---
_id: '6648'
abstract:
- lang: eng
text: "Various kinds of data are routinely represented as discrete probability distributions.
Examples include text documents summarized by histograms of word occurrences and
images represented as histograms of oriented gradients. Viewing a discrete probability
distribution as a point in the standard simplex of the appropriate dimension,
we can understand collections of such objects in geometric and topological terms.
Importantly, instead of using the standard Euclidean distance, we look into dissimilarity
measures with information-theoretic justification, and we develop the theory\r\nneeded
for applying topological data analysis in this setting. In doing so, we emphasize
constructions that enable the usage of existing computational topology software
in this context."
alternative_title:
- LIPIcs
arxiv: 1
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ziga
full_name: Virk, Ziga
last_name: Virk
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information
space. In: 35th International Symposium on Computational Geometry. Vol
129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31'
apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis
in information space. In 35th International Symposium on Computational Geometry
(Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31'
chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data
Analysis in Information Space.” In 35th International Symposium on Computational
Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31.
ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information
space,” in 35th International Symposium on Computational Geometry, Portland,
OR, United States, 2019, vol. 129, p. 31:1-31:14.
ista: 'Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information
space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium
on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14.'
mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.”
35th International Symposium on Computational Geometry, vol. 129, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31.
short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on
Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019,
p. 31:1-31:14.
conference:
end_date: 2019-06-21
location: Portland, OR, United States
name: 'SoCG 2019: Symposium on Computational Geometry'
start_date: 2019-06-18
corr_author: '1'
date_created: 2019-07-17T10:36:09Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2024-10-09T20:58:55Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.4230/LIPICS.SOCG.2019.31
external_id:
arxiv:
- '1903.08510'
file:
- access_level: open_access
checksum: 8ec8720730d4c789bf7b06540f1c29f4
content_type: application/pdf
creator: dernst
date_created: 2019-07-24T06:40:01Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6666'
file_name: 2019_LIPICS_Edelsbrunner.pdf
file_size: 1355179
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 129'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 31:1-31:14
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: 35th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959771047'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Topological data analysis in information space
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: 129
year: '2019'
...
---
_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. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981
apa: Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni,
N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3306346.3322981
chicago: Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni,
and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions
on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.
ieee: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni,
“Volume-aware design of composite molds,” ACM Transactions on Graphics,
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.” ACM
Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981.
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: 2025-04-14T07:28:58Z
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'
...
---
OA_embargo: 6 months
OA_place: publisher
OA_type: hybrid
_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
article_type: original
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. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118
apa: Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives
new gene male germline expression. Genome Research. Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/gr.238824.118
chicago: Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives
New Gene Male Germline Expression.” Genome Research. Cold Spring Harbor
Laboratory Press, 2019. https://doi.org/10.1101/gr.238824.118.
ieee: J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene
male germline expression,” Genome Research, vol. 29, no. 7. Cold Spring
Harbor Laboratory 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.”
Genome Research, vol. 29, no. 7, Cold Spring Harbor Laboratory Press, 2019,
pp. 1115–22, doi:10.1101/gr.238824.118.
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: 2025-05-20T06:25:39Z
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
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1115-1122
publication: Genome Research
publication_identifier:
eissn:
- ' 1549-5469'
issn:
- 1088-9051
publication_status: published
publisher: Cold Spring Harbor Laboratory 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
OA_type: free access
_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.
Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034
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. Bulletin
of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan.
https://doi.org/10.1246/bcsj.20190034
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.” Bulletin of the Chemical Society of Japan. Bulletin
of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034.
ieee: N. Zenmyo et al., “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, 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.” Bulletin
of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical
Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034.
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: 2025-09-10T10:37:21Z
day: '15'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1246/bcsj.20190034
ec_funded: 1
external_id:
isi:
- '000468101800007'
has_accepted_license: '1'
intvolume: ' 92'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1246/bcsj.20190034
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:
- 0009-2673
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992
apa: Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski,
K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3306346.3322992
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.” ACM Transactions
on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992.
ieee: D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,”
ACM Transactions on Graphics, 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.”
ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992.
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: 2025-03-31T15:58:17Z
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. Journal of Applied and Computational
Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8
apa: 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. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8
chicago: Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The
Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.”
Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8.
ieee: J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion,
geodesic convexity and the variation of tangent spaces,” Journal of Applied
and Computational Topology, 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.” Journal of Applied and Computational
Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.
short: J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational
Topology 3 (2019) 29–58.
corr_author: '1'
date_created: 2019-07-24T08:37:29Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-04-14T07:44:06Z
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'
scopus_import: '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: 31st ACM Symposium on Parallelism
in Algorithms and Architectures. ACM; 2019:145-154. doi:10.1145/3323165.3323201'
apa: 'Alistarh, D.-A., Nadiradze, G., & Koval, N. (2019). Efficiency guarantees
for parallel incremental algorithms under relaxed schedulers. In 31st ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 145–154). Phoenix, AZ,
United States: ACM. https://doi.org/10.1145/3323165.3323201'
chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Nikita Koval. “Efficiency Guarantees
for Parallel Incremental Algorithms under Relaxed Schedulers.” In 31st ACM
Symposium on Parallelism in Algorithms and Architectures, 145–54. ACM, 2019.
https://doi.org/10.1145/3323165.3323201.
ieee: D.-A. Alistarh, G. Nadiradze, and N. Koval, “Efficiency guarantees for parallel
incremental algorithms under relaxed schedulers,” in 31st ACM Symposium on
Parallelism in Algorithms and Architectures, 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.” 31st ACM Symposium on Parallelism in
Algorithms and Architectures, ACM, 2019, pp. 145–54, doi:10.1145/3323165.3323201.
short: D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism
in Algorithms and Architectures, ACM, 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: 2026-04-08T07:00:45Z
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
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing. ACM; 2019:986-996. doi:10.1145/3313276.3316407'
apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019).
Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT
Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States:
ACM. https://doi.org/10.1145/3313276.3316407'
chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi
Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM
SIGACT Symposium on Theory of Computing, 986–96. ACM, 2019. https://doi.org/10.1145/3313276.3316407.
ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based
proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing, 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.” Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM, 2019,
pp. 986–96, doi:10.1145/3313276.3316407.
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, 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: 2025-05-14T11:26:07Z
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
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812
apa: Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812
chicago: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on
Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.
ieee: H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment
in a new habitat,” Evolution, 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.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45,
doi:10.1111/evo.13812.
short: H. Sachdeva, Evolution 73 (2019) 1729–1745.
corr_author: '1'
date_created: 2019-07-25T09:08:28Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2024-10-09T20:58:56Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13812
external_id:
isi:
- '000481300600001'
file:
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checksum: 772ce7035965153959b946a1033de1ca
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creator: kschuh
date_created: 2019-09-17T10:56:27Z
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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:
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status: public
scopus_import: '1'
status: public
title: Effect of partial selfing and polygenic selection on establishment in a new
habitat
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name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2019'
...
---
OA_place: publisher
_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:10.15479/AT:ISTA:6681
apa: Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681
chicago: Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.
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. Algorithmic Aspects of Homotopy Theory and Embeddability.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.
short: S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute
of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-07-26T11:14:34Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2026-04-16T12:20:40Z
day: '08'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: UlWa
doi: 10.15479/AT:ISTA:6681
file:
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date_created: 2019-08-07T13:03:34Z
date_updated: 2020-07-14T12:47:37Z
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file_size: 1087004
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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:
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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: ba8df636-2132-11f1-aed0-ed93e2281fdd
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. Annals of botany.
2019;123(7):1119-1131. doi:10.1093/aob/mcy183
apa: Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and
rapid turnover in gene expression in pre-reproductive seedlings of a dioecious
herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183
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.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183.
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,” Annals
of botany, 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.” Annals of Botany, vol.
123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183.
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: 2026-06-18T19:11:56Z
day: '04'
ddc:
- '570'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 123
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. Frontiers in Microbiology. 2019;10.
doi:10.3389/fmicb.2019.01171'
apa: 'Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing
autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology.
Frontiers. https://doi.org/10.3389/fmicb.2019.01171'
chicago: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing
Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology.
Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.'
ieee: 'C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer
controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, 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.” Frontiers in Microbiology,
vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.'
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: 2025-04-14T13:38:17Z
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
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
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th
International Colloquium on Automata, Languages and Programming. Vol 132.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77'
apa: 'Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In
46th International Colloquium on Automata, Languages and Programming (Vol.
132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ICALP.2019.77'
chicago: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.”
In 46th International Colloquium on Automata, Languages and Programming,
132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.
ieee: V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th
International Colloquium on Automata, Languages and Programming, 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: Automata,
Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.'
mla: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th
International Colloquium on Automata, Languages and Programming, vol. 132,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77.
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: 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: 2025-07-10T11:53:47Z
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. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627.
LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9'
apa: 'Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann,
A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019
(Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9'
chicago: 'Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress
in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi,
11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.'
ieee: 'M. Walter, “Sampling the integers with low relative error,” in Progress
in Cryptology – AFRICACRYPT 2019, 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.” Progress
in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627,
Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9.
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: 2025-09-10T10:38:28Z
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
external_id:
isi:
- '001299240700009'
intvolume: ' 11627'
isi: 1
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
eissn:
- 1611-3349
isbn:
- 978-3-0302-3695-3
issn:
- 0302-9743
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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.
IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738
apa: Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible
fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738
chicago: Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible
Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019.
https://doi.org/10.1109/TSP.2019.2944738.
ieee: S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast
polar decoders,” IEEE Transactions on Signal Processing, 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.” IEEE Transactions
on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738.
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: 2025-01-14T14:34:26Z
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:
- 1053-587X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rate-flexible fast polar decoders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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. Journal
of the ACM. 2019;66(4). doi:10.1145/3340295
apa: Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding
games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295
chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration
Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295.
ieee: G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,”
Journal of the ACM, 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.” Journal of the ACM,
vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295.
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: 2025-07-10T11:53:47Z
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: Formal methods for the design and analysis of complex systems
- _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:
- 1557-735X
issn:
- 0004-5411
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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.
Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133'
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. Genome Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz133'
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.” Genome Biology and Evolution.
Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz133.'
ieee: 'M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma
mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome
biology and evolution, vol. 11, no. 7. Oxford University 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.” Genome
Biology and Evolution, vol. 11, no. 7, Oxford University Press, 2019, pp.
1909–22, doi:10.1093/gbe/evz133.'
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: 2025-05-14T11:08:50Z
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 University 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2019'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '6759'
abstract:
- lang: eng
text: "We consider the graph class Grounded-L corresponding to graphs that admit
an intersection representation by L-shaped curves, where additionally the topmost
points of each curve are assumed to belong to a common horizontal line. We prove
that Grounded-L graphs admit an equivalent characterisation in terms of vertex
ordering with forbidden patterns. \r\nWe also compare this class to related intersection
classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max
point-tolerance graphs), or the outer-1-string graphs. We give constructions showing
that these classes are all distinct and satisfy only trivial or previously known
inclusions."
article_number: P3.17
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Vít
full_name: Jelínek, Vít
last_name: Jelínek
- first_name: Martin
full_name: Töpfer, Martin
id: 4B865388-F248-11E8-B48F-1D18A9856A87
last_name: Töpfer
citation:
ama: Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic
Journal of Combinatorics. 2019;26(3). doi:10.37236/8096
apa: Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives.
Electronic Journal of Combinatorics. Electronic Journal of Combinatorics.
https://doi.org/10.37236/8096
chicago: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.”
Electronic Journal of Combinatorics. Electronic Journal of Combinatorics,
2019. https://doi.org/10.37236/8096.
ieee: V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic
Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics,
2019.
ista: Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic
Journal of Combinatorics. 26(3), P3.17.
mla: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.”
Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic
Journal of Combinatorics, 2019, doi:10.37236/8096.
short: V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).
corr_author: '1'
date_created: 2019-08-04T21:59:20Z
date_published: 2019-07-19T00:00:00Z
date_updated: 2025-06-26T12:25:39Z
day: '19'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.37236/8096
ec_funded: 1
external_id:
arxiv:
- '1808.04148'
file:
- access_level: open_access
checksum: 20fc366fc6683ef0b074a019b73a663a
content_type: application/pdf
creator: dernst
date_created: 2019-08-05T06:46:55Z
date_updated: 2020-07-14T12:47:39Z
file_id: '6764'
file_name: 2019_eJourCombinatorics_Jelinek.pdf
file_size: 533697
relation: main_file
file_date_updated: 2020-07-14T12:47:39Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On grounded L-graphs and their relatives
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: 26
year: '2019'
...
---
_id: '6762'
abstract:
- lang: eng
text: "We present and study novel optimal control problems motivated by the search
for photovoltaic materials with high power-conversion efficiency. The material
must perform the first step: convert light (photons) into electronic excitations.
We formulate various desirable properties of the excitations as mathematical control
goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by
the nuclear charge distribution. We prove that nuclear distributions exist which
give rise to optimal HOMO-LUMO excitations, and present illustrative numerical
simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features
such as large electron-hole separation, and a hierarchy of length scales: internal
HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the
doping profiles < system size."
article_processing_charge: No
arxiv: 1
author:
- first_name: Gero
full_name: Friesecke, Gero
last_name: Friesecke
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Friesecke G, Kniely M. New optimal control problems in density functional theory
motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947.
doi:10.1137/18M1207272
apa: Friesecke, G., & Kniely, M. (2019). New optimal control problems in density
functional theory motivated by photovoltaics. Multiscale Modeling and Simulation.
SIAM. https://doi.org/10.1137/18M1207272
chicago: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density
Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation.
SIAM, 2019. https://doi.org/10.1137/18M1207272.
ieee: G. Friesecke and M. Kniely, “New optimal control problems in density functional
theory motivated by photovoltaics,” Multiscale Modeling and Simulation,
vol. 17, no. 3. SIAM, pp. 926–947, 2019.
ista: Friesecke G, Kniely M. 2019. New optimal control problems in density functional
theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3),
926–947.
mla: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density
Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation,
vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.
short: G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.
date_created: 2019-08-04T21:59:21Z
date_published: 2019-07-16T00:00:00Z
date_updated: 2025-07-10T11:53:49Z
day: '16'
department:
- _id: JuFi
doi: 10.1137/18M1207272
external_id:
arxiv:
- '1808.04200'
isi:
- '000487931800002'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.04200
month: '07'
oa: 1
oa_version: Preprint
page: 926-947
publication: Multiscale Modeling and Simulation
publication_identifier:
eissn:
- 1540-3467
issn:
- 1540-3459
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: New optimal control problems in density functional theory motivated by photovoltaics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2019'
...
---
_id: '6763'
abstract:
- lang: eng
text: "When grape-sized aqueous dimers are irradiated in a microwave oven, an intense
electromagnetic hotspot forms at their point of contact, often igniting a plasma.
Here we show that this irradiation can result in the injection of mechanical energy.
By examining irradiated hydrogel dimers through high-speed imaging, we find that
they repeatedly bounce off of each other while irradiated. We determine that an
average of 1 lJ of mechanical energy is injected into the pair during each collision.
Furthermore, a characteristic high-pitched audio signal is found to accompany
each collision.\r\nWe show that both the audio signal and the energy injection
arise via an interplay between vaporization and elastic deformations in the region
of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish
a novel, non-contact method of injecting mechanical energy into soft matter systems,
suggesting application in fields such as soft robotics."
article_processing_charge: No
article_type: original
author:
- first_name: Hamza K.
full_name: Khattak, Hamza K.
last_name: Khattak
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Aaron D.
full_name: Slepkov, Aaron D.
last_name: Slepkov
citation:
ama: Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation
of hydrogel dimers. Soft Matter. 2019;15(29):5804-5809. doi:10.1039/c9sm00756c
apa: Khattak, H. K., Waitukaitis, S. R., & Slepkov, A. D. (2019). Microwave
induced mechanical activation of hydrogel dimers. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c9sm00756c
chicago: Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave
Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter. Royal Society
of Chemistry, 2019. https://doi.org/10.1039/c9sm00756c.
ieee: H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical
activation of hydrogel dimers,” Soft Matter, vol. 15, no. 29. Royal Society
of Chemistry, pp. 5804–5809, 2019.
ista: Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical
activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.
mla: Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel
Dimers.” Soft Matter, vol. 15, no. 29, Royal Society of Chemistry, 2019,
pp. 5804–09, doi:10.1039/c9sm00756c.
short: H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.
date_created: 2019-08-04T21:59:21Z
date_published: 2019-07-15T00:00:00Z
date_updated: 2025-07-10T11:53:49Z
day: '15'
department:
- _id: ScWa
doi: 10.1039/c9sm00756c
external_id:
isi:
- '000476909200002'
pmid:
- '31305853'
intvolume: ' 15'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa_version: None
page: 5804-5809
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microwave induced mechanical activation of hydrogel dimers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...