---
_id: '12330'
abstract:
- lang: eng
text: 'The design and implementation of efficient concurrent data structures has
seen significant attention. However, most of this work has focused on concurrent
data structures providing good worst-case guarantees, although, in real workloads,
objects are often accessed at different rates. Efficient distribution-adaptive
data structures, such as splay-trees, are known in the sequential case; however,
they often are hard to translate efficiently to the concurrent case. We investigate
distribution-adaptive concurrent data structures, and propose a new design called
the splay-list. At a high level, the splay-list is similar to a standard skip-list,
with the key distinction that the height of each element adapts dynamically to
its access rate: popular elements “move up,” whereas rarely-accessed elements
decrease in height. We show that the splay-list provides order-optimal amortized
complexity bounds for a subset of operations, while being amenable to efficient
concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity
for performance, and can outperform the only previously-known distribution-adaptive
concurrent design in certain workloads.'
article_processing_charge: No
article_type: original
author:
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- 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: Alexandra
full_name: Drozdova, Alexandra
last_name: Drozdova
- first_name: Amirkeivan
full_name: Mohtashami, Amirkeivan
last_name: Mohtashami
citation:
ama: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive
concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x'
apa: 'Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The
splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00441-x'
chicago: 'Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan
Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.'
ieee: 'V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list:
A distribution-adaptive concurrent skip-list,” Distributed Computing, vol.
36. Springer Nature, pp. 395–418, 2023.'
ista: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list:
A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.'
mla: 'Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent
Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp.
395–418, doi:10.1007/s00446-022-00441-x.'
short: V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing
36 (2023) 395–418.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-14T12:54:32Z
day: '01'
department:
- _id: DaAl
doi: 10.1007/s00446-022-00441-x
external_id:
arxiv:
- '2008.01009'
isi:
- '000913424000001'
intvolume: ' 36'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2008.01009
month: '09'
oa: 1
oa_version: Preprint
page: 395-418
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The splay-list: A distribution-adaptive concurrent skip-list'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
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: 32
year: '2023'
...
---
_id: '12114'
abstract:
- lang: eng
text: 'Probing the dynamics of aromatic side chains provides important insights
into the behavior of a protein because flips of aromatic rings in a protein’s
hydrophobic core report on breathing motion involving a large part of the protein.
Inherently invisible to crystallography, aromatic motions have been primarily
studied by solution NMR. The question how packing of proteins in crystals affects
ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning
NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a
protein in three different crystal packing environments to shed light onto possible
impact of packing on ring flips. The flips of the two Phe residues in ubiquitin,
both surface exposed, appear remarkably conserved in the different crystal forms,
even though the intermolecular packing is quite different: Phe4 flips on a ca.
10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to
µs motion. Our findings suggest that intramolecular influences are more important
for ring flips than intermolecular (packing) effects.'
acknowledgement: The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within
the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche)
CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research
Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the
Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI
(ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership
for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing
and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg
State University in a form of the grant 92425251 and the access to the MRR, MCT
and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact
that “tensor asymmetry” is better called “tensor biaxiality”.
article_number: '100079'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Olga O.
full_name: Lebedenko, Olga O.
last_name: Lebedenko
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079'
apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R.,
Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079'
chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman
Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in
Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal
of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.'
ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin
protein crystals from MAS NMR and MD,” Journal of Structural Biology: X,
vol. 7. Elsevier, 2023.'
ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR,
Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals
from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.'
mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin
Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X,
vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.'
short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R.
Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).'
date_created: 2023-01-12T11:55:38Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-16T09:37:25Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.yjsbx.2022.100079
external_id:
pmid:
- '36578472'
file:
- access_level: open_access
checksum: b4b1c10a31018aafe053b7d55a470e54
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T09:36:28Z
date_updated: 2023-08-16T09:36:28Z
file_id: '14064'
file_name: 2023_JourStrucBiologyX_Gauto.pdf
file_size: 5132322
relation: main_file
success: 1
file_date_updated: 2023-08-16T09:36:28Z
has_accepted_license: '1'
intvolume: ' 7'
keyword:
- Structural Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Structural Biology: X'
publication_identifier:
issn:
- 2590-1524
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS
NMR and MD
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12163'
abstract:
- lang: eng
text: Small GTPases play essential roles in the organization of eukaryotic cells.
In recent years, it has become clear that their intracellular functions result
from intricate biochemical networks of the GTPase and their regulators that dynamically
bind to a membrane surface. Due to the inherent complexities of their interactions,
however, revealing the underlying mechanisms of action is often difficult to achieve
from in vivo studies. This review summarizes in vitro reconstitution approaches
developed to obtain a better mechanistic understanding of how small GTPase activities
are regulated in space and time.
acknowledgement: The authors acknowledge support from IST Austria and helpful comments
from the anonymous reviewers that helped to improve this manuscript. We apologize
to the authors of primary literature and outstanding research not cited here due
to space restraints.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: Hanifatul R
full_name: Budiman, Hanifatul R
id: 55380f95-15b2-11ec-abd3-aff8e230696b
last_name: Budiman
- first_name: Lukasz M
full_name: Kowalski, Lukasz M
id: e3a512e2-4bbe-11eb-a68a-e3857a7844c2
last_name: Kowalski
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
citation:
ama: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro
reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777.
doi:10.1002/1873-3468.14540
apa: Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic,
I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters.
Wiley. https://doi.org/10.1002/1873-3468.14540
chicago: Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz
M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.
ieee: M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic,
“In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol.
597, no. 6. Wiley, pp. 762–777, 2023.
ista: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In
vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.
mla: Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.
short: M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic,
FEBS Letters 597 (2023) 762–777.
date_created: 2023-01-12T12:09:58Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:32:29Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1002/1873-3468.14540
external_id:
isi:
- '000891573000001'
pmid:
- '36448231'
file:
- access_level: open_access
checksum: 7492244d3f9c5faa1347ef03f6e5bc84
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:31:04Z
date_updated: 2023-08-16T08:31:04Z
file_id: '14063'
file_name: 2023_FEBSLetters_Loose.pdf
file_size: 3148143
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:31:04Z
has_accepted_license: '1'
intvolume: ' 597'
isi: 1
issue: '6'
keyword:
- Cell Biology
- Genetics
- Molecular Biology
- Biochemistry
- Structural Biology
- Biophysics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 762-777
pmid: 1
publication: FEBS Letters
publication_identifier:
eissn:
- 1873-3468
issn:
- 0014-5793
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution of small GTPase regulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 597
year: '2023'
...
---
_id: '12164'
abstract:
- lang: eng
text: 'A shared-memory counter is a widely-used and well-studied concurrent object.
It supports two operations: An Inc operation that increases its value by 1 and
a Read operation that returns its current value. In Jayanti et al (SIAM J Comput,
30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case
step complexity of obstruction-free implementations, from read-write registers,
of a large class of shared objects that includes counters. The lower bound leaves
open the question of finding counter implementations with sub-linear amortized
step complexity. In this work, we address this gap. We show that n-process, wait-free
and linearizable counters can be implemented from read-write registers with O(log2n)
amortized step complexity. This is the first counter algorithm from read-write
registers that provides sub-linear amortized step complexity in executions of
arbitrary length. Since a logarithmic lower bound on the amortized step complexity
of obstruction-free counter implementations exists, our upper bound is within
a logarithmic factor of the optimal. The worst-case step complexity of the construction
remains linear, which is optimal. This is obtained thanks to a new max register
construction with O(logn) amortized step complexity in executions of arbitrary
length in which the value stored in the register does not grow too quickly. We
then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel
[1] in which we “plug” our max register implementation to show that it remains
linearizable while achieving O(log2n) amortized step complexity.'
acknowledgement: A preliminary version of this work appeared in DISC’19. Mirza Ahad
Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes
and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported
by the Israel Science Foundation (Grants 380/18 and 1425/22).
article_processing_charge: No
article_type: original
author:
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Danny
full_name: Hendler, Danny
last_name: Hendler
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5
apa: Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived
counters with polylogarithmic amortized step complexity. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00439-5
chicago: Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers.
“Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.
ieee: M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with
polylogarithmic amortized step complexity,” Distributed Computing, vol.
36. Springer Nature, pp. 29–43, 2023.
ista: Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 36, 29–43.
mla: Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized
Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023,
pp. 29–43, doi:10.1007/s00446-022-00439-5.
short: M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023)
29–43.
date_created: 2023-01-12T12:10:08Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:39:36Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00446-022-00439-5
external_id:
isi:
- '000890138700001'
intvolume: ' 36'
isi: 1
keyword:
- Computational Theory and Mathematics
- Computer Networks and Communications
- Hardware and Architecture
- Theoretical Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://drops.dagstuhl.de/opus/volltexte/2019/11310/
month: '03'
oa: 1
oa_version: Preprint
page: 29-43
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived counters with polylogarithmic amortized step complexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12172'
abstract:
- lang: eng
text: In industrial reactors and equipment, non-ideality is quite a common phenomenon
rather than an exception. These deviations from ideality impact the process's
overall efficiency and the effectiveness of the equipment. To recognize the associated
non-ideality, one needs to have enough understanding of the formulation of the
equations and in-depth knowledge of the residence time distribution (RTD) data
of real reactors. In the current work, step input and pulse input were used to
create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the
aforementioned configuration, experiments were run at various flow rates to validate
the developed characteristic equations. To produce RTD data, distilled water was
utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior
of tracer concentration exits age distribution, and cumulative fraction for each
setup and each input was plotted and experimental results were compared with perfect
behavior. Deviation of concentration exit age distribution and cumulative fractional
distribution from ideal behavior is more in pulse input as compared to a step
input. For ideal cases, the exit age distribution curve and cumulative fraction
curves are independent of the type of input. But a significant difference was
observed for the two cases, which may be due to non-measurable fluctuations in
volumetric flow rate, non-achievement of instant injection of tracer in case of
pulse input, and slight variations in the sampling period. Further, with increasing
flow rate, concentration, exit age, and cumulative fractional curves shifted upward,
and this behavior matches with the actual case.
article_processing_charge: No
article_type: original
author:
- first_name: Bushra
full_name: Khatoon, Bushra
last_name: Khatoon
- first_name: Shoaib
full_name: Kamil, Shoaib
id: 185a19af-dc7d-11ea-9b2f-8eb2201959e9
last_name: Kamil
- first_name: Hitesh
full_name: Babu, Hitesh
last_name: Babu
- first_name: M.
full_name: Siraj Alam, M.
last_name: Siraj Alam
citation:
ama: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade
CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part
1):40-47. doi:10.1016/j.matpr.2022.11.037'
apa: 'Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental
analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings.
Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037'
chicago: 'Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental
Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings.
Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.'
ieee: 'B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis
of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings,
vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.'
ista: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of
Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part
1), 40–47.'
mla: 'Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step
and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier,
2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.'
short: 'B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings
78 (2023) 40–47.'
date_created: 2023-01-12T12:11:26Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T09:08:11Z
day: '20'
department:
- _id: BjHo
doi: 10.1016/j.matpr.2022.11.037
intvolume: ' 78'
issue: Part 1
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 40-47
publication: 'Materials Today: Proceedings'
publication_identifier:
issn:
- 2214-7853
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental analysis of Cascade CSTRs with step and pulse inputs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2023'
...
---
_id: '12515'
abstract:
- lang: eng
text: "Introduction: The olfactory system in most mammals is divided into several
subsystems based on the anatomical locations of the neuroreceptor cells involved
and the receptor families that are expressed. In addition to the main olfactory
system and the vomeronasal system, a range of olfactory subsystems converge onto
the transition zone located between the main olfactory bulb (MOB) and the accessory
olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL
contains specialized glomeruli that receive noncanonical sensory afferences and
which interact with the MOB and AOB. Little is known regarding the olfactory subsystems
of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing
the OL in the red fox by performing general and specific histological stainings
on serial sections, using both single and double immunohistochemical and lectin-histochemical
labeling techniques.\r\nResults: As a result, we have been able to determine that
the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development
and complexity.\r\nDiscussion: This makes this species a novel mammalian model,
the study of which could improve our understanding of the noncanonical pathways
involved in the processing of chemosensory cues."
acknowledgement: This work was partially supported by a grant from “Consello Social
Universidade de Santiago de Compostela” 2022-PU004.We would like to show special
gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing
us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia,
Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación
Galega de Caza for providing the red foxes used in this study.
article_number: '1097467'
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Ortiz-Leal, Irene
last_name: Ortiz-Leal
- first_name: Mateo V.
full_name: Torres, Mateo V.
last_name: Torres
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Luis Eusebio
full_name: Fidalgo, Luis Eusebio
last_name: Fidalgo
- first_name: Ana María
full_name: López-Beceiro, Ana María
last_name: López-Beceiro
- first_name: Jorge A.
full_name: Larriva-Sahd, Jorge A.
last_name: Larriva-Sahd
- first_name: Pablo
full_name: Sánchez-Quinteiro, Pablo
last_name: Sánchez-Quinteiro
citation:
ama: Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of
the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb
pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467
apa: Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro,
A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory
limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory
bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467
chicago: Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio
Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro.
“The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a
Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers,
2023. https://doi.org/10.3389/fnana.2022.1097467.
ieee: I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes
vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers
in Neuroanatomy, vol. 16. Frontiers, 2023.
ista: Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM,
Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox
(Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway.
Frontiers in Neuroanatomy. 16, 1097467.
mla: Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes).
New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in
Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.
short: I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro,
J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).
date_created: 2023-02-05T23:01:00Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2023-08-16T11:37:52Z
day: '10'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.3389/fnana.2022.1097467
external_id:
isi:
- '000919786900001'
pmid:
- '36704406'
file:
- access_level: open_access
checksum: 49cd40f3bda6f267079427042e7d15e3
content_type: application/pdf
creator: dernst
date_created: 2023-02-06T07:56:14Z
date_updated: 2023-02-06T07:56:14Z
file_id: '12518'
file_name: 2022_FrontiersNeuroanatomy_OrtizLeal.pdf
file_size: 21943473
relation: main_file
success: 1
file_date_updated: 2023-02-06T07:56:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neuroanatomy
publication_identifier:
eissn:
- 1662-5129
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding
a noncanonical olfactory bulb pathway
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: 16
year: '2023'
...
---
_id: '12106'
abstract:
- lang: eng
text: Regulation of chromatin states involves the dynamic interplay between different
histone modifications to control gene expression. Recent advances have enabled
mapping of histone marks in single cells, but most methods are constrained to
profile only one histone mark per cell. Here, we present an integrated experimental
and computational framework, scChIX-seq (single-cell chromatin immunocleavage
and unmixing sequencing), to map several histone marks in single cells. scChIX-seq
multiplexes two histone marks together in single cells, then computationally deconvolves
the signal using training data from respective histone mark profiles. This framework
learns the cell-type-specific correlation structure between histone marks, and
therefore does not require a priori assumptions of their genomic distributions.
Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single
cells across a range of mark combinations. Modeling dynamics of in vitro macrophage
differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq
unlocks systematic interrogation of the interplay between histone modifications
in single cells.
acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell
types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg
for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat
and O. Stegle for discussions on multinomial distributions. This work was supported
by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse
Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001)
and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early
Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie
Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term
Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is
part of the Oncode Institute which is financed partly by the Dutch Cancer Society.
article_processing_charge: No
article_type: original
author:
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Buys Anton
full_name: De Barbanson, Buys Anton
last_name: De Barbanson
- first_name: Max D.
full_name: Wellenstein, Max D.
last_name: Wellenstein
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
citation:
ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. scChIX-seq infers dynamic relationships between histone modifications in single
cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3
apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D.,
& Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between
histone modifications in single cells. Nature Biotechnology. Springer Nature.
https://doi.org/10.1038/s41587-022-01560-3
chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max
D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships
between Histone Modifications in Single Cells.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.
ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and
A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications
in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823,
2023.
ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. 2023. scChIX-seq infers dynamic relationships between histone modifications
in single cells. Nature Biotechnology. 41, 813–823.
mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone
Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer
Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.
short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A.
Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.
date_created: 2023-01-08T23:00:53Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-16T11:32:33Z
day: '01'
ddc:
- '570'
department:
- _id: ScienComp
doi: 10.1038/s41587-022-01560-3
external_id:
isi:
- '000909067600003'
file:
- access_level: open_access
checksum: 668447a1c8d360b68f8aaf9e08ed644f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:30:45Z
date_updated: 2023-08-16T11:30:45Z
file_id: '14066'
file_name: 2023_NatureBioTech_Yeung.pdf
file_size: 12040976
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:30:45Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 813–823
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: scChIX-seq infers dynamic relationships between histone modifications in single
cells
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: 41
year: '2023'
...
---
_id: '12183'
abstract:
- lang: eng
text: We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with
Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii
regime, with an optimal bound on the condensate depletion. Moreover, our lower
bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann
bracketing) a lower bound for the ground state energy of N bosons in a large box
[−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.
acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions.
Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3
apa: Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann
boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3
chicago: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.
ieee: C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary
conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560,
2023.
ista: Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary
conditions. Annales Henri Poincare. 24, 1505–1560.
mla: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.
short: C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.
date_created: 2023-01-15T23:00:52Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-08-16T11:34:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00023-022-01252-3
ec_funded: 1
external_id:
arxiv:
- '2205.15284'
isi:
- '000910751800002'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.15284
month: '05'
oa: 1
oa_version: Preprint
page: 1505-1560
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bose Gas in a box with Neumann boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12544'
abstract:
- lang: eng
text: Geometry is crucial in our efforts to comprehend the structures and dynamics
of biomolecules. For example, volume, surface area, and integrated mean and Gaussian
curvature of the union of balls representing a molecule are used to quantify its
interactions with the water surrounding it in the morphometric implicit solvent
models. The Alpha Shape theory provides an accurate and reliable method for computing
these geometric measures. In this paper, we derive homogeneous formulas for the
expressions of these measures and their derivatives with respect to the atomic
coordinates, and we provide algorithms that implement them into a new software
package, AlphaMol. The only variables in these formulas are the interatomic distances,
making them insensitive to translations and rotations. AlphaMol includes a sequential
algorithm and a parallel algorithm. In the parallel version, we partition the
atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree
algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented
by a buffer zone to account for atoms whose ball representations may partially
cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up
compared to an independent serial implementation when using 32 processors. For
instance, it takes 31 s to compute the geometric measures and derivatives of each
atom in a viral capsid with more than 26 million atoms on 32 Intel processors
running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant
computations, which ultimately limit the impact of using multiple processors.
AlphaMol is available as an OpenSource software.
acknowledgement: "P.K. acknowledges support from the University of California Multicampus
Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant
No.1760485). H.E. acknowledges support from the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program, Grant No.
788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31,
and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access
is funded by the Austrian Science Fund (FWF)."
article_processing_charge: No
article_type: original
author:
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean,
and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346
apa: Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume,
surface area, mean, and Gaussian curvatures of molecules and their derivatives.
Journal of Chemical Information and Modeling. American Chemical Society.
https://doi.org/10.1021/acs.jcim.2c01346
chicago: Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the
Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.”
Journal of Chemical Information and Modeling. American Chemical Society,
2023. https://doi.org/10.1021/acs.jcim.2c01346.
ieee: P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface
area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal
of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society,
pp. 973–985, 2023.
ista: Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area,
mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical
Information and Modeling. 63(3), 973–985.
mla: Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian
Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information
and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85,
doi:10.1021/acs.jcim.2c01346.
short: P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and
Modeling 63 (2023) 973–985.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-02-13T00:00:00Z
date_updated: 2023-08-16T12:22:07Z
day: '13'
ddc:
- '510'
- '540'
department:
- _id: HeEd
doi: 10.1021/acs.jcim.2c01346
ec_funded: 1
external_id:
isi:
- '000920370700001'
pmid:
- '36638318'
file:
- access_level: open_access
checksum: 7d20562269edff1e31b9d6019d4983b0
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:21:13Z
date_updated: 2023-08-16T12:21:13Z
file_id: '14070'
file_name: 2023_JCIM_Koehl.pdf
file_size: 8069223
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:21:13Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 973-985
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Journal of Chemical Information and Modeling
publication_identifier:
eissn:
- 1549-960X
issn:
- 1549-9596
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the volume, surface area, mean, and Gaussian curvatures of molecules
and their derivatives
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: 63
year: '2023'
...
---
_id: '12543'
abstract:
- lang: eng
text: Treating sick group members is a hallmark of collective disease defence in
vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness
and epidemiology, it is still largely unknown how pathogens react to the selection
pressure imposed by care intervention. Using social insects and pathogenic fungi,
we here performed a serial passage experiment in the presence or absence of colony
members, which provide social immunity by grooming off infectious spores from
exposed individuals. We found specific effects on pathogen diversity, virulence
and transmission. Under selection of social immunity, pathogens invested into
higher spore production, but spores were less virulent. Notably, they also elicited
a lower grooming response in colony members, compared with spores from the individual
host selection lines. Chemical spore analysis suggested that the spores from social
selection lines escaped the caregivers’ detection by containing lower levels of
ergosterol, a key fungal membrane component. Experimental application of chemically
pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated
cue triggering host social immunity against fungal pathogens. By reducing this
detection cue, pathogens were able to evade the otherwise very effective collective
disease defences of their social hosts.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the
fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team
at ISTA for ant collection and experimental help, in particular H. Leitner, and
the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg
and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the
Social Immunity team for comments on the manuscript. The study was funded by the
German Research Foundation (CR118/3-1) within the Framework of the Priority Program
SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon
2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Michaela
full_name: Hönigsberger, Michaela
id: 953894f3-25bd-11ec-8556-f70a9d38ef60
last_name: Hönigsberger
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Niklas
full_name: Kampleitner, Niklas
id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87
last_name: Kampleitner
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6
apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F.,
Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature
Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6
chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse,
Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt,
and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and
Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.
ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology
and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.
ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner
N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 7, 450–460.
mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology
and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.
short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N.
Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution
7 (2023) 450–460.
date_created: 2023-02-12T23:00:59Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T11:55:48Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
- _id: LifeSc
- _id: JiFr
doi: 10.1038/s41559-023-01981-6
ec_funded: 1
external_id:
isi:
- '000924572800001'
pmid:
- '36732670'
file:
- access_level: open_access
checksum: 8244f4650a0e7aeea488d1bcd4a31702
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:54:59Z
date_updated: 2023-08-16T11:54:59Z
file_id: '14069'
file_name: 2023_NatureEcoEvo_Stock.pdf
file_size: 1600499
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:54:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 450-460
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Nature Ecology and Evolution
publication_identifier:
eissn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/
scopus_import: '1'
status: public
title: Pathogen evasion of social immunity
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: 7
year: '2023'
...
---
_id: '12521'
abstract:
- lang: eng
text: Differentiated X chromosomes are expected to have higher rates of adaptive
divergence than autosomes, if new beneficial mutations are recessive (the “faster-X
effect”), largely because these mutations are immediately exposed to selection
in males. The evolution of X chromosomes after they stop recombining in males,
but before they become hemizygous, has not been well explored theoretically. We
use the diffusion approximation to infer substitution rates of beneficial and
deleterious mutations under such a scenario. Our results show that selection is
less efficient on diploid X loci than on autosomal and hemizygous X loci under
a wide range of parameters. This “slower-X” effect is stronger for genes affecting
primarily (or only) male fitness, and for sexually antagonistic genes. These unusual
dynamics suggest that some of the peculiar features of X chromosomes, such as
the differential accumulation of genes with sex-specific functions, may start
arising earlier than previously appreciated.
acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing
Unit. We also thank two anonymous reviewers for their valuable comments. This work
was supported by the European Research Council under the European Union’s Horizon
2020 research and innovation program (grant agreements no. 715257 and no. 716117).
article_number: qrac004
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- 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: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
2023;7(1). doi:10.1093/evlett/qrac004'
apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X:
Reduced efficiency of selection in the early stages of X chromosome evolution.
Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004'
chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso.
“Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome
Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.'
ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced
efficiency of selection in the early stages of X chromosome evolution,” Evolution
Letters, vol. 7, no. 1. Oxford University Press, 2023.'
ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
7(1), qrac004.'
mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the
Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no.
1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.'
short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).
date_created: 2023-02-06T13:59:12Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-08-16T11:44:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.1093/evlett/qrac004
ec_funded: 1
external_id:
isi:
- '001021692200001'
pmid:
- '37065438'
file:
- access_level: open_access
checksum: a240a041cb9b9b7c8ba93a4706674a3f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:43:33Z
date_updated: 2023-08-16T11:43:33Z
file_id: '14068'
file_name: 2023_EvLetters_Mrnjavac.pdf
file_size: 2592189
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:43:33Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome
evolution'
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: 7
year: '2023'
...
---
_id: '12679'
abstract:
- lang: eng
text: How to generate a brain of correct size and with appropriate cell-type diversity
during development is a major question in Neuroscience. In the developing neocortex,
radial glial progenitor (RGP) cells are the main neural stem cells that produce
cortical excitatory projection neurons, glial cells, and establish the prospective
postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated
developmental program that when disrupted can result in severe cortical malformations
such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms
instructing faithful RGP lineage progression are however not well understood.
This review will summarize recent conceptual advances that contribute to our understanding
of the general principles of RGP lineage progression.
acknowledgement: "I wish to thank all current and past members of the Hippenmeyer
laboratory at ISTA for exciting discussions on the subject of this review. I apologize
to colleagues whose work I could not cite and/or discuss in the frame of the available
space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported
by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council
(ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(grant agree-ment no. 725780 LinPro) to SH."
article_number: '102695'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Hippenmeyer S. Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4).
doi:10.1016/j.conb.2023.102695'
apa: 'Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology.
Elsevier. https://doi.org/10.1016/j.conb.2023.102695'
chicago: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression:
Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology.
Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.'
ieee: 'S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights
from developing cerebral cortex,” Current Opinion in Neurobiology, vol.
79, no. 4. Elsevier, 2023.'
ista: 'Hippenmeyer S. 2023. Principles of neural stem cell lineage progression:
Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4),
102695.'
mla: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights
from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol.
79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.'
short: S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).
date_created: 2023-02-26T12:24:21Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T12:30:25Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.conb.2023.102695
ec_funded: 1
external_id:
isi:
- '000953497700001'
pmid:
- '36842274'
file:
- access_level: open_access
checksum: 4d11c4ca87e6cbc4d2ac46d3225ea615
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:29:06Z
date_updated: 2023-08-16T12:29:06Z
file_id: '14071'
file_name: 2023_CurrentOpinionNeurobio_Hippenmeyer.pdf
file_size: 1787894
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:29:06Z
has_accepted_license: '1'
intvolume: ' 79'
isi: 1
issue: '4'
keyword:
- General Neuroscience
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Principles of neural stem cell lineage progression: Insights from developing
cerebral cortex'
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: 79
year: '2023'
...
---
_id: '12429'
abstract:
- lang: eng
text: In this paper, we consider traces at initial times for functions with mixed
time-space smoothness. Such results are often needed in the theory of evolution
equations. Our result extends and unifies many previous results. Our main improvement
is that we can allow general interpolation couples. The abstract results are applied
to regularity problems for fractional evolution equations and stochastic evolution
equations, where uniform trace estimates on the half-line are shown.
acknowledgement: The first author has been partially supported by the Nachwuchsring—Network
for the promotion of young scientists—at TU Kaiserslautern. The second and third
authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation
for Scientific Research (NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Nick
full_name: Lindemulder, Nick
last_name: Lindemulder
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350.
doi:10.1002/mana.202100192
apa: Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding
and its applications to evolution equations. Mathematische Nachrichten.
Wiley. https://doi.org/10.1002/mana.202100192
chicago: Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding
and Its Applications to Evolution Equations.” Mathematische Nachrichten.
Wiley, 2023. https://doi.org/10.1002/mana.202100192.
ieee: A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its
applications to evolution equations,” Mathematische Nachrichten, vol. 296,
no. 4. Wiley, pp. 1319–1350, 2023.
ista: Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications
to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.
mla: Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution
Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp.
1319–50, doi:10.1002/mana.202100192.
short: A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023)
1319–1350.
date_created: 2023-01-29T23:00:59Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2023-08-16T11:41:42Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1002/mana.202100192
external_id:
arxiv:
- '2104.05063'
isi:
- '000914134900001'
file:
- access_level: open_access
checksum: 6f099f1d064173784d1a27716a2cc795
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:40:02Z
date_updated: 2023-08-16T11:40:02Z
file_id: '14067'
file_name: 2023_MathNachrichten_Agresti.pdf
file_size: 449280
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:40:02Z
has_accepted_license: '1'
intvolume: ' 296'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 1319-1350
publication: Mathematische Nachrichten
publication_identifier:
eissn:
- 1522-2616
issn:
- 0025-584X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the trace embedding and its applications to evolution equations
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: 296
year: '2023'
...
---
_id: '12430'
abstract:
- lang: eng
text: We study the time evolution of the Nelson model in a mean-field limit in which
N nonrelativistic bosons weakly couple (with respect to the particle number) to
a positive or zero mass quantized scalar field. Our main result is the derivation
of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove
the convergence of the approximate wave function to the many-body wave function
in norm, with a convergence rate proportional to the number of corrections taken
into account in the approximation. We prove an analogous result for the unitary
propagator. As an application, we derive a simple system of partial differential
equations describing the time evolution of the first- and second-order approximations
to the one-particle reduced density matrices of the particles and the quantum
field, respectively.
article_number: '2350006'
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Falconi, Marco
last_name: Falconi
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
citation:
ama: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order
corrections for the regularized Nelson model. Reviews in Mathematical Physics.
2023;35(4). doi:10.1142/S0129055X2350006X
apa: Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023).
Bogoliubov dynamics and higher-order corrections for the regularized Nelson model.
Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X
chicago: Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören
P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized
Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing,
2023. https://doi.org/10.1142/S0129055X2350006X.
ieee: M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov
dynamics and higher-order corrections for the regularized Nelson model,” Reviews
in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.
ista: Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics
and higher-order corrections for the regularized Nelson model. Reviews in Mathematical
Physics. 35(4), 2350006.
mla: Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for
the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35,
no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.
short: M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical
Physics 35 (2023).
date_created: 2023-01-29T23:00:59Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-08-16T11:47:27Z
day: '09'
department:
- _id: RoSe
doi: 10.1142/S0129055X2350006X
external_id:
arxiv:
- '2110.00458'
isi:
- '000909760300001'
intvolume: ' 35'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2110.00458'
month: '01'
oa: 1
oa_version: Preprint
publication: Reviews in Mathematical Physics
publication_identifier:
issn:
- 0129-055X
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bogoliubov dynamics and higher-order corrections for the regularized Nelson
model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12762'
abstract:
- lang: eng
text: Neurons in the brain are wired into adaptive networks that exhibit collective
dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches.
Although existing models account for oscillations and avalanches separately, they
typically do not explain both phenomena, are too complex to analyze analytically
or intractable to infer from data rigorously. Here we propose a feedback-driven
Ising-like class of neural networks that captures avalanches and oscillations
simultaneously and quantitatively. In the simplest yet fully microscopic model
version, we can analytically compute the phase diagram and make direct contact
with human brain resting-state activity recordings via tractable inference of
the model’s two essential parameters. The inferred model quantitatively captures
the dynamics over a broad range of scales, from single sensor oscillations to
collective behaviors of extreme events and neuronal avalanches. Importantly, the
inferred parameters indicate that the co-existence of scale-specific (oscillations)
and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical
point at the onset of self-sustained oscillations.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose
of open access, the author has applied a CC BY public copyright licence to any Author
Accepted Manuscript version arising from this submission. The study was supported
by the European Union Horizon 2020 research and innovation program under the Marie
Sklodowska-Curie action (grant agreement No. 754411 to F.L.).
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023).
Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain. Nature Computational Science.
Springer Nature. https://doi.org/10.1038/s43588-023-00410-9
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence
of Avalanches and Oscillations in Resting Human Brain.” Nature Computational
Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical
modeling of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain,” Nature Computational Science, vol. 3. Springer
Nature, pp. 254–263, 2023.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 3, 254–263.
mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks
Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”
Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63,
doi:10.1038/s43588-023-00410-9.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational
Science 3 (2023) 254–263.
date_created: 2023-03-26T22:01:08Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T12:41:53Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
- _id: GradSch
doi: 10.1038/s43588-023-00410-9
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
file:
- access_level: open_access
checksum: 7c63b2b2edfd68aaffe96d70ca6a865a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:39:57Z
date_updated: 2023-08-16T12:39:57Z
file_id: '14073'
file_name: 2023_NatureCompScience_Lombardi.pdf
file_size: 4474284
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:39:57Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 254-263
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: Nature Computational Science
publication_identifier:
eissn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain
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: '2023'
...
---
_id: '12891'
abstract:
- lang: eng
text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning
and the physical processes driving embryo morphogenesis renders\r\nembryonic development
robust, such that key developmental processes can unfold\r\nrelatively normally
even outside of the full embryonic context. For instance, embryonic\r\nstem cell
cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading
to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis
leads to questions on specific contributions of embryo-specific features, such
as\r\nthe presence of extraembryonic tissues, which are inherently involved in
gastrulation\r\nin the full embryonic context. To address this, we established
zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important
player as a signaling\r\nsource and for morphogenesis during gastrulation, as
a model of ex vivo development.\r\nWe found that dorsal-marginal determinants
are required and sufficient in these\r\nexplants to form and pattern all three
germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling
levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues
for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo
gastrulation-like axis elongation. We found that this\r\nelongation movement shows
hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated
with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation
of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting
that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis.
This control is achieved by Nodal signaling, which is critical for\r\neffectively
downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling
is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis,
but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively,
we provide insights into the capacity and organization of signaling and\r\nmorphogenetic
domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full
embryonic context."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
citation:
ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues. 2023. doi:10.15479/at:ista:12891'
apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The
role of extraembryonic tissues. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12891'
chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation:
The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12891.'
ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of
extraembryonic tissues,” Institute of Science and Technology Austria, 2023.'
ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role
of extraembryonic tissues. Institute of Science and Technology Austria.'
mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The
Role of Extraembryonic Tissues. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12891.'
short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of
Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.'
date_created: 2023-05-05T08:48:20Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2023-08-21T06:25:48Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12891
ec_funded: 1
file:
- access_level: closed
checksum: 59b0303dc483f40a96a610a90aab7ee9
content_type: application/pdf
creator: aschauer
date_created: 2023-05-05T13:01:14Z
date_updated: 2023-05-05T13:01:14Z
embargo: 2024-05-05
embargo_to: open_access
file_id: '12907'
file_name: Thesis_Schauer_final.pdf
file_size: 31434230
relation: main_file
- access_level: closed
checksum: 25f54e12479b6adaabd129a20568e6c1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aschauer
date_created: 2023-05-05T13:04:15Z
date_updated: 2023-05-05T13:04:15Z
file_id: '12908'
file_name: Thesis_Schauer_final.docx
file_size: 43809109
relation: source_file
file_date_updated: 2023-05-05T13:04:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8966'
relation: part_of_dissertation
status: public
- id: '7888'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14085'
abstract:
- lang: eng
text: We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow
under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed,
unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm
in general sparse graphs with arbitrarily good approximation guarantee.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic
Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for
a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz
Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There,
he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich
Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster
and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their
insightful comments."
alternative_title:
- LIPIcs
article_number: '69'
article_processing_charge: Yes
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Goranci G, Henzinger MH. Efficient data structures for incremental exact and
approximate maximum flow. In: 50th International Colloquium on Automata, Languages,
and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.ICALP.2023.69'
apa: 'Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for
incremental exact and approximate maximum flow. In 50th International Colloquium
on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69'
chicago: Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for
Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.
ieee: G. Goranci and M. H. Henzinger, “Efficient data structures for incremental
exact and approximate maximum flow,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Goranci G, Henzinger MH. 2023. Efficient data structures for incremental
exact and approximate maximum flow. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: International Colloquium on Automata, Languages,
and Programming, LIPIcs, vol. 261, 69.'
mla: Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental
Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata,
Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.
short: G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:00:49Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.69
ec_funded: 1
external_id:
unknown:
- '2211.09606'
file:
- access_level: open_access
checksum: 074177e815a1656de5d4071c7a3dffa6
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:59:05Z
date_updated: 2023-08-21T06:59:05Z
file_id: '14089'
file_name: 2023_LIPIcsICALP_Goranci.pdf
file_size: 875910
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:59:05Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient data structures for incremental exact and approximate maximum flow
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: 261
year: '2023'
...
---
_id: '14084'
abstract:
- lang: eng
text: "A central problem in computational statistics is to convert a procedure for
sampling combinatorial objects into a procedure for counting those objects, and
vice versa. We will consider sampling problems which come from Gibbs distributions,
which are families of probability distributions over a discrete space Ω with probability
mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor
Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log
Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts
c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²)
samples for integer-valued distributions (ignoring some second-order terms and
parameters), We show this is optimal up to logarithmic factors. We illustrate
with improved algorithms for counting connected subgraphs and perfect matchings
in a graph."
acknowledgement: We thank Heng Guo for helpful explanations of algorithms for sampling
connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the
Wang-Landau algorithm and its use in physics.
alternative_title:
- LIPIcs
article_number: '72'
article_processing_charge: Yes
author:
- first_name: David G.
full_name: Harris, David G.
last_name: Harris
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In:
50th International Colloquium on Automata, Languages, and Programming.
Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72'
apa: 'Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs
distributions. In 50th International Colloquium on Automata, Languages, and
Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72'
chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” In 50th International Colloquium on Automata, Languages, and
Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.
ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
in 50th International Colloquium on Automata, Languages, and Programming,
Paderborn, Germany, 2023, vol. 261.
ista: 'Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions.
50th International Colloquium on Automata, Languages, and Programming. ICALP:
International Colloquium on Automata, Languages, and Programming, LIPIcs, vol.
261, 72.'
mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.
short: D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T06:49:11Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: VlKo
doi: 10.4230/LIPIcs.ICALP.2023.72
external_id:
arxiv:
- '2007.10824'
file:
- access_level: open_access
checksum: 6dee0684245bb1c524b9c955db1e933d
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:45:16Z
date_updated: 2023-08-21T06:45:16Z
file_id: '14088'
file_name: 2023_LIPIcsICALP_Harris.pdf
file_size: 917791
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:45:16Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
tmp:
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
---
_id: '14086'
abstract:
- lang: eng
text: "The maximization of submodular functions have found widespread application
in areas such as machine learning, combinatorial optimization, and economics,
where practitioners often wish to enforce various constraints; the matroid constraint
has been investigated extensively due to its algorithmic properties and expressive
power. Though tight approximation algorithms for general matroid constraints exist
in theory, the running times of such algorithms typically scale quadratically,
and are not practical for truly large scale settings. Recent progress has focused
on fast algorithms for important classes of matroids given in explicit form. Currently,
nearly-linear time algorithms only exist for graphic and partition matroids [Alina
Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone
submodular maximization constrained by graphic, transversal matroids, or laminar
matroids in time near-linear in the size of their representation. Our algorithms
achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate
the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the
running time of our algorithm cannot be improved within the fast continuous greedy
framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák,
2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures
that maintain bases with approximate maximum cardinality and weight under certain
element updates. These data structures need to support a weight decrease operation
and a novel Freeze operation that allows the algorithm to freeze elements (i.e.
force to be contained) in its basis regardless of future data structure operations.
For the laminar matroid, we present a new dynamic data structure using the top
tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et
al., 2005] that maintains the maximum weight basis under insertions and deletions
of elements in O(log n) time. This data structure needs to support certain subtree
query and path update operations that are performed every insertion and deletion
that are non-trivial to handle in conjunction. For the transversal matroid the
Freeze operation corresponds to requiring the data structure to keep a certain
set S of vertices matched, a property that we call S-stability. While there is
a large body of work on dynamic matching algorithms, none are S-stable and maintain
an approximate maximum weight matching under vertex updates. We give the first
such algorithm for bipartite graphs with total running time linear (up to log
factors) in the number of edges."
acknowledgement: " Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast
Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by
NSF Award 2127781."
alternative_title:
- LIPIcs
article_number: '74'
article_processing_charge: Yes
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Paul
full_name: Liu, Paul
last_name: Liu
- first_name: Jan
full_name: Vondrák, Jan
last_name: Vondrák
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
citation:
ama: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for
several classes of matroids. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74'
apa: 'Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster
submodular maximization for several classes of matroids. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74'
chicago: Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular
Maximization for Several Classes of Matroids.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.
ieee: M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization
for several classes of matroids,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization
for several classes of matroids. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: International Colloquium on Automata, Languages, and Programming,
LIPIcs, vol. 261, 74.'
mla: Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes
of Matroids.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.
short: M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2023-07-10
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-21T07:05:47Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.74
ec_funded: 1
external_id:
arxiv:
- '2305.00122'
file:
- access_level: open_access
checksum: a5eef225014e003efbfbe4830fdd23cb
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:04:36Z
date_updated: 2023-08-21T07:04:36Z
file_id: '14090'
file_name: 2023_LIPIcsICALP_HenzingerM.pdf
file_size: 930943
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:04:36Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster submodular maximization for several classes of matroids
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image: /images/cc_by.png
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type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
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...