limitation. The sensitivity
    of the results to assumptions about the nature of polygenic selection are discussed.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Himani
  full_name: Sachdeva, Himani
  id: 42377A0A-F248-11E8-B48F-1D18A9856A87
  last_name: Sachdeva
citation:
  ama: Sachdeva H. Effect of partial selfing and polygenic selection on establishment
    in a new habitat. <i>Evolution</i>. 2019;73(9):1729-1745. doi:<a href="https://doi.org/10.1111/evo.13812">10.1111/evo.13812</a>
  apa: Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment
    in a new habitat. <i>Evolution</i>. Wiley. <a href="https://doi.org/10.1111/evo.13812">https://doi.org/10.1111/evo.13812</a>
  chicago: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on
    Establishment in a New Habitat.” <i>Evolution</i>. Wiley, 2019. <a href="https://doi.org/10.1111/evo.13812">https://doi.org/10.1111/evo.13812</a>.
  ieee: H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment
    in a new habitat,” <i>Evolution</i>, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.
  ista: Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment
    in a new habitat. Evolution. 73(9), 1729–1745.
  mla: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment
    in a New Habitat.” <i>Evolution</i>, vol. 73, no. 9, Wiley, 2019, pp. 1729–45,
    doi:<a href="https://doi.org/10.1111/evo.13812">10.1111/evo.13812</a>.
  short: H. Sachdeva, Evolution 73 (2019) 1729–1745.
date_created: 2019-07-25T09:08:28Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-29T06:43:58Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13812
external_id:
  isi:
  - '000481300600001'
file:
- access_level: open_access
  checksum: 772ce7035965153959b946a1033de1ca
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-09-17T10:56:27Z
  date_updated: 2020-07-14T12:47:37Z
  file_id: '6881'
  file_name: 2019_Evolution_Sachdeva.pdf
  file_size: 937573
  relation: main_file
file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
intvolume: '        73'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1729-1745
publication: Evolution
publication_identifier:
  eissn:
  - 1558-5646
  issn:
  - 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
  record:
  - id: '9802'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Effect of partial selfing and polygenic selection on establishment in a new
  habitat
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2019'
...
---
_id: '6681'
abstract:
- lang: eng
  text: "The first part of the thesis considers the computational aspects of the homotopy
    groups πd(X) of a topological space X. It is well known that there is no algorithm
    to decide whether the fundamental group π1(X) of a given finite simplicial complex
    X is trivial. On the other hand, there are several algorithms that, given a finite
    simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute
    the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms
    come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract
    finitely generated abelian group given by generators and relations, but they work
    with very implicit representations of the elements of πd(X). We present an algorithm
    that, given a simply connected space X, computes πd(X) and represents its elements
    as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed
    d, the algorithm runs in time exponential in size(X), the number of simplices
    of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct
    a family of simply connected spaces X such that for any simplicial map representing
    a generator of πd(X), the size of the triangulation of S d on which the map is
    defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove
    that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋,
    k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable
    range: Given a finite simplicial complex K of dimension k, decide whether there
    exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of
    K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephan Y
  full_name: Zhechev, Stephan Y
  id: 3AA52972-F248-11E8-B48F-1D18A9856A87
  last_name: Zhechev
citation:
  ama: Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019.
    doi:<a href="https://doi.org/10.15479/AT:ISTA:6681">10.15479/AT:ISTA:6681</a>
  apa: Zhechev, S. Y. (2019). <i>Algorithmic aspects of homotopy theory and embeddability</i>.
    Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:6681">https://doi.org/10.15479/AT:ISTA:6681</a>
  chicago: Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.”
    Institute of Science and Technology Austria, 2019. <a href="https://doi.org/10.15479/AT:ISTA:6681">https://doi.org/10.15479/AT:ISTA:6681</a>.
  ieee: S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,”
    Institute of Science and Technology Austria, 2019.
  ista: Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability.
    Institute of Science and Technology Austria.
  mla: Zhechev, Stephan Y. <i>Algorithmic Aspects of Homotopy Theory and Embeddability</i>.
    Institute of Science and Technology Austria, 2019, doi:<a href="https://doi.org/10.15479/AT:ISTA:6681">10.15479/AT:ISTA:6681</a>.
  short: S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute
    of Science and Technology Austria, 2019.
date_created: 2019-07-26T11:14:34Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2023-09-07T13:10:36Z
day: '08'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: UlWa
doi: 10.15479/AT:ISTA:6681
file:
- access_level: open_access
  checksum: 3231e7cbfca3b5687366f84f0a57a0c0
  content_type: application/pdf
  creator: szhechev
  date_created: 2019-08-07T13:02:50Z
  date_updated: 2020-07-14T12:47:37Z
  file_id: '6771'
  file_name: Stephan_Zhechev_thesis.pdf
  file_size: 1464227
  relation: main_file
- access_level: closed
  checksum: 85d65eb27b4377a9e332ee37a70f08b6
  content_type: application/octet-stream
  creator: szhechev
  date_created: 2019-08-07T13:03:22Z
  date_updated: 2020-07-14T12:47:37Z
  file_id: '6772'
  file_name: Stephan_Zhechev_thesis.tex
  file_size: 303988
  relation: source_file
- access_level: closed
  checksum: 86b374d264ca2dd53e712728e253ee75
  content_type: application/zip
  creator: szhechev
  date_created: 2019-08-07T13:03:34Z
  date_updated: 2020-07-14T12:47:37Z
  file_id: '6773'
  file_name: supplementary_material.zip
  file_size: 1087004
  relation: supplementary_material
file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '104'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '6774'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Uli
  full_name: Wagner, Uli
  id: 36690CA2-F248-11E8-B48F-1D18A9856A87
  last_name: Wagner
  orcid: 0000-0002-1494-0568
title: Algorithmic aspects of homotopy theory and embeddability
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6710'
abstract:
- lang: eng
  text: Sexual dimorphism in morphology, physiology or life history traits is common
    in dioecious plants at reproductive maturity, but it is typically inconspicuous
    or absent in juveniles. Although plants of different sexes probably begin to diverge
    in gene expression both before their reproduction commences and before dimorphism
    becomes readily apparent, to our knowledge transcriptome-wide differential gene
    expression has yet to be demonstrated for any angiosperm species.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
  full_name: Cossard, Guillaume
  last_name: Cossard
- first_name: Melissa A
  full_name: Toups, Melissa A
  id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
  last_name: Toups
  orcid: 0000-0002-9752-7380
- first_name: 'John '
  full_name: 'Pannell, John '
  last_name: Pannell
citation:
  ama: Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene
    expression in pre-reproductive seedlings of a dioecious herb. <i>Annals of botany</i>.
    2019;123(7):1119-1131. doi:<a href="https://doi.org/10.1093/aob/mcy183">10.1093/aob/mcy183</a>
  apa: Cossard, G., Toups, M. A., &#38; Pannell, J. (2019). Sexual dimorphism and
    rapid turnover in gene expression in pre-reproductive seedlings of a dioecious
    herb. <i>Annals of Botany</i>. Oxford University Press. <a href="https://doi.org/10.1093/aob/mcy183">https://doi.org/10.1093/aob/mcy183</a>
  chicago: Cossard, Guillaume, Melissa A Toups, and John  Pannell. “Sexual Dimorphism
    and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious
    Herb.” <i>Annals of Botany</i>. Oxford University Press, 2019. <a href="https://doi.org/10.1093/aob/mcy183">https://doi.org/10.1093/aob/mcy183</a>.
  ieee: G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover
    in gene expression in pre-reproductive seedlings of a dioecious herb,” <i>Annals
    of botany</i>, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.
  ista: Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover
    in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of
    botany. 123(7), 1119–1131.
  mla: Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression
    in Pre-Reproductive Seedlings of a Dioecious Herb.” <i>Annals of Botany</i>, vol.
    123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:<a href="https://doi.org/10.1093/aob/mcy183">10.1093/aob/mcy183</a>.
  short: G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.
date_created: 2019-07-28T21:59:15Z
date_published: 2019-06-04T00:00:00Z
date_updated: 2023-08-29T06:42:22Z
day: '04'
department:
- _id: BeVi
doi: 10.1093/aob/mcy183
external_id:
  isi:
  - '000493043500004'
  pmid:
  - '30289430'
intvolume: '       123'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1093/aob/mcy183
month: '06'
oa: 1
oa_version: Published Version
page: 1119-1131
pmid: 1
publication: Annals of botany
publication_identifier:
  eissn:
  - 1095-8290
  issn:
  - 0305-7364
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual dimorphism and rapid turnover in gene expression in pre-reproductive
  seedlings of a dioecious herb
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 123
year: '2019'
...
---
_id: '6713'
abstract:
- lang: eng
  text: Evolutionary studies are often limited by missing data that are critical to
    understanding the history of selection. Selection experiments, which reproduce
    rapid evolution under controlled conditions, are excellent tools to study how
    genomes evolve under selection. Here we present a genomic dissection of the Longshanks
    selection experiment, in which mice were selectively bred over 20 generations
    for longer tibiae relative to body mass, resulting in 13% longer tibiae in two
    replicates. We synthesized evolutionary theory, genome sequences and molecular
    genetics to understand the selection response and found that it involved both
    polygenic adaptation and discrete loci of major effect, with the strongest loci
    tending to be selected in parallel between replicates. We show that selection
    may favor de-repression of bone growth through inactivating two limb enhancers
    of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is
    possible to connect individual base-pair changes to the overall selection response.
article_number: e42014
article_processing_charge: No
author:
- first_name: João Pl
  full_name: Castro, João Pl
  last_name: Castro
- first_name: Michelle N.
  full_name: Yancoskie, Michelle N.
  last_name: Yancoskie
- first_name: Marta
  full_name: Marchini, Marta
  last_name: Marchini
- first_name: Stefanie
  full_name: Belohlavy, Stefanie
  id: 43FE426A-F248-11E8-B48F-1D18A9856A87
  last_name: Belohlavy
  orcid: 0000-0002-9849-498X
- first_name: Layla
  full_name: Hiramatsu, Layla
  last_name: Hiramatsu
- first_name: Marek
  full_name: Kučka, Marek
  last_name: Kučka
- first_name: William H.
  full_name: Beluch, William H.
  last_name: Beluch
- first_name: Ronald
  full_name: Naumann, Ronald
  last_name: Naumann
- first_name: Isabella
  full_name: Skuplik, Isabella
  last_name: Skuplik
- first_name: John
  full_name: Cobb, John
  last_name: Cobb
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
- first_name: Campbell
  full_name: Rolian, Campbell
  last_name: Rolian
- first_name: Yingguang Frank
  full_name: Chan, Yingguang Frank
  last_name: Chan
citation:
  ama: Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis
    of the Longshanks selection experiment for longer limbs in mice. <i>eLife</i>.
    2019;8. doi:<a href="https://doi.org/10.7554/eLife.42014">10.7554/eLife.42014</a>
  apa: Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L.,
    Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks
    selection experiment for longer limbs in mice. <i>ELife</i>. eLife Sciences Publications.
    <a href="https://doi.org/10.7554/eLife.42014">https://doi.org/10.7554/eLife.42014</a>
  chicago: Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy,
    Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic
    Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>.
    eLife Sciences Publications, 2019. <a href="https://doi.org/10.7554/eLife.42014">https://doi.org/10.7554/eLife.42014</a>.
  ieee: J. P. Castro <i>et al.</i>, “An integrative genomic analysis of the Longshanks
    selection experiment for longer limbs in mice,” <i>eLife</i>, vol. 8. eLife Sciences
    Publications, 2019.
  ista: Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch
    WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative
    genomic analysis of the Longshanks selection experiment for longer limbs in mice.
    eLife. 8, e42014.
  mla: Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks
    Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>, vol. 8, e42014,
    eLife Sciences Publications, 2019, doi:<a href="https://doi.org/10.7554/eLife.42014">10.7554/eLife.42014</a>.
  short: J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M.
    Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F.
    Chan, ELife 8 (2019).
date_created: 2019-07-28T21:59:17Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2024-03-25T23:30:11Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7554/eLife.42014
external_id:
  isi:
  - '000473588700001'
  pmid:
  - '31169497'
file:
- access_level: open_access
  checksum: fa0936fe58f0d9e3f8e75038570e5a17
  content_type: application/pdf
  creator: apreinsp
  date_created: 2019-07-29T07:41:18Z
  date_updated: 2020-07-14T12:47:38Z
  file_id: '6721'
  file_name: 2019_eLife_Castro.pdf
  file_size: 6748249
  relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: '         8'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
  record:
  - id: '9804'
    relation: research_data
    status: public
  - id: '11388'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: An integrative genomic analysis of the Longshanks selection experiment for
  longer limbs in mice
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6717'
abstract:
- lang: eng
  text: With the recent publication by Silpe and Bassler (2019), considering phage
    detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many
    as five examples of phage-associated intercellular communication (Table 1). Each
    potentially involves ecological inferences by phages as to concentrations of surrounding
    phage-infected or uninfected bacteria. While the utility of phage detection of
    bacterial QS molecules may at first glance appear to be straightforward, we suggest
    in this commentary that the underlying ecological explanation is unlikely to be
    simple.
article_number: '1171'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Claudia
  full_name: Igler, Claudia
  id: 46613666-F248-11E8-B48F-1D18A9856A87
  last_name: Igler
- first_name: Stephen T.
  full_name: Abedon, Stephen T.
  last_name: Abedon
citation:
  ama: 'Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer
    controls a phage lysis-lysogeny decision. <i>Frontiers in Microbiology</i>. 2019;10.
    doi:<a href="https://doi.org/10.3389/fmicb.2019.01171">10.3389/fmicb.2019.01171</a>'
  apa: 'Igler, C., &#38; Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing
    autoinducer controls a phage lysis-lysogeny decision. <i>Frontiers in Microbiology</i>.
    Frontiers. <a href="https://doi.org/10.3389/fmicb.2019.01171">https://doi.org/10.3389/fmicb.2019.01171</a>'
  chicago: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing
    Autoinducer Controls a Phage Lysis-Lysogeny Decision.” <i>Frontiers in Microbiology</i>.
    Frontiers, 2019. <a href="https://doi.org/10.3389/fmicb.2019.01171">https://doi.org/10.3389/fmicb.2019.01171</a>.'
  ieee: 'C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer
    controls a phage lysis-lysogeny decision,” <i>Frontiers in Microbiology</i>, vol.
    10. Frontiers, 2019.'
  ista: 'Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer
    controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.'
  mla: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing
    Autoinducer Controls a Phage Lysis-Lysogeny Decision.” <i>Frontiers in Microbiology</i>,
    vol. 10, 1171, Frontiers, 2019, doi:<a href="https://doi.org/10.3389/fmicb.2019.01171">10.3389/fmicb.2019.01171</a>.'
  short: C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).
date_created: 2019-07-28T21:59:18Z
date_published: 2019-06-03T00:00:00Z
date_updated: 2023-08-29T06:41:20Z
day: '03'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.3389/fmicb.2019.01171
external_id:
  isi:
  - '000470131200001'
file:
- access_level: open_access
  checksum: 317a06067e9a8e717bb55f23e0d77ba7
  content_type: application/pdf
  creator: apreinsp
  date_created: 2019-07-29T07:51:54Z
  date_updated: 2020-07-14T12:47:38Z
  file_id: '6722'
  file_name: 2019_Frontiers_Igler.pdf
  file_size: 246151
  relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: '        10'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
  grant_number: '24573'
  name: Design principles underlying genetic switch architecture (DOC Fellowship)
publication: Frontiers in Microbiology
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny
  decision'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6725'
abstract:
- lang: eng
  text: "A Valued Constraint Satisfaction Problem (VCSP) provides a common framework
    that can express a wide range of discrete optimization problems. A VCSP instance
    is given by a finite set of variables, a finite domain of labels, and an objective
    function to be minimized. This function is represented as a sum of terms where
    each term depends on a subset of the variables. To obtain different classes of
    optimization problems, one can restrict all terms to come from a fixed set Γ of
    cost functions, called a language. \r\nRecent breakthrough results have established
    a complete complexity classification of such classes with respect to language
    Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances
    can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately,
    testing this condition for a given language Γ is known to be NP-hard. We thus
    study exponential algorithms for this meta-problem. We show that the tractability
    condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ)))
    time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also
    obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH).
    More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm,
    assuming that SETH holds."
alternative_title:
- LIPIcs
arxiv: 1
author:
- first_name: Vladimir
  full_name: Kolmogorov, Vladimir
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
citation:
  ama: 'Kolmogorov V. Testing the complexity of a valued CSP language. In: <i>46th
    International Colloquium on Automata, Languages and Programming</i>. Vol 132.
    Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:<a href="https://doi.org/10.4230/LIPICS.ICALP.2019.77">10.4230/LIPICS.ICALP.2019.77</a>'
  apa: 'Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In
    <i>46th International Colloquium on Automata, Languages and Programming</i> (Vol.
    132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
    <a href="https://doi.org/10.4230/LIPICS.ICALP.2019.77">https://doi.org/10.4230/LIPICS.ICALP.2019.77</a>'
  chicago: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.”
    In <i>46th International Colloquium on Automata, Languages and Programming</i>,
    132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href="https://doi.org/10.4230/LIPICS.ICALP.2019.77">https://doi.org/10.4230/LIPICS.ICALP.2019.77</a>.
  ieee: V. Kolmogorov, “Testing the complexity of a valued CSP language,” in <i>46th
    International Colloquium on Automata, Languages and Programming</i>, Patras, Greece,
    2019, vol. 132, p. 77:1-77:12.
  ista: 'Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th
    International Colloquium on Automata, Languages and Programming. ICALP 2019: International
    Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.'
  mla: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” <i>46th
    International Colloquium on Automata, Languages and Programming</i>, vol. 132,
    Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:<a
    href="https://doi.org/10.4230/LIPICS.ICALP.2019.77">10.4230/LIPICS.ICALP.2019.77</a>.
  short: V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages
    and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.
conference:
  end_date: 2019-07-12
  location: Patras, Greece
  name: 'ICALP 2019: International Colloquim on Automata, Languages and Programming'
  start_date: 2019-07-08
date_created: 2019-07-29T12:23:29Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2021-01-12T08:08:40Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.4230/LIPICS.ICALP.2019.77
ec_funded: 1
external_id:
  arxiv:
  - '1803.02289'
file:
- access_level: open_access
  checksum: f5ebee8eec6ae09e30365578ee63a492
  content_type: application/pdf
  creator: dernst
  date_created: 2019-07-31T07:01:45Z
  date_updated: 2020-07-14T12:47:38Z
  file_id: '6738'
  file_name: 2019_LIPICS_Kolmogorov.pdf
  file_size: 575475
  relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: '       132'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 77:1-77:12
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '616160'
  name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 46th International Colloquium on Automata, Languages and Programming
publication_identifier:
  isbn:
  - 978-3-95977-109-2
  issn:
  - 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Testing the complexity of a valued CSP language
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2019'
...
---
_id: '6726'
abstract:
- lang: eng
  text: Randomness is an essential part of any secure cryptosystem, but many constructions
    rely on distributions that are not uniform. This is particularly true for lattice
    based cryptosystems, which more often than not make use of discrete Gaussian distributions
    over the integers. For practical purposes it is crucial to evaluate the impact
    that approximation errors have on the security of a scheme to provide the best
    possible trade-off between security and performance. Recent years have seen surprising
    results allowing to use relatively low precision while maintaining high levels
    of security. A key insight in these results is that sampling a distribution with
    low relative error can provide very strong security guarantees. Since floating
    point numbers provide guarantees on the relative approximation error, they seem
    a suitable tool in this setting, but it is not obvious which sampling algorithms
    can actually profit from them. While previous works have shown that inversion
    sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES
    2014; Prest, ASIACRYPT 2017), other works have called into question if this is
    possible for other sampling techniques (Zheng et al., Eprint report 2018/309).
    In this work, we consider all sampling algorithms that are popular in the cryptographic
    setting and analyze the relationship of floating point precision and the resulting
    relative error. We show that all of the algorithms either natively achieve a low
    relative error or can be adapted to do so.
article_processing_charge: No
author:
- first_name: Michael
  full_name: Walter, Michael
  id: 488F98B0-F248-11E8-B48F-1D18A9856A87
  last_name: Walter
  orcid: 0000-0003-3186-2482
citation:
  ama: 'Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj
    A, Rachidi T, eds. <i>Progress in Cryptology – AFRICACRYPT 2019</i>. Vol 11627.
    LNCS. Cham: Springer Nature; 2019:157-180. doi:<a href="https://doi.org/10.1007/978-3-030-23696-0_9">10.1007/978-3-030-23696-0_9</a>'
  apa: 'Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann,
    A. Nitaj, &#38; T. Rachidi (Eds.), <i>Progress in Cryptology – AFRICACRYPT 2019</i>
    (Vol. 11627, pp. 157–180). Cham: Springer Nature. <a href="https://doi.org/10.1007/978-3-030-23696-0_9">https://doi.org/10.1007/978-3-030-23696-0_9</a>'
  chicago: 'Walter, Michael. “Sampling the Integers with Low Relative Error.” In <i>Progress
    in Cryptology – AFRICACRYPT 2019</i>, edited by J Buchmann, A Nitaj, and T Rachidi,
    11627:157–80. LNCS. Cham: Springer Nature, 2019. <a href="https://doi.org/10.1007/978-3-030-23696-0_9">https://doi.org/10.1007/978-3-030-23696-0_9</a>.'
  ieee: 'M. Walter, “Sampling the integers with low relative error,” in <i>Progress
    in Cryptology – AFRICACRYPT 2019</i>, vol. 11627, J. Buchmann, A. Nitaj, and T.
    Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.'
  ista: 'Walter M. 2019.Sampling the integers with low relative error. In: Progress
    in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.'
  mla: Walter, Michael. “Sampling the Integers with Low Relative Error.” <i>Progress
    in Cryptology – AFRICACRYPT 2019</i>, edited by J Buchmann et al., vol. 11627,
    Springer Nature, 2019, pp. 157–80, doi:<a href="https://doi.org/10.1007/978-3-030-23696-0_9">10.1007/978-3-030-23696-0_9</a>.
  short: M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology
    – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.
conference:
  end_date: 2019-07-11
  location: Rabat, Morocco
  name: 'AFRICACRYPT: International Conference on Cryptology in Africa'
  start_date: 2019-07-09
date_created: 2019-07-29T12:25:31Z
date_published: 2019-06-29T00:00:00Z
date_updated: 2023-02-23T12:50:15Z
day: '29'
department:
- _id: KrPi
doi: 10.1007/978-3-030-23696-0_9
ec_funded: 1
editor:
- first_name: J
  full_name: Buchmann, J
  last_name: Buchmann
- first_name: A
  full_name: Nitaj, A
  last_name: Nitaj
- first_name: T
  full_name: Rachidi, T
  last_name: Rachidi
intvolume: '     11627'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2019/068
month: '06'
oa: 1
oa_version: Preprint
page: 157-180
place: Cham
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
publication: Progress in Cryptology – AFRICACRYPT 2019
publication_identifier:
  eisbn:
  - 978-3-0302-3696-0
  isbn:
  - 978-3-0302-3695-3
  issn:
  - 0302-9743
  - 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Sampling the integers with low relative error
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11627
year: '2019'
...
---
_id: '6750'
abstract:
- lang: eng
  text: 'Polar codes have gained extensive attention during the past few years and
    recently they have been selected for the next generation of wireless communications
    standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC
    list (SCL) and SC flip (SCF), provide a reasonable error performance for polar
    codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC,
    Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code
    graph off-line, produce a list of operations, store the list in memory, and feed
    the list to the decoder to decode the constituent codes in order efficiently,
    thus increasing the decoding speed. However, the list of operations is dependent
    on the code rate and as the rate changes, a new list is produced, making fast
    SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible
    fast SC-based decoder by creating the list of operations directly in hardware,
    with low implementation complexity. We further propose a hardware architecture
    implementing the proposed method and show that the area occupation of the rate-flexible
    fast SC-based decoder in this paper is only 38% of the total area of the memory-based
    base-line decoder when 5G code rates are supported. '
article_number: '8854897'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Seyyed Ali
  full_name: Hashemi, Seyyed Ali
  last_name: Hashemi
- first_name: Carlo
  full_name: Condo, Carlo
  last_name: Condo
- first_name: Marco
  full_name: Mondelli, Marco
  id: 27EB676C-8706-11E9-9510-7717E6697425
  last_name: Mondelli
  orcid: 0000-0002-3242-7020
- first_name: Warren J
  full_name: Gross, Warren J
  last_name: Gross
citation:
  ama: Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders.
    <i>IEEE Transactions on Signal Processing</i>. 2019;67(22). doi:<a href="https://doi.org/10.1109/TSP.2019.2944738">10.1109/TSP.2019.2944738</a>
  apa: Hashemi, S. A., Condo, C., Mondelli, M., &#38; Gross, W. J. (2019). Rate-flexible
    fast polar decoders. <i>IEEE Transactions on Signal Processing</i>. IEEE. <a href="https://doi.org/10.1109/TSP.2019.2944738">https://doi.org/10.1109/TSP.2019.2944738</a>
  chicago: Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible
    Fast Polar Decoders.” <i>IEEE Transactions on Signal Processing</i>. IEEE, 2019.
    <a href="https://doi.org/10.1109/TSP.2019.2944738">https://doi.org/10.1109/TSP.2019.2944738</a>.
  ieee: S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast
    polar decoders,” <i>IEEE Transactions on Signal Processing</i>, vol. 67, no. 22.
    IEEE, 2019.
  ista: Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar
    decoders. IEEE Transactions on Signal Processing. 67(22), 8854897.
  mla: Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” <i>IEEE Transactions
    on Signal Processing</i>, vol. 67, no. 22, 8854897, IEEE, 2019, doi:<a href="https://doi.org/10.1109/TSP.2019.2944738">10.1109/TSP.2019.2944738</a>.
  short: S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal
    Processing 67 (2019).
date_created: 2019-07-31T09:51:14Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2021-01-12T08:08:51Z
day: '15'
department:
- _id: MaMo
doi: 10.1109/TSP.2019.2944738
external_id:
  arxiv:
  - '1903.09203'
intvolume: '        67'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1903.09203
month: '11'
oa: 1
oa_version: Preprint
publication: IEEE Transactions on Signal Processing
publication_identifier:
  issn:
  - 1053587X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: 1
status: public
title: Rate-flexible fast polar decoders
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 67
year: '2019'
...
---
_id: '6752'
abstract:
- lang: eng
  text: 'Two-player games on graphs are widely studied in formal methods, as they
    model the interaction between a system and its environment. The game is played
    by moving a token throughout a graph to produce an infinite path. There are several
    common modes to determine how the players move the token through the graph; e.g.,
    in turn-based games the players alternate turns in moving the token. We study
    the bidding mode of moving the token, which, to the best of our knowledge, has
    never been studied in infinite-duration games. The following bidding rule was
    previously defined and called Richman bidding. Both players have separate budgets,
    which sum up to 1. In each turn, a bidding takes place: Both players submit bids
    simultaneously, where a bid is legal if it does not exceed the available budget,
    and the higher bidder pays his bid to the other player and moves the token. The
    central question studied in bidding games is a necessary and sufficient initial
    budget for winning the game: a threshold budget in a vertex is a value t ∈ [0,
    1] such that if Player 1’s budget exceeds t, he can win the game; and if Player
    2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously
    shown to exist in every vertex of a reachability game, which have an interesting
    connection with random-turn games—a sub-class of simple stochastic games in which
    the player who moves is chosen randomly. We show the existence of threshold budgets
    for a qualitative class of infinite-duration games, namely parity games, and a
    quantitative class, namely mean-payoff games. The key component of the proof is
    a quantitative solution to strongly connected mean-payoff bidding games in which
    we extend the connection with random-turn games to these games, and construct
    explicit optimal strategies for both players.'
article_number: '31'
article_processing_charge: No
arxiv: 1
author:
- first_name: Guy
  full_name: Avni, Guy
  id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
  last_name: Avni
  orcid: 0000-0001-5588-8287
- 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: Ventsislav K
  full_name: Chonev, Ventsislav K
  id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
  last_name: Chonev
citation:
  ama: Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. <i>Journal
    of the ACM</i>. 2019;66(4). doi:<a href="https://doi.org/10.1145/3340295">10.1145/3340295</a>
  apa: Avni, G., Henzinger, T. A., &#38; Chonev, V. K. (2019). Infinite-duration bidding
    games. <i>Journal of the ACM</i>. ACM. <a href="https://doi.org/10.1145/3340295">https://doi.org/10.1145/3340295</a>
  chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration
    Bidding Games.” <i>Journal of the ACM</i>. ACM, 2019. <a href="https://doi.org/10.1145/3340295">https://doi.org/10.1145/3340295</a>.
  ieee: G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,”
    <i>Journal of the ACM</i>, vol. 66, no. 4. ACM, 2019.
  ista: Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal
    of the ACM. 66(4), 31.
  mla: Avni, Guy, et al. “Infinite-Duration Bidding Games.” <i>Journal of the ACM</i>,
    vol. 66, no. 4, 31, ACM, 2019, doi:<a href="https://doi.org/10.1145/3340295">10.1145/3340295</a>.
  short: G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).
date_created: 2019-08-04T21:59:16Z
date_published: 2019-07-16T00:00:00Z
date_updated: 2023-08-29T07:02:13Z
day: '16'
department:
- _id: ToHe
doi: 10.1145/3340295
external_id:
  arxiv:
  - '1705.01433'
  isi:
  - '000487714900008'
intvolume: '        66'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1705.01433
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02369
  name: Formal Methods meets Algorithmic Game Theory
publication: Journal of the ACM
publication_identifier:
  eissn:
  - 1557735X
  issn:
  - '00045411'
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
  record:
  - id: '950'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Infinite-duration bidding games
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 66
year: '2019'
...
---
_id: '6755'
abstract:
- lang: eng
  text: 'Differentiated sex chromosomes are accompanied by a difference in gene dose
    between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked
    genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic
    mechanisms and results into expression level equalization. Schistosoma mansoni
    has been previously described as a ZW species (i.e., female heterogamety, in opposition
    to XY male heterogametic species) with a partial dosage compensation, but underlying
    mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and
    epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in
    free larval cercariae and intravertebrate parasitic stages. For the first time,
    we describe differences in dosage compensation status in ZW females, depending
    on the parasitic status: free cercariae display global dosage compensation, whereas
    intravertebrate stages show a partial dosage compensation. We also highlight regional
    differences of gene expression along the Z chromosome in cercariae, but not in
    the intravertebrate stages. Finally, we feature a consistent permissive chromatin
    landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation
    in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific
    region.'
acknowledged_ssus:
- _id: CampIT
article_processing_charge: No
article_type: original
author:
- first_name: Marion A L
  full_name: Picard, Marion A L
  id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
  last_name: Picard
  orcid: 0000-0002-8101-2518
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
- first_name: David
  full_name: Roquis, David
  last_name: Roquis
- first_name: Ingo
  full_name: Bulla, Ingo
  last_name: Bulla
- first_name: Ronaldo C.
  full_name: Augusto, Ronaldo C.
  last_name: Augusto
- first_name: Nathalie
  full_name: Arancibia, Nathalie
  last_name: Arancibia
- first_name: Christoph
  full_name: Grunau, Christoph
  last_name: Grunau
- first_name: Jérôme
  full_name: Boissier, Jérôme
  last_name: Boissier
- first_name: Céline
  full_name: Cosseau, Céline
  last_name: Cosseau
citation:
  ama: 'Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the
    Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome.
    <i>Genome biology and evolution</i>. 2019;11(7):1909-1922. doi:<a href="https://doi.org/10.1093/gbe/evz133">10.1093/gbe/evz133</a>'
  apa: 'Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia,
    N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni
    lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome Biology
    and Evolution</i>. Oxford Academic Press. <a href="https://doi.org/10.1093/gbe/evz133">https://doi.org/10.1093/gbe/evz133</a>'
  chicago: 'Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo
    C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline
    Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific
    Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>.
    Oxford Academic Press, 2019. <a href="https://doi.org/10.1093/gbe/evz133">https://doi.org/10.1093/gbe/evz133</a>.'
  ieee: 'M. A. L. Picard <i>et al.</i>, “Dosage compensation throughout the Schistosoma
    mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” <i>Genome
    biology and evolution</i>, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922,
    2019.'
  ista: 'Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau
    C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma
    mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology
    and evolution. 11(7), 1909–1922.'
  mla: 'Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma
    Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome
    Biology and Evolution</i>, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22,
    doi:<a href="https://doi.org/10.1093/gbe/evz133">10.1093/gbe/evz133</a>.'
  short: M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia,
    C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.
date_created: 2019-08-04T21:59:18Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:53:58Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evz133
external_id:
  isi:
  - '000484039500018'
  pmid:
  - '31273378'
file:
- access_level: open_access
  checksum: f9e8f6863a406dcc5a36b2be001c138c
  content_type: application/pdf
  creator: dernst
  date_created: 2019-08-05T07:55:02Z
  date_updated: 2020-07-14T12:47:39Z
  file_id: '6765'
  file_name: 2019_GenomeBiology_Picard.pdf
  file_size: 580205
  relation: main_file
file_date_updated: 2020-07-14T12:47:39Z
has_accepted_license: '1'
intvolume: '        11'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1909-1922
pmid: 1
publication: Genome biology and evolution
publication_identifier:
  eissn:
  - 1759-6653
publication_status: published
publisher: Oxford Academic Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific
  chromatin landscape of the Z chromosome'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2019'
...
---
_id: '6756'
abstract:
- lang: eng
  text: "We study the topology generated by the temperature fluctuations of the cosmic
    microwave background (CMB) radiation, as quantified by the number of components
    and holes, formally given by the Betti numbers, in the growing excursion sets.
    We compare CMB maps observed by the Planck satellite with a thousand simulated
    maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations.
    The comparison is multi-scale, being performed on a sequence of degraded maps
    with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over
    \U0001D54A2 is incomplete due to obfuscation effects by bright point sources and
    other extended foreground objects like our own galaxy. To deal with such situations,
    where analysis in the presence of “masks” is of importance, we introduce the concept
    of relative homology. The parametric χ2-test shows differences between observations
    and simulations, yielding p-values at percent to less than permil levels roughly
    between 2 and 7°, with the difference in the number of components and holes peaking
    at more than 3σ sporadically at these scales. The highest observed deviation between
    the observations and simulations for b0 and b1 is approximately between 3σ and
    4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler
    characteristic at 3.66° in the literature, computed from independent measurements
    of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave
    Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler
    characteristic is phenomenologically related to the strongly anomalous behaviour
    of components and holes, or the zeroth and first Betti numbers, respectively.
    Further, since these topological descriptors show consistent anomalous behaviour
    over independent measurements of Planck and WMAP, instrumental and systematic
    errors may be an unlikely source. These are also the scales at which the observed
    maps exhibit low variance compared to the simulations, and approximately the range
    of scales at which the power spectrum exhibits a dip with respect to the theoretical
    model. Non-parametric tests show even stronger differences at almost all scales.
    Crucially, Gaussian simulations based on power-spectrum matching the characteristics
    of the observed dipped power spectrum are not able to resolve the anomaly. Understanding
    the origin of the anomalies in the CMB, whether cosmological in nature or arising
    due to late-time effects, is an extremely challenging task. Regardless, beyond
    the trivial possibility that this may still be a manifestation of an extreme Gaussian
    case, these observations, along with the super-horizon scales involved, may motivate
    the study of primordial non-Gaussianity. Alternative scenarios worth exploring
    may be models with non-trivial topology, including topological defect models."
article_number: A163
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Pratyush
  full_name: Pranav, Pratyush
  last_name: Pranav
- first_name: Robert J.
  full_name: Adler, Robert J.
  last_name: Adler
- first_name: Thomas
  full_name: Buchert, Thomas
  last_name: Buchert
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Bernard J.T.
  full_name: Jones, Bernard J.T.
  last_name: Jones
- first_name: Armin
  full_name: Schwartzman, Armin
  last_name: Schwartzman
- first_name: Hubert
  full_name: Wagner, Hubert
  id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
  last_name: Wagner
- first_name: Rien
  full_name: Van De Weygaert, Rien
  last_name: Van De Weygaert
citation:
  ama: Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature
    fluctuations in the cosmic microwave background. <i>Astronomy and Astrophysics</i>.
    2019;627. doi:<a href="https://doi.org/10.1051/0004-6361/201834916">10.1051/0004-6361/201834916</a>
  apa: Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman,
    A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations
    in the cosmic microwave background. <i>Astronomy and Astrophysics</i>. EDP Sciences.
    <a href="https://doi.org/10.1051/0004-6361/201834916">https://doi.org/10.1051/0004-6361/201834916</a>
  chicago: Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner,
    Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert.
    “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.”
    <i>Astronomy and Astrophysics</i>. EDP Sciences, 2019. <a href="https://doi.org/10.1051/0004-6361/201834916">https://doi.org/10.1051/0004-6361/201834916</a>.
  ieee: P. Pranav <i>et al.</i>, “Unexpected topology of the temperature fluctuations
    in the cosmic microwave background,” <i>Astronomy and Astrophysics</i>, vol. 627.
    EDP Sciences, 2019.
  ista: Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner
    H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations
    in the cosmic microwave background. Astronomy and Astrophysics. 627, A163.
  mla: Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations
    in the Cosmic Microwave Background.” <i>Astronomy and Astrophysics</i>, vol. 627,
    A163, EDP Sciences, 2019, doi:<a href="https://doi.org/10.1051/0004-6361/201834916">10.1051/0004-6361/201834916</a>.
  short: P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman,
    H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).
date_created: 2019-08-04T21:59:18Z
date_published: 2019-07-17T00:00:00Z
date_updated: 2023-08-29T07:01:48Z
day: '17'
ddc:
- '520'
- '530'
department:
- _id: HeEd
doi: 10.1051/0004-6361/201834916
external_id:
  arxiv:
  - '1812.07678'
  isi:
  - '000475839300003'
file:
- access_level: open_access
  checksum: 83b9209ed9eefbdcefd89019c5a97805
  content_type: application/pdf
  creator: dernst
  date_created: 2019-08-05T08:08:59Z
  date_updated: 2020-07-14T12:47:39Z
  file_id: '6766'
  file_name: 2019_AstronomyAstrophysics_Pranav.pdf
  file_size: 14420451
  relation: main_file
file_date_updated: 2020-07-14T12:47:39Z
has_accepted_license: '1'
intvolume: '       627'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 265683E4-B435-11E9-9278-68D0E5697425
  grant_number: M62909-18-1-2038
  name: Toward Computational Information Topology
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I02979-N35
  name: Persistence and stability of geometric complexes
publication: Astronomy and Astrophysics
publication_identifier:
  eissn:
  - '14320746'
  issn:
  - '00046361'
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unexpected topology of the temperature fluctuations in the cosmic microwave
  background
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 627
year: '2019'
...
