---
_id: '9287'
abstract:
- lang: eng
text: "The phytohormone auxin and its directional transport through tissues are
intensively studied. However, a mechanistic understanding of auxin-mediated feedback
on endocytosis and polar distribution of PIN auxin transporters remains limited
due to contradictory observations and interpretations. Here, we used state-of-the-art
methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used
high auxin concentrations or longer treatments versus lower concentrations and
shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish
between specific and nonspecific effects. Longer treatments of both auxins interfere
with Brefeldin A-mediated intracellular PIN2 accumulation and also with general
aggregation of endomembrane compartments. NAA treatment decreased the internalization
of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the
number, distribution, and compartment identity of the early endosome/trans-Golgi
network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations
unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the
endomembrane system, we opted for alternative approaches visualizing the endocytic
events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence
(TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the
incidence and dynamics of clathrin foci, implying that these treatments do not
affect the overall endocytosis rate. However, both NAA and IAA at low concentrations
rapidly and specifically promoted endocytosis of photo-converted PIN2 from the
PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis,
thus contributing to its\r\npolarity maintenance and furthermore illustrate that
high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
acknowledgement: 'We thank Ivan Kulik for developing the Chip’n’Dale apparatus with
Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent
support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help;
Barbara Casillas-Perez for her help with statistics. This project has received funding
from the European Research Council (ERC) under the European Union''s Horizon 2020
research and innovation program (grant agreement No 742985). A.J. is supported by
funding from the Austrian Science Fund (FWF): I3630B25 to J.F. '
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- 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: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: E
full_name: Himschoot, E
last_name: Himschoot
- first_name: R
full_name: Wang, R
last_name: Wang
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
- first_name: J
full_name: Sánchez-Simarro, J
last_name: Sánchez-Simarro
- first_name: F
full_name: Aniento, F
last_name: Aniento
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and
nonspecific auxin effects on endocytosis and trafficking. Plant Physiology.
2021;186(2):1122–1142. doi:10.1093/plphys/kiab134
apa: Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li,
L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin
effects on endocytosis and trafficking. Plant Physiology. Oxford University
Press. https://doi.org/10.1093/plphys/kiab134
chicago: Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson,
Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis
of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant
Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134.
ieee: M. Narasimhan et al., “Systematic analysis of specific and nonspecific
auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186,
no. 2. Oxford University Press, pp. 1122–1142, 2021.
ista: Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez
Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento
F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific
auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.
mla: Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific
Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186,
no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134.
short: M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li,
L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro,
F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.
date_created: 2021-03-26T12:08:38Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2024-03-27T23:30:43Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/plphys/kiab134
ec_funded: 1
external_id:
isi:
- '000671555900031'
pmid:
- '33734402'
file:
- access_level: open_access
checksum: 532bb9469d3b665907f06df8c383eade
content_type: application/pdf
creator: cziletti
date_created: 2021-11-11T15:07:51Z
date_updated: 2021-11-11T15:07:51Z
file_id: '10273'
file_name: 2021_PlantPhysio_Narasimhan.pdf
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has_accepted_license: '1'
intvolume: ' 186'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1122–1142
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
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: 10.1093/plphys/kiab380
record:
- id: '11626'
relation: dissertation_contains
status: public
- id: '10083'
relation: dissertation_contains
status: public
status: public
title: Systematic analysis of specific and nonspecific auxin effects on endocytosis
and trafficking
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: 186
year: '2021'
...
---
_id: '10083'
abstract:
- lang: eng
text: "Plant motions occur across a wide spectrum of timescales, ranging from seed
dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term
adaptation of gross architecture. Relatively fast motions include water-driven
growth as exemplified by root cell expansion under abiotic/biotic stresses or
during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered
by the phytohormone auxin. However, the cellular and molecular mechanisms are
still largely unknown. This thesis covers the studies about this topic as follows.
By taking advantage of microfluidics combined with live imaging, pharmaceutical
tools, and transgenic lines, we examined the kinetics of and causal relationship
among various auxininduced rapid cellular changes in root growth, apoplastic pH,
cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology.
We revealed that CMT reorientation and vacuolar constriction are the consequence
of growth itself instead of responding directly to auxin. In contrast, auxin induces
apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered
apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+
inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling.
To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined
microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct
a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway
is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we
uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface
signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during
auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly
activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract
instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and
TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and
TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore
the relation of two signaling pathways. Assisted with biochemistry and fluorescent
imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with
each other. The ability of TIR1/AFB binding to membrane lipid provides a basis
for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides,
transgenic analysis combined with genetic engineering and biochemistry showed
that vi\r\nthey do function in the same pathway. Particularly, auxin-induced
TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely,
TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling.
To follow the study of rapid growth regulation, we analyzed another rapid growth
regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid
and reversible growth inhibition caused by H + influx, highly resembling but not
dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression
of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1
hour, contributing to the sustained RALF1-triggered growth inhibition. These studies
collectively contribute to understanding rapid regulation on plant cell\r\ngrowth,
novel auxin signaling pathway as well as auxin-peptide crosstalk. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
last_name: Li
citation:
ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083
apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083
chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of
Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.
ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science
and Technology Austria, 2021.
ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science
and Technology Austria.
mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of
Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.
short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science
and Technology Austria, 2021.
date_created: 2021-10-04T13:33:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-10-31T19:30:02Z
day: '06'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:10083
ec_funded: 1
file:
- access_level: open_access
checksum: 3b2f55b3b8ae05337a0dcc1cd8595b10
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T08:00:07Z
date_updated: 2022-12-20T23:30:03Z
embargo: 2022-10-14
file_id: '10138'
file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf
file_size: 8616142
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creator: cchlebak
date_created: 2021-10-14T08:00:13Z
date_updated: 2022-12-20T23:30:03Z
embargo_to: open_access
file_id: '10139'
file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014.docx
file_size: 15058499
relation: source_file
file_date_updated: 2022-12-20T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _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_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '442'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '9287'
relation: part_of_dissertation
status: public
- id: '8283'
relation: part_of_dissertation
status: public
- id: '8986'
relation: part_of_dissertation
status: public
- id: '6627'
relation: part_of_dissertation
status: public
- id: '10095'
relation: part_of_dissertation
status: public
- id: '10015'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Rapid cell growth regulation in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10015'
abstract:
- lang: eng
text: "Auxin plays a dual role in growth regulation and, depending on the tissue
and concentration of the hormone, it can either promote or inhibit division and
expansion processes in plants. Recent studies have revealed that, beyond transcriptional
reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here,
we explored the impact of different concentrations of the synthetic auxin NAA
that establish growth-promoting and -repressing conditions on the root tip proteome
and phosphoproteome, generating a unique resource. From the phosphoproteome data,
we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results,
together with previously published studies, suggest that auxin, H+-ATPases, cell
wall modifications and cell wall sensing receptor-like kinases are tightly embedded
in a pathway regulating cell elongation. Furthermore, our study assigned a novel
role to MKK2 as a regulator of primary root growth and a (potential) regulator
of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31
phosphorylation site for growth regulation in the Arabidopsis root tip."
acknowledgement: We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem
for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by
the Austrian Science Fund (FWF).
alternative_title:
- Protein Phosphorylation and Cell Signaling in Plants
article_number: '1665 '
article_processing_charge: Yes
article_type: original
author:
- first_name: N
full_name: Nikonorova, N
last_name: Nikonorova
- first_name: E
full_name: Murphy, E
last_name: Murphy
- first_name: CF
full_name: Fonseca de Lima, CF
last_name: Fonseca de Lima
- first_name: S
full_name: Zhu, S
last_name: Zhu
- first_name: B
full_name: van de Cotte, B
last_name: van de Cotte
- first_name: LD
full_name: Vu, LD
last_name: Vu
- first_name: D
full_name: Balcerowicz, D
last_name: Balcerowicz
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: X
full_name: Kong, X
last_name: Kong
- first_name: G
full_name: De Rop, G
last_name: De Rop
- first_name: T
full_name: Beeckman, T
last_name: Beeckman
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: K
full_name: Vissenberg, K
last_name: Vissenberg
- first_name: PC
full_name: Morris, PC
last_name: Morris
- first_name: Z
full_name: Ding, Z
last_name: Ding
- first_name: I
full_name: De Smet, I
last_name: De Smet
citation:
ama: Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip
(phospho)proteomes at growth-promoting versus growth-repressing conditions reveal
novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665
apa: Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B.,
Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting
versus growth-repressing conditions reveal novel root growth regulators. Cells.
MDPI. https://doi.org/10.3390/cells10071665
chicago: Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD
Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting
versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071665.
ieee: N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes
at growth-promoting versus growth-repressing conditions reveal novel root growth
regulators,” Cells, vol. 10. MDPI, 2021.
ista: Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz
D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z,
De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting
versus growth-repressing conditions reveal novel root growth regulators. Cells.
10, 1665.
mla: Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting
versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells,
vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665.
short: N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L.
Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg,
P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).
date_created: 2021-09-14T11:36:20Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2024-03-27T23:30:43Z
day: '02'
ddc:
- '575'
department:
- _id: JiFr
doi: 10.3390/cells10071665
ec_funded: 1
external_id:
isi:
- '000676604700001'
pmid:
- '34359847'
file:
- access_level: open_access
checksum: 2a9f534b9c2200e72e2cde95afaf4eed
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-16T09:07:06Z
date_updated: 2021-09-16T09:07:06Z
file_id: '10021'
file_name: 2021_Cells_Nikonorova.pdf
file_size: 2667848
relation: main_file
success: 1
file_date_updated: 2021-09-16T09:07:06Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- primary root
- (phospho)proteomics
- auxin
- (receptor) kinase
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Cells
publication_identifier:
issn:
- 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
status: public
title: The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing
conditions reveal novel root growth regulators
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: 10
year: '2021'
...
---
_id: '10095'
abstract:
- lang: eng
text: Growth regulation tailors plant development to its environment. A showcase
is response to gravity, where shoots bend up and roots 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 phospho-proteomics
in Arabidopsis thaliana, we advance our understanding how auxin inhibits root
growth. We show that auxin activates two distinct, antagonistically acting signalling
pathways that converge on the rapid regulation of the apoplastic pH, a causative
growth determinant. 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 alkalinisation. The simultaneous activation
of these two counteracting mechanisms poises the root for a rapid, fine-tuned
growth modulation while navigating complex soil environment.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance
and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge 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) 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.), the 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 the Marie Skłodowska-Curie Grant Agreement No. 665385
and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship
Council to J.C.
article_number: '266395'
article_processing_charge: No
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. Research Square. doi:10.21203/rs.3.rs-266395/v3
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling
for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3
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.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+-fluxes in root growth,” Research Square. .
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. Cell surface and intracellular auxin signalling
for H+-fluxes in root growth. Research Square, 266395.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes
in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.
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, Research Square (n.d.).
date_created: 2021-10-06T08:56:22Z
date_published: 2021-09-09T00:00:00Z
date_updated: 2024-03-27T23:30:43Z
day: '09'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.21203/rs.3.rs-266395/v3
ec_funded: 1
language:
- iso: eng
main_file_link:
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url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _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: 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: Research Square
publication_identifier:
issn:
- 2693-5015
publication_status: accepted
related_material:
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relation: dissertation_contains
status: public
status: public
title: Cell surface and intracellular auxin signalling for H+-fluxes in root growth
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10293'
abstract:
- lang: eng
text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism
for explaining the evolution of cooperation among unrelated individuals. In contrast
to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally
cooperating by using their own experiences, indirect reciprocity is based on individuals’
reputations. If a player helps another, this increases the helper’s public standing,
benefitting them in the future. This lets cooperation in the population emerge
without individuals having to meet more than once. While the two modes of reciprocity
are intertwined, they are difficult to compare. Thus, they are usually studied
in isolation. Direct reciprocity can maintain cooperation with simple strategies,
and is robust against noise even when players do not remember more\r\nthan their
partner’s last action. Meanwhile, indirect reciprocity requires its successful
strategies, or social norms, to be more complex. Exhaustive search previously
identified eight such norms, called the “leading eight”, which excel at maintaining
cooperation. However, as the first result of this thesis, we show that the leading
eight break down once we remove the fundamental assumption that information is
synchronized and public, such that everyone agrees on reputations. Once we consider
a more realistic scenario of imperfect information, where reputations are private,
and individuals occasionally misinterpret or miss observations, the leading eight
do not promote cooperation anymore. Instead, minor initial disagreements can proliferate,
fragmenting populations into subgroups. In a next step, we consider ways to mitigate
this issue. We first explore whether introducing “generosity” can stabilize cooperation
when players use the leading eight strategies in noisy environments. This approach
of modifying strategies to include probabilistic elements for coping with errors
is known to work well in direct reciprocity. However, as we show here, it fails
for the more complex norms of indirect reciprocity. Imperfect information still
prevents cooperation from evolving. On the other hand, we succeeded to show in
this thesis that modifying the leading eight to use “quantitative assessment”,
i.e. tracking reputation scores on a scale beyond good and bad, and making overall
judgments of others based on a threshold, is highly successful, even when noise
increases in the environment. Cooperation can flourish when reputations\r\nare
more nuanced, and players have a broader understanding what it means to be “good.”
Finally, we present a single theoretical framework that unites the two modes of
reciprocity despite their differences. Within this framework, we identify a novel
simple and successful strategy for indirect reciprocity, which can cope with noisy
environments and has an analogue in direct reciprocity. We can also analyze decision
making when different sources of information are available. Our results help highlight
that for sustaining cooperation, already the most simple rules of reciprocity
can be sufficient."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
citation:
ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect
information. 2021. doi:10.15479/at:ista:10293
apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293
chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.
ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect
information,” Institute of Science and Technology Austria, 2021.
ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria.
mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:10293.
short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect
Information, Institute of Science and Technology Austria, 2021.
date_created: 2021-11-15T17:12:57Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-11-07T08:28:29Z
day: '17'
ddc:
- '519'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrCh
doi: 10.15479/at:ista:10293
ec_funded: 1
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oa: 1
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page: '171'
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9997'
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status: public
- id: '2'
relation: part_of_dissertation
status: public
- id: '9402'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Evolution of cooperation via (in)direct reciprocity under imperfect information
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9997'
abstract:
- lang: eng
text: Indirect reciprocity is a mechanism for the evolution of cooperation based
on social norms. This mechanism requires that individuals in a population observe
and judge each other’s behaviors. Individuals with a good reputation are more
likely to receive help from others. Previous work suggests that indirect reciprocity
is only effective when all relevant information is reliable and publicly available.
Otherwise, individuals may disagree on how to assess others, even if they all
apply the same social norm. Such disagreements can lead to a breakdown of cooperation.
Here we explore whether the predominantly studied ‘leading eight’ social norms
of indirect reciprocity can be made more robust by equipping them with an element
of generosity. To this end, we distinguish between two kinds of generosity. According
to assessment generosity, individuals occasionally assign a good reputation to
group members who would usually be regarded as bad. According to action generosity,
individuals occasionally cooperate with group members with whom they would usually
defect. Using individual-based simulations, we show that the two kinds of generosity
have a very different effect on the resulting reputation dynamics. Assessment
generosity tends to add to the overall noise and allows defectors to invade. In
contrast, a limited amount of action generosity can be beneficial in a few cases.
However, even when action generosity is beneficial, the respective simulations
do not result in full cooperation. Our results suggest that while generosity can
favor cooperation when individuals use the most simple strategies of reciprocity,
it is disadvantageous when individuals use more complex social norms.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science
Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).'
article_number: '17443'
article_processing_charge: Yes
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Pouya
full_name: Shati, Pouya
last_name: Shati
- first_name: Christian
full_name: Hilbe, Christian
last_name: Hilbe
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity
under action and assessment generosity. Scientific Reports. 2021;11(1).
doi:10.1038/s41598-021-96932-1
apa: Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution
of indirect reciprocity under action and assessment generosity. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1
chicago: Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee.
“The Evolution of Indirect Reciprocity under Action and Assessment Generosity.”
Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1.
ieee: L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect
reciprocity under action and assessment generosity,” Scientific Reports,
vol. 11, no. 1. Springer Nature, 2021.
ista: Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect
reciprocity under action and assessment generosity. Scientific Reports. 11(1),
17443.
mla: Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and
Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer
Nature, 2021, doi:10.1038/s41598-021-96932-1.
short: L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).
date_created: 2021-09-11T16:22:02Z
date_published: 2021-08-31T00:00:00Z
date_updated: 2024-03-27T23:30:44Z
day: '31'
ddc:
- '003'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1038/s41598-021-96932-1
ec_funded: 1
external_id:
isi:
- '000692406400018'
pmid:
- '34465830'
file:
- access_level: open_access
checksum: 19df8816cf958b272b85841565c73182
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-13T10:31:21Z
date_updated: 2021-09-13T10:31:21Z
file_id: '10006'
file_name: 2021_ScientificReports_Schmid.pdf
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file_date_updated: 2021-09-13T10:31:21Z
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intvolume: ' 11'
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issue: '1'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10293'
relation: dissertation_contains
status: public
status: public
title: The evolution of indirect reciprocity under action and assessment generosity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9402'
abstract:
- lang: eng
text: Direct and indirect reciprocity are key mechanisms for the evolution of cooperation.
Direct reciprocity means that individuals use their own experience to decide whether
to cooperate with another person. Indirect reciprocity means that they also consider
the experiences of others. Although these two mechanisms are intertwined, they
are typically studied in isolation. Here, we introduce a mathematical framework
that allows us to explore both kinds of reciprocity simultaneously. We show that
the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural
analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium
analysis, we characterize under which conditions either of the two strategies
can maintain cooperation. With simulations, we additionally explore which kind
of reciprocity evolves when members of a population engage in social learning
to adapt to their environment. Our results draw unexpected connections between
direct and indirect reciprocity while highlighting important differences regarding
their evolvability.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph
Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT
(to C.H.). The funders had no role in study design, data collection and analysis,
decision to publish or preparation of the manuscript.'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and
indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8
apa: Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified
framework of direct and indirect reciprocity. Nature Human Behaviour. Springer
Nature. https://doi.org/10.1038/s41562-021-01114-8
chicago: Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak.
“A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour.
Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8.
ieee: L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework
of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no.
10. Springer Nature, pp. 1292–1302, 2021.
ista: Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct
and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.
mla: Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.”
Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302,
doi:10.1038/s41562-021-01114-8.
short: L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5
(2021) 1292–1302.
date_created: 2021-05-18T16:56:57Z
date_published: 2021-05-13T00:00:00Z
date_updated: 2024-03-27T23:30:44Z
day: '13'
ddc:
- '000'
department:
- _id: KrCh
- _id: GradSch
doi: 10.1038/s41562-021-01114-8
ec_funded: 1
external_id:
isi:
- '000650304000002'
pmid:
- '33986519'
file:
- access_level: open_access
checksum: 34f55e173f90dc1dab731063458ac780
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T08:27:23Z
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language:
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month: '05'
oa: 1
oa_version: Submitted Version
page: 1292–1302
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Nature Human Behaviour
publication_identifier:
eissn:
- 2397-3374
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/the-emergence-of-cooperation/
record:
- id: '10293'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A unified framework of direct and indirect reciprocity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2021'
...
---
_id: '9817'
abstract:
- lang: eng
text: Elastic bending of initially flat slender elements allows the realization
and economic fabrication of intriguing curved shapes. In this work, we derive
an intuitive but rigorous geometric characterization of the design space of plane
elastic rods with variable stiffness. It enables designers to determine which
shapes are physically viable with active bending by visual inspection alone. Building
on these insights, we propose a method for efficiently designing the geometry
of a flat elastic rod that realizes a target equilibrium curve, which only requires
solving a linear program. We implement this method in an interactive computational
design tool that gives feedback about the feasibility of a design, and computes
the geometry of the structural elements necessary to realize it within an instant.
The tool also offers an iterative optimization routine that improves the fabricability
of a model while modifying it as little as possible. In addition, we use our geometric
characterization to derive an algorithm for analyzing and recovering the stability
of elastic curves that would otherwise snap out of their unstable equilibrium
shapes by buckling. We show the efficacy of our approach by designing and manufacturing
several physical models that are assembled from flat elements.
acknowledgement: "We thank the anonymous reviewers for their generous feedback, and
Michal Piovarči for his help in producing the supplemental video. This project has
received funding from the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n"
article_number: '126'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions
on Graphics. 2021;40(4). doi:10.1145/3450626.3459800
apa: 'Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves.
ACM Transactions on Graphics. Virtual: Association for Computing Machinery.
https://doi.org/10.1145/3450626.3459800'
chicago: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic
Curves.” ACM Transactions on Graphics. Association for Computing Machinery,
2021. https://doi.org/10.1145/3450626.3459800.
ieee: C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM
Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery,
2021.
ista: Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions
on Graphics. 40(4), 126.
mla: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.”
ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing
Machinery, 2021, doi:10.1145/3450626.3459800.
short: C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).
conference:
end_date: 2021-08-13
location: Virtual
name: 'SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2021-08-09
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-19T00:00:00Z
date_updated: 2024-03-27T23:30:45Z
day: '19'
ddc:
- '516'
department:
- _id: BeBi
doi: 10.1145/3450626.3459800
ec_funded: 1
external_id:
isi:
- '000674930900091'
file:
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creator: chafner
date_created: 2021-10-18T10:42:15Z
date_updated: 2021-10-18T10:42:15Z
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file_size: 17064290
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success: 1
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content_type: application/pdf
creator: chafner
date_created: 2021-10-18T10:42:22Z
date_updated: 2021-10-18T10:42:22Z
file_id: '10151'
file_name: elastic-curves-supp.pdf
file_size: 547156
relation: supplementary_material
file_date_updated: 2021-10-18T10:42:22Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
keyword:
- Computing methodologies
- shape modeling
- modeling and simulation
- theory of computation
- computational geometry
- mathematics of computing
- mathematical optimization
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published 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'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/designing-with-elastic-structures/
record:
- id: '12897'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The design space of plane elastic curves
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'
...
---
_id: '10135'
abstract:
- lang: eng
text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically
throughout their whole life and thereby flexibly adapt to ever-changing environmental
conditions. Plant hormones auxin and cytokinin are the main regulators of the
lateral root organogenesis. Additionally to their solo activities, the interaction
between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root
development and growth. In particular, cytokinin modulates auxin distribution
within the developing lateral root by affecting the endomembrane trafficking of
auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al.,
2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore,
it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational
level. Impact of cytokinin and other plant hormones on auxin transporters (including
PIN1) on the posttranslational level is described in detail in the introduction
part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights
into the molecular machinery underlying cytokinin effect on the endomembrane trafficking
in the plant cell, in particular on the PIN1 degradation, we conducted two large
proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical
proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin
treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A).
We found that DRP2A plays a role in cytokinin regulated processes during the plant
growth and that cytokinin treatment promotes destabilization of DRP2A protein.
However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In
the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial
role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation.
Altogether, we identified proteins, which bind to cytokinin and proteins that
in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation
pattern. By combining information from these two screens, we can pave our way
towards understanding of noncanonical cytokinin effects."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hana
full_name: Semerádová, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semerádová
citation:
ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135
apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:10135
chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:10135.
ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis,” Institute of Science and Technology
Austria, 2021.
ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria.
mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:10135.
short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology
Austria, 2021.
date_created: 2021-10-13T13:42:48Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-01-25T10:53:29Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10135
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date_updated: 2022-12-20T23:30:05Z
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date_created: 2021-10-27T07:45:57Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-10-28
file_id: '10187'
file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf
file_size: 10623525
relation: main_file
file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
publication_identifier:
isbn:
- 978-3-99078-014-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to
coordinate plant organogenesis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9728'
abstract:
- lang: eng
text: "Most real-world flows are multiphase, yet we know little about them compared
to their single-phase counterparts. Multiphase flows are more difficult to investigate
as their dynamics occur in large parameter space and involve complex phenomena
such as preferential concentration, turbulence modulation, non-Newtonian rheology,
etc. Over the last few decades, experiments in particle-laden flows have taken
a back seat in favour of ever-improving computational resources. However, computers
are still not powerful enough to simulate a real-world fluid with millions of
finite-size particles. Experiments are essential not only because they offer a
reliable way to investigate real-world multiphase flows but also because they
serve to validate numerical studies and steer the research in a relevant direction.
In this work, we have experimentally investigated particle-laden flows in pipes,
and in particular, examined the effect of particles on the laminar-turbulent transition
and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows,
an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic)
transition that occurs via localised turbulent structures called puffs is affected
by the addition of particles. In this study, in addition to this known transition,
we found a super-critical transition to a globally fluctuating state with increasing
particle concentration. At the same time, the Newtonian-type transition via puffs
is delayed to larger Reynolds numbers. At an even higher concentration, only the
globally fluctuating state is found. The dynamics of particle-laden flows are
hence determined by two competing instabilities that give rise to three flow regimes:
Newtonian-type turbulence at low, a particle-induced globally fluctuating state
at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect
of particles on turbulent drag is ambiguous, with studies reporting drag reduction,
no net change, and even drag increase. The ambiguity arises because, in addition
to particle concentration, particle shape, size, and density also affect the net
drag. Even similar particles might affect the flow dissimilarly in different Reynolds
number and concentration ranges. In the present study, we explored a wide range
of both Reynolds number and concentration, using spherical as well as cylindrical
particles. We found that the spherical particles do not reduce drag while the
cylindrical particles are drag-reducing within a specific Reynolds number interval.
The interval strongly depends on the particle concentration and the relative size
of the pipe and particles. Within this interval, the magnitude of drag reduction
reaches a maximum. These drag reduction maxima appear to fall onto a distinct
power-law curve irrespective of the pipe diameter and particle concentration,
and this curve can be considered as the maximum drag reduction asymptote for a
given fibre shape. Such an asymptote is well known for polymeric flows but had
not been identified for particle-laden flows prior to this work."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nishchal
full_name: Agrawal, Nishchal
id: 469E6004-F248-11E8-B48F-1D18A9856A87
last_name: Agrawal
citation:
ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe
flows. 2021. doi:10.15479/at:ista:9728
apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728
chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.
ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden
pipe flows,” Institute of Science and Technology Austria, 2021.
ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria.
mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.
short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows, Institute of Science and Technology Austria, 2021.
date_created: 2021-07-27T13:40:30Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2024-02-28T13:14:39Z
day: '29'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:9728
file:
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creator: nagrawal
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date_updated: 2022-07-29T22:30:05Z
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file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip
file_size: 22859658
relation: source_file
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checksum: 72a891d7daba85445c29b868c22575ed
content_type: application/pdf
creator: nagrawal
date_created: 2021-07-28T13:32:05Z
date_updated: 2022-07-29T22:30:05Z
embargo: 2022-07-28
file_id: '9745'
file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf
file_size: 18658048
relation: main_file
file_date_updated: 2022-07-29T22:30:05Z
has_accepted_license: '1'
keyword:
- Drag Reduction
- Transition to Turbulence
- Multiphase Flows
- particle Laden Flows
- Complex Flows
- Experiments
- Fluid Dynamics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '118'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6189'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Transition to turbulence and drag reduction in particle-laden pipe flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10673'
abstract:
- lang: eng
text: We propose a neural information processing system obtained by re-purposing
the function of a biological neural circuit model to govern simulated and real-world
control tasks. Inspired by the structure of the nervous system of the soil-worm,
C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model
of biological neural circuits reparameterized for the control of alternative tasks.
We first demonstrate that ONCs realize networks with higher maximum flow compared
to arbitrary wired networks. We then learn instances of ONCs to control a series
of robotic tasks, including the autonomous parking of a real-world rover robot.
For reconfiguration of the purpose of the neural circuit, we adopt a search-based
optimization algorithm. Ordinary neural circuits perform on par and, in some cases,
significantly surpass the performance of contemporary deep learning models. ONC
networks are compact, 77% sparser than their counterpart neural controllers, and
their neural dynamics are fully interpretable at the cell-level.
acknowledgement: "RH and RG are partially supported by Horizon-2020 ECSEL Project
grant No. 783163 (iDev40), Productive 4.0, and ATBMBFW CPS-IoT Ecosystem. ML was
supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein
Award). AA is supported by the National Science Foundation (NSF) Graduate Research
Fellowship\r\nProgram. RH and DR are partially supported by The Boeing Company and
JP Morgan Chase. This research work is\r\npartially drawn from the PhD dissertation
of RH.\r\n"
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner:
Reinforcement learning with ordinary neural circuits. In: Proceedings of the
37th International Conference on Machine Learning. PMLR. ; 2020:4082-4093.'
apa: 'Hasani, R., Lechner, M., Amini, A., Rus, D., & Grosu, R. (2020). A natural
lottery ticket winner: Reinforcement learning with ordinary neural circuits. In
Proceedings of the 37th International Conference on Machine Learning (pp.
4082–4093). Virtual.'
chicago: 'Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu
Grosu. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary
Neural Circuits.” In Proceedings of the 37th International Conference on Machine
Learning, 4082–93. PMLR, 2020.'
ieee: 'R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery
ticket winner: Reinforcement learning with ordinary neural circuits,” in Proceedings
of the 37th International Conference on Machine Learning, Virtual, 2020, pp.
4082–4093.'
ista: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2020. A natural lottery ticket
winner: Reinforcement learning with ordinary neural circuits. Proceedings of the
37th International Conference on Machine Learning. ML: Machine LearningPMLR, PMLR,
, 4082–4093.'
mla: 'Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning
with Ordinary Neural Circuits.” Proceedings of the 37th International Conference
on Machine Learning, 2020, pp. 4082–93.'
short: R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the
37th International Conference on Machine Learning, 2020, pp. 4082–4093.
conference:
end_date: 2020-07-18
location: Virtual
name: 'ML: Machine Learning'
start_date: 2020-07-12
date_created: 2022-01-25T15:50:34Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2022-01-26T11:14:27Z
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
file:
- access_level: open_access
checksum: c9a4a29161777fc1a89ef451c040e3b1
content_type: application/pdf
creator: cchlebak
date_created: 2022-01-26T11:08:51Z
date_updated: 2022-01-26T11:08:51Z
file_id: '10691'
file_name: 2020_PMLR_Hasani.pdf
file_size: 2329798
relation: main_file
success: 1
file_date_updated: 2022-01-26T11:08:51Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/3.0/
main_file_link:
- open_access: '1'
url: http://proceedings.mlr.press/v119/hasani20a.html
oa: 1
oa_version: Published Version
page: 4082-4093
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the 37th International Conference on Machine Learning
publication_identifier:
issn:
- 2640-3498
publication_status: published
quality_controlled: '1'
scopus_import: '1'
series_title: PMLR
status: public
title: 'A natural lottery ticket winner: Reinforcement learning with ordinary neural
circuits'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '7272'
abstract:
- lang: eng
text: "Many systems rely on optimistic concurrent search trees for multi-core scalability.
In principle, optimistic trees have a simple performance story: searches are read-only
and so run in parallel, with writes to shared memory occurring only when modifying
the data structure. However, this paper shows that in practice, obtaining the
full performance benefits of optimistic search trees is not so simple.\r\n\r\nWe
focus on optimistic binary search trees (BSTs) and perform a detailed performance
analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both
microbenchmarks and an in-memory database system. We find and explain significant
unexpected performance differences between BSTs with similar tree structure and
search implementations, which we trace to subtle performance-degrading interactions
of BSTs with systems software and hardware subsystems. We further derive a prescriptive
approach to avoid this performance degradation, as well as algorithmic insights
on optimistic BST design. Our work underlines the gap between the theory and practice
of multi-core performance, and calls for further research to help bridge this
gap."
article_processing_charge: No
author:
- first_name: Maya
full_name: Arbel-Raviv, Maya
last_name: Arbel-Raviv
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Adam
full_name: Morrison, Adam
last_name: Morrison
citation:
ama: 'Arbel-Raviv M, Brown TA, Morrison A. Getting to the root of concurrent binary
search tree performance. In: Proceedings of the 2018 USENIX Annual Technical
Conference. USENIX Association; 2020:295-306.'
apa: 'Arbel-Raviv, M., Brown, T. A., & Morrison, A. (2020). Getting to the root
of concurrent binary search tree performance. In Proceedings of the 2018 USENIX
Annual Technical Conference (pp. 295–306). Boston, MA, United States: USENIX
Association.'
chicago: Arbel-Raviv, Maya, Trevor A Brown, and Adam Morrison. “Getting to the Root
of Concurrent Binary Search Tree Performance.” In Proceedings of the 2018 USENIX
Annual Technical Conference, 295–306. USENIX Association, 2020.
ieee: M. Arbel-Raviv, T. A. Brown, and A. Morrison, “Getting to the root of concurrent
binary search tree performance,” in Proceedings of the 2018 USENIX Annual Technical
Conference, Boston, MA, United States, 2020, pp. 295–306.
ista: 'Arbel-Raviv M, Brown TA, Morrison A. 2020. Getting to the root of concurrent
binary search tree performance. Proceedings of the 2018 USENIX Annual Technical
Conference. USENIX: Annual Technical Conference, 295–306.'
mla: Arbel-Raviv, Maya, et al. “Getting to the Root of Concurrent Binary Search
Tree Performance.” Proceedings of the 2018 USENIX Annual Technical Conference,
USENIX Association, 2020, pp. 295–306.
short: M. Arbel-Raviv, T.A. Brown, A. Morrison, in:, Proceedings of the 2018 USENIX
Annual Technical Conference, USENIX Association, 2020, pp. 295–306.
conference:
end_date: 2018-07-13
location: Boston, MA, United States
name: 'USENIX: Annual Technical Conference'
start_date: 2018-07-11
date_created: 2020-01-14T07:27:08Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2021-01-11T15:25:48Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.usenix.org/system/files/conference/atc18/atc18-arbel-raviv.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 295-306
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Proceedings of the 2018 USENIX Annual Technical Conference
publication_identifier:
isbn:
- '9781939133021'
publication_status: published
publisher: USENIX Association
quality_controlled: '1'
scopus_import: '1'
status: public
title: Getting to the root of concurrent binary search tree performance
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7346'
abstract:
- lang: eng
text: 'The Price of Anarchy (PoA) is a well-established game-theoretic concept to
shed light on coordination issues arising in open distributed systems. Leaving
agents to selfishly optimize comes with the risk of ending up in sub-optimal states
(in terms of performance and/or costs), compared to a centralized system design.
However, the PoA relies on strong assumptions about agents'' rationality (e.g.,
resources and information) and interactions, whereas in many distributed systems
agents interact locally with bounded resources. They do so repeatedly over time
(in contrast to "one-shot games"), and their strategies may evolve. Using a more
realistic evolutionary game model, this paper introduces a realized evolutionary
Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection
in dynamic distributed systems with multiple equilibria, based on local interactions
of simple memoryless agents. Considering a fundamental game related to virus propagation
on networks, we present analytical bounds on the ePoA in basic network topologies
and for different strategy update dynamics. In particular, deriving stationary
distributions of the stochastic evolutionary process, we find that the Nash equilibria
are not always the most abundant states, and that different processes can feature
significant off-equilibrium behavior, leading to a significantly higher ePoA compared
to the PoA studied traditionally in the literature. '
alternative_title:
- LIPIcs
article_number: '21'
article_processing_charge: No
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Schmid L, Chatterjee K, Schmid S. The evolutionary price of anarchy: Locally
bounded agents in a dynamic virus game. In: Proceedings of the 23rd International
Conference on Principles of Distributed Systems. Vol 153. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.OPODIS.2019.21'
apa: 'Schmid, L., Chatterjee, K., & Schmid, S. (2020). The evolutionary price
of anarchy: Locally bounded agents in a dynamic virus game. In Proceedings
of the 23rd International Conference on Principles of Distributed Systems
(Vol. 153). Neuchâtel, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.OPODIS.2019.21'
chicago: 'Schmid, Laura, Krishnendu Chatterjee, and Stefan Schmid. “The Evolutionary
Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” In Proceedings
of the 23rd International Conference on Principles of Distributed Systems,
Vol. 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.OPODIS.2019.21.'
ieee: 'L. Schmid, K. Chatterjee, and S. Schmid, “The evolutionary price of anarchy:
Locally bounded agents in a dynamic virus game,” in Proceedings of the 23rd
International Conference on Principles of Distributed Systems, Neuchâtel,
Switzerland, 2020, vol. 153.'
ista: 'Schmid L, Chatterjee K, Schmid S. 2020. The evolutionary price of anarchy:
Locally bounded agents in a dynamic virus game. Proceedings of the 23rd International
Conference on Principles of Distributed Systems. OPODIS: International Conference
on Principles of Distributed Systems, LIPIcs, vol. 153, 21.'
mla: 'Schmid, Laura, et al. “The Evolutionary Price of Anarchy: Locally Bounded
Agents in a Dynamic Virus Game.” Proceedings of the 23rd International Conference
on Principles of Distributed Systems, vol. 153, 21, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2020, doi:10.4230/LIPIcs.OPODIS.2019.21.'
short: L. Schmid, K. Chatterjee, S. Schmid, in:, Proceedings of the 23rd International
Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2020.
conference:
end_date: 2019-12-19
location: Neuchâtel, Switzerland
name: 'OPODIS: International Conference on Principles of Distributed Systems'
start_date: 2019-12-17
date_created: 2020-01-21T16:00:26Z
date_published: 2020-02-10T00:00:00Z
date_updated: 2023-02-23T13:05:49Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.OPODIS.2019.21
external_id:
arxiv:
- '1906.00110'
file:
- access_level: open_access
checksum: 9a91916ac2c21ab42458fcda39ef0b8d
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T09:14:06Z
date_updated: 2020-07-14T12:47:56Z
file_id: '7608'
file_name: 2019_LIPIcS_Schmid.pdf
file_size: 630752
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 153'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the 23rd International Conference on Principles of Distributed
Systems
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The evolutionary price of anarchy: Locally bounded agents in a dynamic virus
game'
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: 153
year: '2020'
...
---
_id: '7348'
abstract:
- lang: eng
text: 'The monitoring of event frequencies can be used to recognize behavioral anomalies,
to identify trends, and to deduce or discard hypotheses about the underlying system.
For example, the performance of a web server may be monitored based on the ratio
of the total count of requests from the least and most active clients. Exact frequency
monitoring, however, can be prohibitively expensive; in the above example it would
require as many counters as there are clients. In this paper, we propose the efficient
probabilistic monitoring of common frequency properties, including the mode (i.e.,
the most common event) and the median of an event sequence. We define a logic
to express composite frequency properties as a combination of atomic frequency
properties. Our main contribution is an algorithm that, under suitable probabilistic
assumptions, can be used to monitor these important frequency properties with
four counters, independent of the number of different events. Our algorithm samples
longer and longer subwords of an infinite event sequence. We prove the almost-sure
convergence of our algorithm by generalizing ergodic theory from increasing-length
prefixes to increasing-length subwords of an infinite sequence. A similar algorithm
could be used to learn a connected Markov chain of a given structure from observing
its outputs, to arbitrary precision, for a given confidence. '
alternative_title:
- LIPIcs
article_number: '20'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
citation:
ama: 'Ferrere T, Henzinger TA, Kragl B. Monitoring event frequencies. In: 28th
EACSL Annual Conference on Computer Science Logic. Vol 152. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.CSL.2020.20'
apa: 'Ferrere, T., Henzinger, T. A., & Kragl, B. (2020). Monitoring event frequencies.
In 28th EACSL Annual Conference on Computer Science Logic (Vol. 152). Barcelona,
Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2020.20'
chicago: Ferrere, Thomas, Thomas A Henzinger, and Bernhard Kragl. “Monitoring Event
Frequencies.” In 28th EACSL Annual Conference on Computer Science Logic,
Vol. 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.CSL.2020.20.
ieee: T. Ferrere, T. A. Henzinger, and B. Kragl, “Monitoring event frequencies,”
in 28th EACSL Annual Conference on Computer Science Logic, Barcelona, Spain,
2020, vol. 152.
ista: 'Ferrere T, Henzinger TA, Kragl B. 2020. Monitoring event frequencies. 28th
EACSL Annual Conference on Computer Science Logic. CSL: Computer Science Logic,
LIPIcs, vol. 152, 20.'
mla: Ferrere, Thomas, et al. “Monitoring Event Frequencies.” 28th EACSL Annual
Conference on Computer Science Logic, vol. 152, 20, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2020, doi:10.4230/LIPIcs.CSL.2020.20.
short: T. Ferrere, T.A. Henzinger, B. Kragl, in:, 28th EACSL Annual Conference on
Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.
conference:
end_date: 2020-01-16
location: Barcelona, Spain
name: 'CSL: Computer Science Logic'
start_date: 2020-01-13
date_created: 2020-01-21T11:22:21Z
date_published: 2020-01-15T00:00:00Z
date_updated: 2021-01-12T08:13:12Z
day: '15'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CSL.2020.20
external_id:
arxiv:
- '1910.06097'
file:
- access_level: open_access
checksum: b9a691d658d075c6369d3304d17fb818
content_type: application/pdf
creator: bkragl
date_created: 2020-01-21T11:21:04Z
date_updated: 2020-07-14T12:47:56Z
file_id: '7349'
file_name: main.pdf
file_size: 617206
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 152'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 28th EACSL Annual Conference on Computer Science Logic
publication_identifier:
isbn:
- '9783959771320'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Monitoring event frequencies
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: 152
year: '2020'
...
---
_id: '7567'
abstract:
- lang: eng
text: Coxeter triangulations are triangulations of Euclidean space based on a single
simplex. By this we mean that given an individual simplex we can recover the entire
triangulation of Euclidean space by inductively reflecting in the faces of the
simplex. In this paper we establish that the quality of the simplices in all Coxeter
triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate
the Delaunay property for these triangulations. Moreover, we consider an extension
of the Delaunay property, namely protection, which is a measure of non-degeneracy
of a Delaunay triangulation. In particular, one family of Coxeter triangulations
achieves the protection O(1/d2). We conjecture that both bounds are optimal for
triangulations in Euclidean space.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Aruni
full_name: Choudhary, Aruni
last_name: Choudhary
- first_name: Siargey
full_name: Kachanovich, Siargey
last_name: Kachanovich
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Choudhary A, Kachanovich S, Wintraecken M. Coxeter triangulations have good
quality. Mathematics in Computer Science. 2020;14:141-176. doi:10.1007/s11786-020-00461-5
apa: Choudhary, A., Kachanovich, S., & Wintraecken, M. (2020). Coxeter triangulations
have good quality. Mathematics in Computer Science. Springer Nature. https://doi.org/10.1007/s11786-020-00461-5
chicago: Choudhary, Aruni, Siargey Kachanovich, and Mathijs Wintraecken. “Coxeter
Triangulations Have Good Quality.” Mathematics in Computer Science. Springer
Nature, 2020. https://doi.org/10.1007/s11786-020-00461-5.
ieee: A. Choudhary, S. Kachanovich, and M. Wintraecken, “Coxeter triangulations
have good quality,” Mathematics in Computer Science, vol. 14. Springer
Nature, pp. 141–176, 2020.
ista: Choudhary A, Kachanovich S, Wintraecken M. 2020. Coxeter triangulations have
good quality. Mathematics in Computer Science. 14, 141–176.
mla: Choudhary, Aruni, et al. “Coxeter Triangulations Have Good Quality.” Mathematics
in Computer Science, vol. 14, Springer Nature, 2020, pp. 141–76, doi:10.1007/s11786-020-00461-5.
short: A. Choudhary, S. Kachanovich, M. Wintraecken, Mathematics in Computer Science
14 (2020) 141–176.
date_created: 2020-03-05T13:30:18Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2021-01-12T08:14:13Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s11786-020-00461-5
ec_funded: 1
file:
- access_level: open_access
checksum: 1d145f3ab50ccee735983cb89236e609
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T10:18:02Z
date_updated: 2020-11-20T10:18:02Z
file_id: '8783'
file_name: 2020_MathCompScie_Choudhary.pdf
file_size: 872275
relation: main_file
success: 1
file_date_updated: 2020-11-20T10:18:02Z
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 141-176
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Mathematics in Computer Science
publication_identifier:
eissn:
- 1661-8289
issn:
- 1661-8270
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coxeter triangulations have good quality
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: 14
year: '2020'
...
---
_id: '7594'
abstract:
- lang: eng
text: The concept of the entanglement between spin and orbital degrees of freedom
plays a crucial role in our understanding of various phases and exotic ground
states in a broad class of materials, including orbitally ordered materials and
spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator
depends on the value of the spin-orbit coupling of the relativistic origin. To
this end, we numerically diagonalize a one-dimensional spin-orbital model with
Kugel-Khomskii exchange interactions between spins and orbitals on different sites
supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit
coupling with regard to the spin-orbital exchange, the ground state to a large
extent resembles the one obtained in the limit of vanishing spin-orbit coupling.
On the other hand, for large spin-orbit coupling the ground state can, depending
on the model parameters, either still show negligible spin-orbital entanglement
or evolve to a highly spin-orbitally-entangled phase with completely distinct
properties that are described by an effective XXZ model. The presented results
suggest that (i) the spin-orbital entanglement may be induced by large on-site
spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates;
(ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as,
e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground
state can, in the first order of perturbation theory, be neglected.
article_number: '013353'
article_processing_charge: No
article_type: original
author:
- first_name: Dorota
full_name: Gotfryd, Dorota
last_name: Gotfryd
- first_name: Ekaterina
full_name: Paerschke, Ekaterina
id: 8275014E-6063-11E9-9B7F-6338E6697425
last_name: Paerschke
orcid: 0000-0003-0853-8182
- first_name: Jiri
full_name: Chaloupka, Jiri
last_name: Chaloupka
- first_name: Andrzej M.
full_name: Oles, Andrzej M.
last_name: Oles
- first_name: Krzysztof
full_name: Wohlfeld, Krzysztof
last_name: Wohlfeld
citation:
ama: Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. How spin-orbital
entanglement depends on the spin-orbit coupling in a Mott insulator. Physical
Review Research. 2020;2(1). doi:10.1103/PhysRevResearch.2.013353
apa: Gotfryd, D., Paerschke, E., Chaloupka, J., Oles, A. M., & Wohlfeld, K.
(2020). How spin-orbital entanglement depends on the spin-orbit coupling in a
Mott insulator. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.2.013353
chicago: Gotfryd, Dorota, Ekaterina Paerschke, Jiri Chaloupka, Andrzej M. Oles,
and Krzysztof Wohlfeld. “How Spin-Orbital Entanglement Depends on the Spin-Orbit
Coupling in a Mott Insulator.” Physical Review Research. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevResearch.2.013353.
ieee: D. Gotfryd, E. Paerschke, J. Chaloupka, A. M. Oles, and K. Wohlfeld, “How
spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator,”
Physical Review Research, vol. 2, no. 1. American Physical Society, 2020.
ista: Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. 2020. How spin-orbital
entanglement depends on the spin-orbit coupling in a Mott insulator. Physical
Review Research. 2(1), 013353.
mla: Gotfryd, Dorota, et al. “How Spin-Orbital Entanglement Depends on the Spin-Orbit
Coupling in a Mott Insulator.” Physical Review Research, vol. 2, no. 1,
013353, American Physical Society, 2020, doi:10.1103/PhysRevResearch.2.013353.
short: D. Gotfryd, E. Paerschke, J. Chaloupka, A.M. Oles, K. Wohlfeld, Physical
Review Research 2 (2020).
date_created: 2020-03-20T15:21:10Z
date_published: 2020-03-20T00:00:00Z
date_updated: 2021-01-12T08:14:23Z
day: '20'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.2.013353
ec_funded: 1
file:
- access_level: open_access
checksum: 1be551fd5f5583635076017d7391ffdc
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T10:18:38Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7610'
file_name: 2020_PhysRevResearch_Gotfryd.pdf
file_size: 1436735
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: How spin-orbital entanglement depends on the spin-orbit coupling in a Mott
insulator
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: 2
year: '2020'
...
---
_id: '7605'
abstract:
- lang: eng
text: 'Union-Find (or Disjoint-Set Union) is one of the fundamental problems in
computer science; it has been well-studied from both theoretical and practical
perspectives in the sequential case. Recently, there has been mounting interest
in analyzing this problem in the concurrent scenario, and several asymptotically-efficient
algorithms have been proposed. Yet, to date, there is very little known about
the practical performance of concurrent Union-Find. This work addresses this gap.
We evaluate and analyze the performance of several concurrent Union-Find algorithms
and optimization strategies across a wide range of platforms (Intel, AMD, and
ARM) and workloads (social, random, and road networks, as well as integrations
into more complex algorithms). We first observe that, due to the limited computational
cost, the number of induced cache misses is the critical determining factor for
the performance of existing algorithms. We introduce new techniques to reduce
this cost by storing node priorities implicitly and by using plain reads and writes
in a way that does not affect the correctness of the algorithms. Finally, we show
that Union-Find implementations are an interesting application for Transactional
Memory (TM): one of the fastest algorithm variants we discovered is a sequential
one that uses coarse-grained locking with the lock elision optimization to reduce
synchronization cost and increase scalability. '
alternative_title:
- LIPIcs
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: Alexander
full_name: Fedorov, Alexander
last_name: Fedorov
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
citation:
ama: 'Alistarh D-A, Fedorov A, Koval N. In search of the fastest concurrent union-find
algorithm. In: 23rd International Conference on Principles of Distributed Systems.
Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020:15:1-15:16. doi:10.4230/LIPIcs.OPODIS.2019.15'
apa: 'Alistarh, D.-A., Fedorov, A., & Koval, N. (2020). In search of the fastest
concurrent union-find algorithm. In 23rd International Conference on Principles
of Distributed Systems (Vol. 153, p. 15:1-15:16). Neuchatal, Switzerland:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2019.15'
chicago: Alistarh, Dan-Adrian, Alexander Fedorov, and Nikita Koval. “In Search of
the Fastest Concurrent Union-Find Algorithm.” In 23rd International Conference
on Principles of Distributed Systems, 153:15:1-15:16. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2020. https://doi.org/10.4230/LIPIcs.OPODIS.2019.15.
ieee: D.-A. Alistarh, A. Fedorov, and N. Koval, “In search of the fastest concurrent
union-find algorithm,” in 23rd International Conference on Principles of Distributed
Systems, Neuchatal, Switzerland, 2020, vol. 153, p. 15:1-15:16.
ista: 'Alistarh D-A, Fedorov A, Koval N. 2020. In search of the fastest concurrent
union-find algorithm. 23rd International Conference on Principles of Distributed
Systems. OPODIS: International Conference on Principles of Distributed Systems,
LIPIcs, vol. 153, 15:1-15:16.'
mla: Alistarh, Dan-Adrian, et al. “In Search of the Fastest Concurrent Union-Find
Algorithm.” 23rd International Conference on Principles of Distributed Systems,
vol. 153, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16,
doi:10.4230/LIPIcs.OPODIS.2019.15.
short: D.-A. Alistarh, A. Fedorov, N. Koval, in:, 23rd International Conference
on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2020, p. 15:1-15:16.
conference:
end_date: 2019-12-19
location: Neuchatal, Switzerland
name: 'OPODIS: International Conference on Principles of Distributed Systems'
start_date: 2019-12-17
date_created: 2020-03-22T23:00:46Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-02-23T13:12:12Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2019.15
external_id:
arxiv:
- '1911.06347'
file:
- access_level: open_access
checksum: d66f07ecb609d9f02433e39f80a447e9
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T09:22:48Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7609'
file_name: 2019_LIPIcs_Alistarh.pdf
file_size: 13074131
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 153'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 15:1-15:16
publication: 23rd International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959771337'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: In search of the fastest concurrent union-find algorithm
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2020'
...
---
_id: '7601'
abstract:
- lang: eng
text: Plasmodesmata (PD) are crucial structures for intercellular communication
in multicellular plants with remorins being their crucial plant-specific structural
and functional constituents. The PD biogenesis is an intriguing but poorly understood
process. By expressing an Arabidopsis remorin protein in mammalian cells, we have
reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting
neighboring cells physically and physiologically. Notably, RFs are capable of
transporting macromolecules intercellularly, in a way similar to plant PD. With
further super-resolution microscopic analysis and biochemical characterization,
we found that RFs are also composed of actin filaments, forming the core skeleton
structure, aligned with the remorin protein. This unique heterologous filamentous
structure might explain the molecular mechanism for remorin function as well as
PD construction. Furthermore, remorin protein exhibits a specific distribution
manner in the plasma membrane in mammalian cells, representing a lipid nanodomain,
depending on its lipid modification status. Our studies not only provide crucial
insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental
mechanistic and evolutionary links between intercellular communication systems
of plants and animals.
article_processing_charge: No
author:
- first_name: Zhuang
full_name: Wei, Zhuang
last_name: Wei
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Tao
full_name: Liu, Tao
last_name: Liu
- first_name: Yuan
full_name: Wu, Yuan
last_name: Wu
- first_name: Ji-Gang
full_name: Lei, Ji-Gang
last_name: Lei
- first_name: ZhengJun
full_name: Chen, ZhengJun
last_name: Chen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
- first_name: Kan
full_name: Liao, Kan
last_name: Liao
citation:
ama: Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by
plant remorin in animal cells. bioRxiv. 2020. doi:10.1101/791137
apa: Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020).
Plasmodesmata-like intercellular connections by plant remorin in animal cells.
bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/791137
chicago: Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen,
Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections
by Plant Remorin in Animal Cells.” BioRxiv. Cold Spring Harbor Laboratory,
2020. https://doi.org/10.1101/791137.
ieee: Z. Wei et al., “Plasmodesmata-like intercellular connections by plant
remorin in animal cells,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020.
Plasmodesmata-like intercellular connections by plant remorin in animal cells.
bioRxiv, 10.1101/791137.
mla: Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant
Remorin in Animal Cells.” BioRxiv, Cold Spring Harbor Laboratory, 2020,
doi:10.1101/791137.
short: Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K.
Liao, BioRxiv (2020).
date_created: 2020-03-21T16:34:42Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2021-01-12T08:14:26Z
day: '19'
department:
- _id: JiFr
doi: 10.1101/791137
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/791137
month: '02'
oa: 1
oa_version: Preprint
page: '22'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Plasmodesmata-like intercellular connections by plant remorin in animal cells
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7651'
abstract:
- lang: eng
text: The growth of snail shells can be described by simple mathematical rules.
Variation in a few parameters can explain much of the diversity of shell shapes
seen in nature. However, empirical studies of gastropod shell shape variation
typically use geometric morphometric approaches, which do not capture this growth
pattern. We have developed a way to infer a set of developmentally descriptive
shape parameters based on three-dimensional logarithmic helicospiral growth and
using landmarks from two-dimensional shell images as input. We demonstrate the
utility of this approach, and compare it to the geometric morphometric approach,
using a large set of Littorina saxatilis shells in which locally adapted populations
differ in shape. Our method can be modified easily to make it applicable to a
wide range of shell forms, which would allow for investigations of the similarities
and differences between and within many different species of gastropods.
article_number: '20190721'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Larsson, J.
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: S.
full_name: Bengmark, S.
last_name: Bengmark
- first_name: T.
full_name: Lundh, T.
last_name: Lundh
- first_name: R. K.
full_name: Butlin, R. K.
last_name: Butlin
citation:
ama: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive
method for quantifying shape in gastropod shells. Journal of The Royal Society
Interface. 2020;17(163). doi:10.1098/rsif.2019.0721
apa: Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020).
A developmentally descriptive method for quantifying shape in gastropod shells.
Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721
chicago: Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A
Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.”
Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721.
ieee: J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally
descriptive method for quantifying shape in gastropod shells,” Journal of The
Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020.
ista: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally
descriptive method for quantifying shape in gastropod shells. Journal of The Royal
Society Interface. 17(163), 20190721.
mla: Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape
in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17,
no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721.
short: J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of
The Royal Society Interface 17 (2020).
date_created: 2020-04-08T15:19:17Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2021-01-12T08:14:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsif.2019.0721
file:
- access_level: open_access
checksum: 4eb102304402f5c56432516b84df86d6
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T12:31:16Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7660'
file_name: 2020_JournRoyalSociety_Larsson.pdf
file_size: 1556190
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '163'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Journal of The Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
issn:
- 1742-5689
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: 1
status: public
title: A developmentally descriptive method for quantifying shape in gastropod shells
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: 17
year: '2020'
...
---
_id: '7803'
abstract:
- lang: eng
text: "We settle the complexity of the (Δ+1)-coloring and (Δ+1)-list coloring problems
in the CONGESTED CLIQUE model by presenting a simple deterministic algorithm for
both problems running in a constant number of rounds. This matches the complexity
of the recent breakthrough randomized constant-round (Δ+1)-list coloring algorithm
due to Chang et al. (PODC'19), and significantly improves upon the state-of-the-art
O(logΔ)-round deterministic (Δ+1)-coloring bound of Parter (ICALP'18).\r\nA remarkable
property of our algorithm is its simplicity. Whereas the state-of-the-art randomized
algorithms for this problem are based on the quite involved local coloring algorithm
of Chang et al. (STOC'18), our algorithm can be described in just a few lines.
At a high level, it applies a careful derandomization of a recursive procedure
which partitions the nodes and their respective palettes into separate bins. We
show that after O(1) recursion steps, the remaining uncolored subgraph within
each bin has linear size, and thus can be solved locally by collecting it to a
single node. This algorithm can also be implemented in the Massively Parallel
Computation (MPC) model provided that each machine has linear (in n, the number
of nodes in the input graph) space.\r\nWe also show an extension of our algorithm
to the MPC regime in which machines have sublinear space: we present the first
deterministic (Δ+1)-list coloring algorithm designed for sublinear-space MPC,
which runs in O(logΔ+loglogn) rounds."
article_processing_charge: No
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
orcid: 0000-0002-5646-9524
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
citation:
ama: 'Czumaj A, Davies P, Parter M. Simple, deterministic, constant-round coloring
in the congested clique. In: Proceedings of the 2020 ACM Symposium on Principles
of Distributed Computing. Association for Computing Machinery; 2020:309-318.
doi:10.1145/3382734.3405751'
apa: 'Czumaj, A., Davies, P., & Parter, M. (2020). Simple, deterministic, constant-round
coloring in the congested clique. In Proceedings of the 2020 ACM Symposium
on Principles of Distributed Computing (pp. 309–318). Salerno, Italy: Association
for Computing Machinery. https://doi.org/10.1145/3382734.3405751'
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Simple, Deterministic,
Constant-Round Coloring in the Congested Clique.” In Proceedings of the 2020
ACM Symposium on Principles of Distributed Computing, 309–18. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405751.
ieee: A. Czumaj, P. Davies, and M. Parter, “Simple, deterministic, constant-round
coloring in the congested clique,” in Proceedings of the 2020 ACM Symposium
on Principles of Distributed Computing, Salerno, Italy, 2020, pp. 309–318.
ista: 'Czumaj A, Davies P, Parter M. 2020. Simple, deterministic, constant-round
coloring in the congested clique. Proceedings of the 2020 ACM Symposium on Principles
of Distributed Computing. PODC: Symposium on Principles of Distributed Computing,
309–318.'
mla: Czumaj, Artur, et al. “Simple, Deterministic, Constant-Round Coloring in the
Congested Clique.” Proceedings of the 2020 ACM Symposium on Principles of Distributed
Computing, Association for Computing Machinery, 2020, pp. 309–18, doi:10.1145/3382734.3405751.
short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2020 ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery, 2020,
pp. 309–318.
conference:
end_date: 2020-08-07
location: Salerno, Italy
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2020-08-03
date_created: 2020-05-06T09:02:14Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2021-01-12T08:15:37Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3382734.3405751
ec_funded: 1
external_id:
arxiv:
- '2009.06043'
file:
- access_level: open_access
checksum: 46fe4fc58a64eb04068115573f631d4c
content_type: application/pdf
creator: pdavies
date_created: 2020-10-08T08:17:36Z
date_updated: 2020-10-08T08:17:36Z
file_id: '8624'
file_name: ColoringArxiv.pdf
file_size: 520051
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:17:36Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 309-318
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Simple, deterministic, constant-round coloring in the congested clique
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...