---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2024-10-21T06:02:05Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
- access_level: open_access
checksum: d99fcd51aebde19c21314e3de0148007
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
scopus_import: '1'
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10166'
abstract:
- lang: eng
text: While sexual reproduction is widespread among many taxa, asexual lineages
have repeatedly evolved from sexual ancestors. Despite extensive research on the
evolution of sex, it is still unclear whether this switch represents a major transition
requiring major molecular reorganization, and how convergent the changes involved
are. In this study, we investigated the phylogenetic relationship and patterns
of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp,
to assess how gene expression patterns are affected by the transition to asexuality.
We find only a few genes that are consistently associated with the evolution of
asexuality, suggesting that this shift may not require an extensive overhauling
of the meiotic machinery. While genes with sex-biased expression have high rates
of expression divergence within Eurasian Artemia, neither female- nor male-biased
genes appear to show unusual evolutionary patterns after sexuality is lost, contrary
to theoretical expectations.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander
for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate
and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific
Computing Group for their support. This work was supported by the European Research
Council under the European Union's Horizon 2020 research and innovation program
(grant agreement no. 715257).
article_number: '20211720'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720'
apa: 'Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions
to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings
of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720'
chicago: 'Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso.
“Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”
Proceedings of the Royal Society B: Biological Sciences. The Royal Society,
2021. https://doi.org/10.1098/rspb.2021.1720.'
ieee: 'A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp,” Proceedings of the
Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society,
2021.'
ista: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 288(1959), 20211720.'
mla: 'Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene
Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological
Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720.'
short: 'A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal
Society B: Biological Sciences 288 (2021).'
date_created: 2021-10-21T07:46:06Z
date_published: 2021-09-22T00:00:00Z
date_updated: 2025-04-14T07:41:20Z
day: '22'
ddc:
- '595'
department:
- _id: BeVi
doi: 10.1098/rspb.2021.1720
ec_funded: 1
external_id:
isi:
- '000697643700001'
pmid:
- '34547909'
file:
- access_level: open_access
checksum: 76e7f253b7040bca2ad76f82bd7c45c0
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-22T11:48:02Z
date_updated: 2021-10-22T11:48:02Z
file_id: '10172'
file_name: 2021_ProRoSocBBioSci_Huylmans.pdf
file_size: 995806
relation: main_file
success: 1
file_date_updated: 2021-10-22T11:48:02Z
has_accepted_license: '1'
intvolume: ' 288'
isi: 1
issue: '1959'
keyword:
- asexual reproduction
- parthenogenesis
- sex-biased genes
- sexual conflict
- automixis
- crustaceans
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://doi.org/10.6084/m9.figshare.c.5615488.v1
record:
- id: '9949'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Transitions to asexuality and evolution of gene expression in Artemia brine
shrimp
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 288
year: '2021'
...
---
_id: '10176'
abstract:
- lang: eng
text: "We give a combinatorial model for r-spin surfaces with parameterized boundary
based on Novak (“Lattice topological field theories in two dimensions,” Ph.D.
thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of
ℤ\U0001D45F-valued indices assigned to the edges of a polygonal decomposition.
This combinatorial model is designed for our state-sum construction of two-dimensional
topological field theories on r-spin surfaces. We show that an example of such
a topological field theory computes the Arf-invariant of an r-spin surface as
introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka
J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant
is constant on orbits of the mapping class group, providing an alternative proof
of that fact."
acknowledgement: We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse,
Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and
Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG
Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum
Field Theory.”
article_number: '102302'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ingo
full_name: Runkel, Ingo
last_name: Runkel
- first_name: Lorant
full_name: Szegedy, Lorant
id: 7943226E-220E-11EA-94C7-D59F3DDC885E
last_name: Szegedy
orcid: 0000-0003-2834-5054
citation:
ama: Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant.
Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826
apa: Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces
and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing.
https://doi.org/10.1063/5.0037826
chicago: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces
and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing,
2021. https://doi.org/10.1063/5.0037826.
ieee: I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and
the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP
Publishing, 2021.
ista: Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and
the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.
mla: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces
and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10,
102302, AIP Publishing, 2021, doi:10.1063/5.0037826.
short: I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).
corr_author: '1'
date_created: 2021-10-24T22:01:32Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2025-07-10T11:49:44Z
day: '01'
department:
- _id: MiLe
doi: 10.1063/5.0037826
external_id:
arxiv:
- '1802.09978'
isi:
- '000755638500010'
intvolume: ' 62'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.09978
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological field theory on r-spin surfaces and the Arf-invariant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2021'
...
---
_id: '10179'
abstract:
- lang: eng
text: Inhibitory GABAergic interneurons migrate over long distances from their extracortical
origin into the developing cortex. In humans, this process is uniquely slow and
prolonged, and it is unclear whether guidance cues unique to humans govern the
various phases of this complex developmental process. Here, we use fused cerebral
organoids to identify key roles of neurotransmitter signaling pathways in guiding
the migratory behavior of human cortical interneurons. We use scRNAseq to reveal
expression of GABA, glutamate, glycine, and serotonin receptors along distinct
maturation trajectories across interneuron migration. We develop an image analysis
software package, TrackPal, to simultaneously assess 48 parameters for entire
migration tracks of individual cells. By chemical screening, we show that different
modes of interneuron migration depend on distinct neurotransmitter signaling pathways,
linking transcriptional maturation of interneurons with their migratory behavior.
Altogether, our study provides a comprehensive quantitative analysis of human
interneuron migration and its functional modulation by neurotransmitter signaling.
acknowledgement: We thank all Knoblich laboratory members for continued support and
discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek,
Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service,
in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas
Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in
particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility,
notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon
Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance
with slice culture setups, Oliver L. Eichmueller for discussions and assistance
with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical
assistance regarding generation of cerebral organoids. This project received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in
J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education,
Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research
Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European
Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020
program (grant agreement no. 695642).
article_number: e108714
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sunanjay
full_name: Bajaj, Sunanjay
last_name: Bajaj
- first_name: Joshua A.
full_name: Bagley, Joshua A.
last_name: Bagley
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Abel
full_name: Vertesy, Abel
last_name: Vertesy
- first_name: Sakurako
full_name: Nagumo Wong, Sakurako
last_name: Nagumo Wong
- first_name: Veronica
full_name: Krenn, Veronica
last_name: Krenn
- first_name: Julie
full_name: Lévi-Strauss, Julie
last_name: Lévi-Strauss
- first_name: Juergen A.
full_name: Knoblich, Juergen A.
last_name: Knoblich
citation:
ama: Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates
distinct phases of multimodal human interneuron migration. EMBO Journal.
2021;40(23). doi:10.15252/embj.2021108714
apa: Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn,
V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases
of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714
chicago: Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako
Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter
Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.”
EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714.
ieee: S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases
of multimodal human interneuron migration,” EMBO Journal, vol. 40, no.
23. Embo Press, 2021.
ista: Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss
J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of
multimodal human interneuron migration. EMBO Journal. 40(23), e108714.
mla: Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases
of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no.
23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714.
short: S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn,
J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).
date_created: 2021-10-24T22:01:34Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2023-08-14T08:05:23Z
day: '18'
ddc:
- '610'
department:
- _id: Bio
doi: 10.15252/embj.2021108714
external_id:
isi:
- '000708012800001'
pmid:
- '34661293'
file:
- access_level: open_access
checksum: 78d2d02e775322297e774f72810a41a4
content_type: application/pdf
creator: alisjak
date_created: 2021-12-13T14:54:14Z
date_updated: 2021-12-13T14:54:14Z
file_id: '10541'
file_name: 2021_EMBO_Bajaj.pdf
file_size: 7819881
relation: main_file
success: 1
file_date_updated: 2021-12-13T14:54:14Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '23'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neurotransmitter signaling regulates distinct phases of multimodal human interneuron
migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
OA_place: publisher
_id: '10180'
abstract:
- lang: eng
text: The growing energy and performance costs of deep learning have driven the
community to reduce the size of neural networks by selectively pruning components.
Similarly to their biological counterparts, sparse networks generalize just as
well, sometimes even better than, the original dense networks. Sparsity promises
to reduce the memory footprint of regular networks to fit mobile devices, as well
as shorten training time for ever growing networks. In this paper, we survey prior
work on sparsity in deep learning and provide an extensive tutorial of sparsification
for both inference and training. We describe approaches to remove and add elements
of neural networks, different training strategies to achieve model sparsity, and
mechanisms to exploit sparsity in practice. Our work distills ideas from more
than 300 research papers and provides guidance to practitioners who wish to utilize
sparsity today, as well as to researchers whose goal is to push the frontier forward.
We include the necessary background on mathematical methods in sparsification,
describe phenomena such as early structure adaptation, the intricate relations
between sparsity and the training process, and show techniques for achieving acceleration
on real hardware. We also define a metric of pruned parameter efficiency that
could serve as a baseline for comparison of different sparse networks. We close
by speculating on how sparsity can improve future workloads and outline major
open problems in the field.
acknowledgement: "We thank Doug Burger, Steve Scott, Marco Heddes, and the respective
teams at Microsoft for inspiring discussions on the topic. We thank Angelika Steger
for uplifting debates about the connections to biological brains, Sidak Pal Singh
for his support regarding experimental results, and Utku Evci as well as Xin Wang
for comments on previous versions of this\r\nwork. Special thanks go to Bernhard
Schölkopf, our JMLR editor Samy Bengio, and the three anonymous reviewers who provided
excellent comprehensive, pointed, and deep review comments that improved the quality
of our manuscript significantly."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- 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: Tal
full_name: Ben-Nun, Tal
last_name: Ben-Nun
- first_name: Nikoli
full_name: Dryden, Nikoli
last_name: Dryden
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
citation:
ama: 'Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Krumes A. Sparsity in deep learning:
Pruning and growth for efficient inference and training in neural networks. Journal
of Machine Learning Research. 2021;22(241):1-124.'
apa: 'Hoefler, T., Alistarh, D.-A., Ben-Nun, T., Dryden, N., & Krumes, A. (2021).
Sparsity in deep learning: Pruning and growth for efficient inference and training
in neural networks. Journal of Machine Learning Research. ML Research Press.'
chicago: 'Hoefler, Torsten, Dan-Adrian Alistarh, Tal Ben-Nun, Nikoli Dryden, and
Alexandra Krumes. “Sparsity in Deep Learning: Pruning and Growth for Efficient
Inference and Training in Neural Networks.” Journal of Machine Learning Research.
ML Research Press, 2021.'
ieee: 'T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, and A. Krumes, “Sparsity
in deep learning: Pruning and growth for efficient inference and training in neural
networks,” Journal of Machine Learning Research, vol. 22, no. 241. ML Research
Press, pp. 1–124, 2021.'
ista: 'Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Krumes A. 2021. Sparsity in
deep learning: Pruning and growth for efficient inference and training in neural
networks. Journal of Machine Learning Research. 22(241), 1–124.'
mla: 'Hoefler, Torsten, et al. “Sparsity in Deep Learning: Pruning and Growth for
Efficient Inference and Training in Neural Networks.” Journal of Machine Learning
Research, vol. 22, no. 241, ML Research Press, 2021, pp. 1–124.'
short: T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, A. Krumes, Journal of
Machine Learning Research 22 (2021) 1–124.
corr_author: '1'
date_created: 2021-10-24T22:01:34Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2025-06-26T11:53:12Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '2102.00554'
file:
- access_level: open_access
checksum: 3389d9d01fc58f8fb4c1a53e14a8abbf
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T15:34:18Z
date_updated: 2021-10-27T15:34:18Z
file_id: '10192'
file_name: 2021_JMachLearnRes_Hoefler.pdf
file_size: 3527521
relation: main_file
success: 1
file_date_updated: 2021-10-27T15:34:18Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '241'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.jmlr.org/papers/v22/21-0366.html
month: '09'
oa: 1
oa_version: Published Version
page: 1-124
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
issn:
- 1532-4435
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Sparsity in deep learning: Pruning and growth for efficient inference and
training in neural networks'
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: 22
year: '2021'
...
---
_id: '10184'
abstract:
- lang: eng
text: "We introduce a novel technique to automatically decompose an input object’s
volume into a set of parts that can be represented by two opposite height fields.
Such decomposition enables the manufacturing of individual parts using two-piece
reusable rigid molds. Our decomposition strategy relies on a new energy formulation
that utilizes a pre-computed signal on the mesh volume representing the accessibility
for a predefined set of extraction directions. Thanks to this novel formulation,
our method allows for efficient optimization of a fabrication-aware partitioning
of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our
approach by generating valid volume partitionings for a wide range of complex
objects and physically reproducing several of them."
acknowledgement: 'The authors thank Marco Callieri for all his precious help with
the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning
Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research
was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent
fabrication-oriented computational design and modeling (grant no. 715767).'
article_number: '272'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
citation:
ama: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6).
doi:10.1145/3478513.3480555
apa: Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021).
Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics.
Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555
chicago: Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico
Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions
on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555.
ieee: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition
for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no.
6. Association for Computing Machinery, 2021.
ista: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.
mla: Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.”
ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing
Machinery, 2021, doi:10.1145/3478513.3480555.
short: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-10-27T07:08:19Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2025-04-14T07:28:57Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3478513.3480555
ec_funded: 1
external_id:
isi:
- '000729846700077'
file:
- access_level: open_access
checksum: 384ece7a9ad1026787ba9560b04336d5
content_type: application/pdf
creator: bbickel
date_created: 2021-10-27T07:08:07Z
date_updated: 2021-10-27T07:08:07Z
file_id: '10185'
file_name: rigidmolds-authorversion.pdf
file_size: 107708317
relation: main_file
file_date_updated: 2021-10-27T07:08:07Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://vcg.isti.cnr.it/Publications/2021/AMBCP21
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '1557-7368 '
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Volume decomposition for two-piece rigid casting
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2021'
...
---
_id: '10203'
abstract:
- lang: eng
text: Single photon emitters in atomically-thin semiconductors can be deterministically
positioned using strain induced by underlying nano-structures. Here, we couple
monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas
providing both optical enhancement and monolayer deformation. For single photon
emitters formed on such nano-antennas, we find very low (femto-Joule) saturation
pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed
on low-refractive-index SiO2 pillars. We show that the key to these observations
is the increase on average by a factor of 5 of the quantum efficiency of the emitters
coupled to the nano-antennas. This further allows us to gain new insights into
their photoluminescence dynamics, revealing the roles of the dark exciton reservoir
and Auger processes. We also find that the coherence time of such emitters is
limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas
as a platform for high-efficiency quantum light generation in monolayer semiconductors.
acknowledgement: L.S., P.G.Z., and A.I.T. thank the financial support of the European
Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1.
L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation
programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108.
P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation
programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C.,
S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P.,
A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1.
S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid
(SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.
article_number: '6063'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Luca
full_name: Sortino, Luca
last_name: Sortino
- first_name: Panaiot G.
full_name: Zotev, Panaiot G.
last_name: Zotev
- first_name: Catherine L.
full_name: Phillips, Catherine L.
last_name: Phillips
- first_name: Alistair J.
full_name: Brash, Alistair J.
last_name: Brash
- first_name: Javier
full_name: Cambiasso, Javier
last_name: Cambiasso
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: A. Mark
full_name: Fox, A. Mark
last_name: Fox
- first_name: Stefan A.
full_name: Maier, Stefan A.
last_name: Maier
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
- first_name: Alexander I.
full_name: Tartakovskii, Alexander I.
last_name: Tartakovskii
citation:
ama: Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with
enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3
apa: Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi,
E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced
quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3
chicago: Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash,
Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza,
and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum
Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.”
Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3.
ieee: L. Sortino et al., “Bright single photon emitters with enhanced quantum
efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,”
Nature Communications, vol. 12. Springer Nature, 2021.
ista: Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM,
Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with
enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. 12, 6063.
mla: Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum
Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.”
Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3.
short: L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi,
A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12
(2021).
date_created: 2021-10-31T23:01:30Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2023-08-14T08:12:12Z
day: '18'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1038/s41467-021-26262-3
external_id:
arxiv:
- '2103.16986'
isi:
- '000708601800015'
file:
- access_level: open_access
checksum: 8580d128389860f732028c521cd5949e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-03T11:31:24Z
date_updated: 2021-11-03T11:31:24Z
file_id: '10212'
file_name: 2021_NatComm_Sortino.pdf
file_size: 1434201
relation: main_file
success: 1
file_date_updated: 2021-11-03T11:31:24Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bright single photon emitters with enhanced quantum efficiency in a two-dimensional
semiconductor coupled with dielectric nano-antennas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10204'
abstract:
- lang: eng
text: Two common representations of close packings of identical spheres consisting
of hexagonal layers, called Barlow stackings, appear abundantly in minerals and
metals. These motifs, however, occupy an identical portion of space and bear identical
first-order topological signatures as measured by persistent homology. Here we
present a novel method based on k-fold covers that unambiguously distinguishes
between these patterns. Moreover, our approach provides topological evidence that
the FCC motif is the more stable of the two in the context of evolving experimental
sphere packings during the transition from disordered to an ordered state. We
conclude that our approach can be generalised to distinguish between various Barlow
stackings manifested in minerals and metals.
acknowledgement: MS acknowledges the support by Australian Research Council funding
through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour
and N. Francois for their input and valuable discussions. This project has received
funding from the European Research Council (ERC) under the European Union's Horizon
2020 research and innovation programme, grant no. 788183 and from the Wittgenstein
Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.
article_processing_charge: No
article_type: original
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mohammad
full_name: Saadatfar, Mohammad
last_name: Saadatfar
citation:
ama: Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability
of hexagonal close packing and Barlow stackings. Soft Matter. 2021;17(40):9107-9115.
doi:10.1039/d1sm00774b
apa: Osang, G. F., Edelsbrunner, H., & Saadatfar, M. (2021). Topological signatures
and stability of hexagonal close packing and Barlow stackings. Soft Matter.
Royal Society of Chemistry . https://doi.org/10.1039/d1sm00774b
chicago: Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological
Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft
Matter. Royal Society of Chemistry , 2021. https://doi.org/10.1039/d1sm00774b.
ieee: G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and
stability of hexagonal close packing and Barlow stackings,” Soft Matter,
vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.
ista: Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability
of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.
mla: Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal
Close Packing and Barlow Stackings.” Soft Matter, vol. 17, no. 40, Royal
Society of Chemistry , 2021, pp. 9107–15, doi:10.1039/d1sm00774b.
short: G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115.
date_created: 2021-10-31T23:01:30Z
date_published: 2021-10-20T00:00:00Z
date_updated: 2025-04-15T07:16:52Z
day: '20'
ddc:
- '540'
department:
- _id: HeEd
doi: 10.1039/d1sm00774b
ec_funded: 1
external_id:
isi:
- '000700090000001'
pmid:
- '34569592'
file:
- access_level: open_access
checksum: b4da0c420530295e61b153960f6cb350
content_type: application/pdf
creator: dernst
date_created: 2023-10-03T09:21:42Z
date_updated: 2023-10-03T09:21:42Z
file_id: '14385'
file_name: 2021_SoftMatter_acceptedversion_Osang.pdf
file_size: 4678788
relation: main_file
success: 1
file_date_updated: 2023-10-03T09:21:42Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 9107-9115
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: Mathematics, Computer Science
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological signatures and stability of hexagonal close packing and Barlow
stackings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10206'
abstract:
- lang: eng
text: Neural-network classifiers achieve high accuracy when predicting the class
of an input that they were trained to identify. Maintaining this accuracy in dynamic
environments, where inputs frequently fall outside the fixed set of initially
known classes, remains a challenge. The typical approach is to detect inputs from
novel classes and retrain the classifier on an augmented dataset. However, not
only the classifier but also the detection mechanism needs to adapt in order to
distinguish between newly learned and yet unknown input classes. To address this
challenge, we introduce an algorithmic framework for active monitoring of a neural
network. A monitor wrapped in our framework operates in parallel with the neural
network and interacts with a human user via a series of interpretable labeling
queries for incremental adaptation. In addition, we propose an adaptive quantitative
monitor to improve precision. An experimental evaluation on a diverse set of benchmarks
with varying numbers of classes confirms the benefits of our active monitoring
framework in dynamic scenarios.
acknowledgement: We thank Christoph Lampert and Alex Greengold for fruitful discussions.
This research was supported in part by the Simons Institute for the Theory of Computing,
the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the
European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural
networks. In: 21st International Conference on Runtime Verification. Vol
12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3'
apa: 'Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown:
active monitoring of neural networks. In 21st International Conference on Runtime
Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3'
chicago: 'Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown:
Active Monitoring of Neural Networks.” In 21st International Conference on
Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3.'
ieee: 'A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring
of neural networks,” in 21st International Conference on Runtime Verification,
Virtual, 2021, vol. 12974, pp. 42–61.'
ista: 'Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring
of neural networks. 21st International Conference on Runtime Verification. RV:
Runtime Verification, LNCS, vol. 12974, 42–61.'
mla: 'Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.”
21st International Conference on Runtime Verification, vol. 12974, Springer
Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3.'
short: A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference
on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
corr_author: '1'
date_created: 2021-10-31T23:01:31Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2025-04-15T06:26:14Z
day: '06'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_3
ec_funded: 1
external_id:
arxiv:
- '2009.06429'
isi:
- '000719383800003'
isi: 1
keyword:
- monitoring
- neural networks
- novelty detection
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06429
month: '10'
oa: 1
oa_version: Preprint
page: 42-61
place: Cham
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: 21st International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 9-783-0308-8493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13234'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: 'Into the unknown: active monitoring of neural networks'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12974 '
year: '2021'
...
---
_id: '10216'
abstract:
- lang: eng
text: 'This paper reports a new concurrent graph data structure that supports updates
of both edges and vertices and queries: Breadth-first search, Single-source shortest-path,
and Betweenness centrality. The operations are provably linearizable and non-blocking.'
acknowledgement: "This work was partially funded by National Supercomputing Mission,
Govt. of India under the project “Concurrent and Distributed Programming primitives
and algorithms for Temporal Graphs”(DST/NSM/R&D_Exascale/2021/16).\r\n"
alternative_title:
- LIPIcs
article_number: '52'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Sathya
full_name: Peri, Sathya
last_name: Peri
- first_name: Muktikanta
full_name: Sa, Muktikanta
last_name: Sa
citation:
ama: 'Chatterjee B, Peri S, Sa M. Brief announcement: Non-blocking dynamic unbounded
graphs with worst-case amortized bounds. In: 35th International Symposium on
Distributed Computing. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2021. doi:10.4230/LIPIcs.DISC.2021.52'
apa: 'Chatterjee, B., Peri, S., & Sa, M. (2021). Brief announcement: Non-blocking
dynamic unbounded graphs with worst-case amortized bounds. In 35th International
Symposium on Distributed Computing (Vol. 209). Freiburg, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2021.52'
chicago: 'Chatterjee, Bapi, Sathya Peri, and Muktikanta Sa. “Brief Announcement:
Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” In 35th
International Symposium on Distributed Computing, Vol. 209. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.DISC.2021.52.'
ieee: 'B. Chatterjee, S. Peri, and M. Sa, “Brief announcement: Non-blocking dynamic
unbounded graphs with worst-case amortized bounds,” in 35th International Symposium
on Distributed Computing, Freiburg, Germany, 2021, vol. 209.'
ista: 'Chatterjee B, Peri S, Sa M. 2021. Brief announcement: Non-blocking dynamic
unbounded graphs with worst-case amortized bounds. 35th International Symposium
on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 52.'
mla: 'Chatterjee, Bapi, et al. “Brief Announcement: Non-Blocking Dynamic Unbounded
Graphs with Worst-Case Amortized Bounds.” 35th International Symposium on Distributed
Computing, vol. 209, 52, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2021, doi:10.4230/LIPIcs.DISC.2021.52.'
short: B. Chatterjee, S. Peri, M. Sa, in:, 35th International Symposium on Distributed
Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.
conference:
end_date: 2021-10-08
location: Freiburg, Germany
name: 'DISC: Distributed Computing'
start_date: 2021-10-04
date_created: 2021-11-07T23:01:23Z
date_published: 2021-10-04T00:00:00Z
date_updated: 2025-05-14T10:54:39Z
day: '04'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.DISC.2021.52
external_id:
arxiv:
- '2003.01697'
file:
- access_level: open_access
checksum: 76546df112a0ba1166c864d33d7834e2
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-12T09:23:22Z
date_updated: 2021-11-12T09:23:22Z
file_id: '10276'
file_name: 2021_LIPIcsDISC_BChatterjee.pdf
file_size: 795860
relation: main_file
success: 1
file_date_updated: 2021-11-12T09:23:22Z
has_accepted_license: '1'
intvolume: ' 209'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: 35th International Symposium on Distributed Computing
publication_identifier:
isbn:
- 9-783-9597-7210-5
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief announcement: Non-blocking dynamic unbounded graphs with worst-case
amortized bounds'
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: 209
year: '2021'
...
---
_id: '10217'
abstract:
- lang: eng
text: This paper gives tight logarithmic lower bounds on the solo step complexity
of leader election in an asynchronous shared-memory model with single-writer multi-reader
(SWMR) registers, for both deterministic and randomized obstruction-free algorithms.
The approach extends to lower bounds for deterministic and randomized obstruction-free
algorithms using multi-writer registers under bounded write concurrency, showing
a trade-off between the solo step complexity of a leader election algorithm, and
the worst-case number of stalls incurred by a processor in an execution.
acknowledgement: "Dan Alistarh: Supported in part by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). Giorgi Nadiradze: Supported in part by the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement No 805223 ScaleML). The authors would
like to thank the DISC anonymous reviewers for their useful\r\nfeedback and comments."
alternative_title:
- LIPIcs
article_number: '4'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: 'Alistarh D-A, Gelashvili R, Nadiradze G. Lower bounds for shared-memory leader
election under bounded write contention. In: 35th International Symposium on
Distributed Computing. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2021. doi:10.4230/LIPIcs.DISC.2021.4'
apa: 'Alistarh, D.-A., Gelashvili, R., & Nadiradze, G. (2021). Lower bounds
for shared-memory leader election under bounded write contention. In 35th International
Symposium on Distributed Computing (Vol. 209). Freiburg, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2021.4'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Giorgi Nadiradze. “Lower Bounds
for Shared-Memory Leader Election under Bounded Write Contention.” In 35th
International Symposium on Distributed Computing, Vol. 209. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.DISC.2021.4.
ieee: D.-A. Alistarh, R. Gelashvili, and G. Nadiradze, “Lower bounds for shared-memory
leader election under bounded write contention,” in 35th International Symposium
on Distributed Computing, Freiburg, Germany, 2021, vol. 209.
ista: 'Alistarh D-A, Gelashvili R, Nadiradze G. 2021. Lower bounds for shared-memory
leader election under bounded write contention. 35th International Symposium on
Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 4.'
mla: Alistarh, Dan-Adrian, et al. “Lower Bounds for Shared-Memory Leader Election
under Bounded Write Contention.” 35th International Symposium on Distributed
Computing, vol. 209, 4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2021, doi:10.4230/LIPIcs.DISC.2021.4.
short: D.-A. Alistarh, R. Gelashvili, G. Nadiradze, in:, 35th International Symposium
on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.
conference:
end_date: 2021-10-08
location: Freiburg, Germany
name: 'DISC: Distributed Computing'
start_date: 2021-10-04
date_created: 2021-11-07T23:01:23Z
date_published: 2021-10-04T00:00:00Z
date_updated: 2025-05-14T10:54:30Z
day: '04'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.DISC.2021.4
ec_funded: 1
file:
- access_level: open_access
checksum: b4cdc6668c899a601c5e6a96b8ca54d9
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-12T09:33:26Z
date_updated: 2021-11-12T09:33:26Z
file_id: '10277'
file_name: 2021_LIPIcsDISC_Alistarh.pdf
file_size: 706791
relation: main_file
success: 1
file_date_updated: 2021-11-12T09:33:26Z
has_accepted_license: '1'
intvolume: ' 209'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th International Symposium on Distributed Computing
publication_identifier:
isbn:
- 9-783-9597-7210-5
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower bounds for shared-memory leader election under bounded write contention
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: 209
year: '2021'
...
---
_id: '10218'
abstract:
- lang: eng
text: 'Let G be a graph on n nodes. In the stochastic population protocol model,
a collection of n indistinguishable, resource-limited nodes collectively solve
tasks via pairwise interactions. In each interaction, two randomly chosen neighbors
first read each other’s states, and then update their local states. A rich line
of research has established tight upper and lower bounds on the complexity of
fundamental tasks, such as majority and leader election, in this model, when G
is a clique. Specifically, in the clique, these tasks can be solved fast, i.e.,
in n polylog n pairwise interactions, with high probability, using at most polylog
n states per node. In this work, we consider the more general setting where G
is an arbitrary graph, and present a technique for simulating protocols designed
for fully-connected networks in any connected regular graph. Our main result is
a simulation that is efficient on many interesting graph families: roughly, the
simulation overhead is polylogarithmic in the number of nodes, and quadratic in
the conductance of the graph. As an example, this implies that, in any regular
graph with conductance φ, both leader election and exact majority can be solved
in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at
most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient
population protocols for leader election and exact majority on graphs with good
expansion properties.'
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No 840605.
alternative_title:
- LIPIcs
article_number: '43'
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: 'Alistarh D-A, Gelashvili R, Rybicki J. Brief announcement: Fast graphical
population protocols. In: 35th International Symposium on Distributed Computing.
Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.DISC.2021.43'
apa: 'Alistarh, D.-A., Gelashvili, R., & Rybicki, J. (2021). Brief announcement:
Fast graphical population protocols. In 35th International Symposium on Distributed
Computing (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2021.43'
chicago: 'Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Brief Announcement:
Fast Graphical Population Protocols.” In 35th International Symposium on Distributed
Computing, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.
https://doi.org/10.4230/LIPIcs.DISC.2021.43.'
ieee: 'D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Brief announcement: Fast
graphical population protocols,” in 35th International Symposium on Distributed
Computing, Freiburg, Germany, 2021, vol. 209.'
ista: 'Alistarh D-A, Gelashvili R, Rybicki J. 2021. Brief announcement: Fast graphical
population protocols. 35th International Symposium on Distributed Computing. DISC:
Distributed Computing , LIPIcs, vol. 209, 43.'
mla: 'Alistarh, Dan-Adrian, et al. “Brief Announcement: Fast Graphical Population
Protocols.” 35th International Symposium on Distributed Computing, vol.
209, 43, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.DISC.2021.43.'
short: D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, 35th International Symposium
on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.
conference:
end_date: 2021-10-08
location: Freiburg, Germany
name: 'DISC: Distributed Computing '
start_date: 2021-10-04
date_created: 2021-11-07T23:01:24Z
date_published: 2021-10-04T00:00:00Z
date_updated: 2025-04-14T07:50:55Z
day: '04'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.DISC.2021.43
ec_funded: 1
external_id:
arxiv:
- '2102.08808'
file:
- access_level: open_access
checksum: fd2a690f6856d21247e9aa952b0e2885
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-12T08:16:44Z
date_updated: 2021-11-12T08:16:44Z
file_id: '10274'
file_name: 2021_LIPIcsDISC_Alistarh.pdf
file_size: 534219
relation: main_file
success: 1
file_date_updated: 2021-11-12T08:16:44Z
has_accepted_license: '1'
intvolume: ' 209'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: 35th International Symposium on Distributed Computing
publication_identifier:
isbn:
- 9-783-9597-7210-5
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief announcement: Fast graphical population protocols'
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 209
year: '2021'
...
---
_id: '10219'
abstract:
- lang: eng
text: We show that any algorithm that solves the sinkless orientation problem in
the supported LOCAL model requires Ω(log n) rounds, and this is tight. The supported
LOCAL is at least as strong as the usual LOCAL model, and as a corollary this
also gives a new, short and elementary proof that shows that the round complexity
of the sinkless orientation problem in the deterministic LOCAL model is Ω(log
n).
acknowledgement: "Janne H. Korhonen: Project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement No 805223 ScaleML). Ami Paz: We acknowledge the Austrian
Science Fund (FWF) and netIDEE SCIENCE project P 33775-N. Stefan Schmid: Research
supported by the Austrian Science Fund (FWF) project ADVISE, I 4800-N, 2020-2023.\r\n"
alternative_title:
- LIPIcs
article_number: '58'
article_processing_charge: No
arxiv: 1
author:
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Ami
full_name: Paz, Ami
last_name: Paz
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
citation:
ama: 'Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. Brief announcement: Sinkless
orientation is hard also in the supported LOCAL model. In: 35th International
Symposium on Distributed Computing. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2021. doi:10.4230/LIPIcs.DISC.2021.58'
apa: 'Korhonen, J., Paz, A., Rybicki, J., Schmid, S., & Suomela, J. (2021).
Brief announcement: Sinkless orientation is hard also in the supported LOCAL model.
In 35th International Symposium on Distributed Computing (Vol. 209). Freiburg,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2021.58'
chicago: 'Korhonen, Janne, Ami Paz, Joel Rybicki, Stefan Schmid, and Jukka Suomela.
“Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL
Model.” In 35th International Symposium on Distributed Computing, Vol.
209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.DISC.2021.58.'
ieee: 'J. Korhonen, A. Paz, J. Rybicki, S. Schmid, and J. Suomela, “Brief announcement:
Sinkless orientation is hard also in the supported LOCAL model,” in 35th International
Symposium on Distributed Computing, Freiburg, Germany, 2021, vol. 209.'
ista: 'Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. 2021. Brief announcement:
Sinkless orientation is hard also in the supported LOCAL model. 35th International
Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol.
209, 58.'
mla: 'Korhonen, Janne, et al. “Brief Announcement: Sinkless Orientation Is Hard
Also in the Supported LOCAL Model.” 35th International Symposium on Distributed
Computing, vol. 209, 58, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2021, doi:10.4230/LIPIcs.DISC.2021.58.'
short: J. Korhonen, A. Paz, J. Rybicki, S. Schmid, J. Suomela, in:, 35th International
Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2021.
conference:
end_date: 2021-10-08
location: Freiburg, Germany
name: 'DISC: Distributed Computing '
start_date: 2021-10-04
date_created: 2021-11-07T23:01:24Z
date_published: 2021-10-04T00:00:00Z
date_updated: 2025-05-14T10:54:13Z
day: '04'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.DISC.2021.58
ec_funded: 1
external_id:
arxiv:
- '2108.02655'
file:
- access_level: open_access
checksum: c43188dc2070bbd2bf5fd6fdaf9ce36d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-12T08:27:42Z
date_updated: 2021-11-12T08:27:42Z
file_id: '10275'
file_name: 2021_LIPIcsDISC_Korhonen.pdf
file_size: 474242
relation: main_file
success: 1
file_date_updated: 2021-11-12T08:27:42Z
has_accepted_license: '1'
intvolume: ' 209'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th International Symposium on Distributed Computing
publication_identifier:
isbn:
- 9-783-9597-7210-5
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief announcement: Sinkless orientation is hard also in the supported LOCAL
model'
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: 209
year: '2021'
...
---
_id: '10220'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex K can be mapped
to ℝd without higher-multiplicity intersections. An almost r-embedding is a map
f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not
have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then
there is a counterexample to the topological Tverberg conjecture, i.e., there
is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on
previous constructions of counterexamples (for d ≥ 3r) based on a series of papers
by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second
and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving
the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite
2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only
if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection
number of the f-images of any r pairwise disjoint simplices of K is zero. This
result can be restated in terms of a cohomological obstruction and extends an
analogous codimension 3 criterion by the second and fourth authors. As another
application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt
follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous
criterion for r = 2 is false. We prove a lemma on singular higher-dimensional
Borromean rings, yielding an elementary proof of the counterexample."
acknowledgement: Research supported by the Swiss National Science Foundation (Project
SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the
Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169),
by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would
like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner
and anonymous referees for helpful comments and discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
orcid: 0000-0002-7840-5062
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Arkadiy B.
full_name: Skopenkov, Arkadiy B.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity
intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534.
doi:10.1007/s11856-021-2216-z
apa: Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating
higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics.
Springer Nature. https://doi.org/10.1007/s11856-021-2216-z
chicago: Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner.
“Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel
Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z.
ieee: S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections. III. Codimension 2,” Israel Journal of Mathematics, vol.
245. Springer Nature, pp. 501–534, 2021.
ista: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity
intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III.
Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature,
2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.
short: S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of
Mathematics 245 (2021) 501–534.
corr_author: '1'
date_created: 2021-11-07T23:01:24Z
date_published: 2021-10-30T00:00:00Z
date_updated: 2025-07-02T10:54:52Z
day: '30'
department:
- _id: UlWa
doi: 10.1007/s11856-021-2216-z
external_id:
arxiv:
- '1511.03501'
isi:
- '000712942100013'
intvolume: ' 245'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '10'
oa: 1
oa_version: Preprint
page: '501–534 '
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9308'
relation: earlier_version
status: public
- id: '8183'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Eliminating higher-multiplicity intersections. III. Codimension 2
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 245
year: '2021'
...
---
_id: '10221'
abstract:
- lang: eng
text: We prove that any deterministic matrix is approximately the identity in the
eigenbasis of a large random Wigner matrix with very high probability and with
an optimal error inversely proportional to the square root of the dimension. Our
theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch
(Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner
ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity
(QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing
previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278,
2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020).
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for
Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048.
doi:10.1007/s00220-021-04239-z
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization
hypothesis for Wigner matrices. Communications in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s00220-021-04239-z
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization
Hypothesis for Wigner Matrices.” Communications in Mathematical Physics.
Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis
for Wigner matrices,” Communications in Mathematical Physics, vol. 388,
no. 2. Springer Nature, pp. 1005–1048, 2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis
for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.
mla: Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner
Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer
Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics
388 (2021) 1005–1048.
corr_author: '1'
date_created: 2021-11-07T23:01:25Z
date_published: 2021-10-29T00:00:00Z
date_updated: 2025-04-15T06:53:08Z
day: '29'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-021-04239-z
external_id:
arxiv:
- '2012.13215'
isi:
- '000712232700001'
file:
- access_level: open_access
checksum: a2c7b6f5d23b5453cd70d1261272283b
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-02T10:19:55Z
date_updated: 2022-02-02T10:19:55Z
file_id: '10715'
file_name: 2021_CommunMathPhys_Cipolloni.pdf
file_size: 841426
relation: main_file
success: 1
file_date_updated: 2022-02-02T10:19:55Z
has_accepted_license: '1'
intvolume: ' 388'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1005–1048
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eigenstate thermalization hypothesis for Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 388
year: '2021'
...
---
_id: '10222'
abstract:
- lang: eng
text: Consider a random set of points on the unit sphere in ℝd, which can be either
uniformly sampled or a Poisson point process. Its convex hull is a random inscribed
polytope, whose boundary approximates the sphere. We focus on the case d = 3,
for which there are elementary proofs and fascinating formulas for metric properties.
In particular, we study the fraction of acute facets, the expected intrinsic volumes,
the total edge length, and the distance to a fixed point. Finally we generalize
the results to the ellipsoid with homeoid density.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
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\nWe
are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and
for directing us to relevant references. We also thank to Anton Mellit for a useful
discussion on Bessel functions."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- 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
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed
in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459
apa: Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random
polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and
Francis. https://doi.org/10.1080/10586458.2021.1980459
chicago: Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty
of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics.
Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459.
ieee: A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes
inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis,
pp. 1–15, 2021.
ista: Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes
inscribed in the 2-sphere. Experimental Mathematics., 1–15.
mla: Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.”
Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.
short: A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021)
1–15.
corr_author: '1'
date_created: 2021-11-07T23:01:25Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2025-04-15T07:45:32Z
day: '25'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1080/10586458.2021.1980459
ec_funded: 1
external_id:
arxiv:
- '2007.07783'
isi:
- '000710893500001'
file:
- access_level: open_access
checksum: 3514382e3a1eb87fa6c61ad622874415
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T11:55:10Z
date_updated: 2023-08-14T11:55:10Z
file_id: '14053'
file_name: 2023_ExperimentalMath_Akopyan.pdf
file_size: 1966019
relation: main_file
success: 1
file_date_updated: 2023-08-14T11:55:10Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1-15
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: Mathematics, Computer Science
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Persistent Homology, Algorithms and Stochastic Geometry
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Experimental Mathematics
publication_identifier:
eissn:
- 1944-950X
issn:
- 1058-6458
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: The beauty of random polytopes inscribed in the 2-sphere
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
year: '2021'
...
---
_id: '10223'
abstract:
- lang: eng
text: Growth regulation tailors development in plants to their environment. A prominent
example of this is the response to gravity, in which shoots bend up and roots
bend down1. This paradox is based on opposite effects of the phytohormone auxin,
which promotes cell expansion in shoots while inhibiting it in roots via a yet
unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic
engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding
of how auxin inhibits root growth. We show that auxin activates two distinct,
antagonistically acting signalling pathways that converge on rapid regulation
of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE
KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma
membrane H+-ATPases for apoplast acidification, while intracellular canonical
auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization.
Simultaneous activation of these two counteracting mechanisms poises roots for
rapid, fine-tuned growth modulation in navigating complex soil environments.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank N. Gnyliukh and L. Hörmayer for technical assistance and
N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science,
Machine Shop and Bioimaging Facilities of IST Austria. This project has received
funding from the European Research Council Advanced Grant (ETAP-742985) and the
Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of
Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research
(NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N)
and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R.,
the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research
to M.R. and D.W., the Australian Research Council and China National Distinguished
Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685)
and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and
innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and
the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship
Council to J.C.
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Lana
full_name: Shabala, Lana
last_name: Shabala
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Hong
full_name: Ren, Hong
last_name: Ren
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Sergey
full_name: Shabala, Sergey
last_name: Shabala
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: William M.
full_name: Gray, William M.
last_name: Gray
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin
signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277.
doi:10.1038/s41586-021-04037-6
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6
chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez
Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin
Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature,
2021. https://doi.org/10.1038/s41586-021-04037-6.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer
Nature, pp. 273–277, 2021.
ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J,
Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D,
Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. 599(7884), 273–277.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+
Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021,
pp. 273–77, doi:10.1038/s41586-021-04037-6.
short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J.
Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel,
D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.
corr_author: '1'
date_created: 2021-11-07T23:01:25Z
date_published: 2021-11-11T00:00:00Z
date_updated: 2025-07-10T11:49:46Z
day: '11'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.1038/s41586-021-04037-6
ec_funded: 1
external_id:
isi:
- '000713338100006'
pmid:
- '34707283'
intvolume: ' 599'
isi: 1
issue: '7884'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '11'
oa: 1
oa_version: Preprint
page: 273-277
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/stop-and-grow/
record:
- id: '10095'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Cell surface and intracellular auxin signalling for H+ fluxes in
root growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 599
year: '2021'
...
---
_id: '10224'
abstract:
- lang: eng
text: We investigate the Fröhlich polaron model on a three-dimensional torus, and
give a proof of the second-order quantum corrections to its ground-state energy
in the strong-coupling limit. Compared to previous work in the confined case,
the translational symmetry (and its breaking in the Pekar approximation) makes
the analysis substantially more challenging.
acknowledgement: "Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged. We
would also like to thank Rupert Frank for many helpful discussions, especially related
to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding
provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum
corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis.
2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7'
apa: 'Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron
on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7'
chicago: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron
on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational
Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.'
ieee: 'D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus:
Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics
and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.'
ista: 'Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus:
Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and
Analysis. 242(3), 1835–1906.'
mla: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on
the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational
Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906,
doi:10.1007/s00205-021-01715-7.'
short: D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis
242 (2021) 1835–1906.
date_created: 2021-11-07T23:01:26Z
date_published: 2021-10-25T00:00:00Z
date_updated: 2025-04-14T09:11:09Z
day: '25'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00205-021-01715-7
ec_funded: 1
external_id:
arxiv:
- '2101.12566'
isi:
- '000710850600001'
file:
- access_level: open_access
checksum: 672e9c21b20f1a50854b7c821edbb92f
content_type: application/pdf
creator: alisjak
date_created: 2021-12-14T08:35:42Z
date_updated: 2021-12-14T08:35:42Z
file_id: '10544'
file_name: 2021_Springer_Feliciangeli.pdf
file_size: 990529
relation: main_file
success: 1
file_date_updated: 2021-12-14T08:35:42Z
has_accepted_license: '1'
intvolume: ' 242'
isi: 1
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1835–1906
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9787'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'The strongly coupled polaron on the torus: Quantum corrections to the Pekar
asymptotics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 242
year: '2021'
...
---
_id: '10267'
abstract:
- lang: eng
text: Tropisms are among the most important growth responses for plant adaptation
to the surrounding environment. One of the most common tropisms is root gravitropism.
Root gravitropism enables the plant to anchor securely to the soil enabling the
absorption of water and nutrients. Most of the knowledge related to the plant
gravitropism has been acquired from the flowering plants, due to limited research
in non-seed plants. Limited research on non-seed plants is due in large part to
the lack of standard research methods. Here, we describe the experimental methods
to evaluate gravitropism in representative non-seed plant species, including the
non-vascular plant moss Physcomitrium patens, the early diverging extant vascular
plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In
addition, we introduce the methods used for statistical analysis of the root gravitropism
in non-seed plant species.
acknowledgement: The Ceratopteris richardii spores were obtained from the lab of Jo
Ann Banks at Purdue University. This work was supported by funding from the European
Union’s Horizon 2020 research and innovation program (ERC grant agreement number
742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program
and DOC Fellowship of the Austrian Academy of Sciences.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In:
Blancaflor EB, ed. Plant Gravitropism. Vol 2368. MIMB. Springer Nature;
2021:43-51. doi:10.1007/978-1-0716-1677-2_2'
apa: Zhang, Y., Li, L., & Friml, J. (2021). Evaluation of gravitropism in non-seed
plants. In E. B. Blancaflor (Ed.), Plant Gravitropism (Vol. 2368, pp. 43–51).
Springer Nature. https://doi.org/10.1007/978-1-0716-1677-2_2
chicago: Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in
Non-Seed Plants.” In Plant Gravitropism, edited by Elison B Blancaflor,
2368:43–51. MIMB. Springer Nature, 2021. https://doi.org/10.1007/978-1-0716-1677-2_2.
ieee: Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,”
in Plant Gravitropism, vol. 2368, E. B. Blancaflor, Ed. Springer Nature,
2021, pp. 43–51.
ista: 'Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants.
In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51.'
mla: Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” Plant
Gravitropism, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021,
pp. 43–51, doi:10.1007/978-1-0716-1677-2_2.
short: Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism,
Springer Nature, 2021, pp. 43–51.
corr_author: '1'
date_created: 2021-11-11T09:26:10Z
date_published: 2021-10-14T00:00:00Z
date_updated: 2025-04-14T07:45:00Z
day: '14'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-1677-2_2
ec_funded: 1
editor:
- first_name: Elison B
full_name: Blancaflor, Elison B
last_name: Blancaflor
external_id:
pmid:
- '34647246'
intvolume: ' 2368'
language:
- iso: eng
month: '10'
oa_version: None
page: 43-51
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Plant Gravitropism
publication_identifier:
eisbn:
- 978-1-0716-1677-2
isbn:
- 978-1-0716-1676-5
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Evaluation of gravitropism in non-seed plants
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2368
year: '2021'
...
---
_id: '10268'
abstract:
- lang: eng
text: The analysis of dynamic cellular processes such as plant cytokinesis stands
and falls with live-cell time-lapse confocal imaging. Conventional approaches
to time-lapse imaging of cell division in Arabidopsis root tips are tedious and
have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous
imaging of multiple root tips on a vertical-stage confocal microscope with automated
root tracking. We also provide modifications of the basic protocol to implement
this imaging method in the analysis of genetic, pharmacological or laser ablation
wounding-mediated experimental manipulations. Our method dramatically improves
the efficiency of cell division time-lapse imaging by increasing the throughput,
while reducing the person-hour requirements of such experiments.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank B. De Rybel for allowing M.G. to work on this manuscript
during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term
fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support
by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading
and correcting the manuscript.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
citation:
ama: 'Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy.
In: Plant Cell Division. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:10.1007/978-1-0716-1744-1_6'
apa: Hörmayer, L., Friml, J., & Glanc, M. (2021). Automated time-lapse imaging
and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal
microscopy. In Plant Cell Division (Vol. 2382, pp. 105–114). Humana Press.
https://doi.org/10.1007/978-1-0716-1744-1_6
chicago: Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging
and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal
Microscopy.” In Plant Cell Division, 2382:105–14. MIMB. Humana Press, 2021.
https://doi.org/10.1007/978-1-0716-1744-1_6.
ieee: L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,”
in Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–114.
ista: 'Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy.
In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.'
mla: Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell
Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” Plant
Cell Division, vol. 2382, Humana Press, 2021, pp. 105–14, doi:10.1007/978-1-0716-1744-1_6.
short: L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press,
2021, pp. 105–114.
date_created: 2021-11-11T10:03:30Z
date_published: 2021-10-28T00:00:00Z
date_updated: 2022-06-03T06:47:06Z
day: '28'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-1744-1_6
external_id:
pmid:
- '34705235'
intvolume: ' 2382'
language:
- iso: eng
month: '10'
oa_version: None
page: 105-114
pmid: 1
publication: Plant Cell Division
publication_identifier:
eisbn:
- 978-1-0716-1744-1
eissn:
- 1940-6029
isbn:
- 978-1-0716-1743-4
issn:
- 1064-3745
publication_status: published
publisher: Humana Press
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis
roots by vertical-stage confocal microscopy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2382
year: '2021'
...