---
_id: '9647'
abstract:
- lang: eng
text: 'Gene expression is regulated by the set of transcription factors (TFs) that
bind to the promoter. The ensuing regulating function is often represented as
a combinational logic circuit, where output (gene expression) is determined by
current input values (promoter bound TFs) only. However, the simultaneous arrival
of TFs is a strong assumption, since transcription and translation of genes introduce
intrinsic time delays and there is no global synchronisation among the arrival
times of different molecular species at their targets. We present an experimentally
implementable genetic circuit with two inputs and one output, which in the presence
of small delays in input arrival, exhibits qualitatively distinct population-level
phenotypes, over timescales that are longer than typical cell doubling times.
From a dynamical systems point of view, these phenotypes represent long-lived
transients: although they converge to the same value eventually, they do so after
a very long time span. The key feature of this toy model genetic circuit is that,
despite having only two inputs and one output, it is regulated by twenty-three
distinct DNA-TF configurations, two of which are more stable than others (DNA
looped states), one promoting and another blocking the expression of the output
gene. Small delays in input arrival time result in a majority of cells in the
population quickly reaching the stable state associated with the first input,
while exiting of this stable state occurs at a slow timescale. In order to mechanistically
model the behaviour of this genetic circuit, we used a rule-based modelling language,
and implemented a grid-search to find parameter combinations giving rise to long-lived
transients. Our analysis shows that in the absence of feedback, there exist path-dependent
gene regulatory mechanisms based on the long timescale of transients. The behaviour
of this toy model circuit suggests that gene regulatory networks can exploit event
timing to create phenotypes, and it opens the possibility that they could use
event timing to memorise events, without regulatory feedback. The model reveals
the importance of (i) mechanistically modelling the transitions between the different
DNA-TF states, and (ii) employing transient analysis thereof.'
acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced
Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science,
Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence
2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia
Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences.
Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award).'
article_processing_charge: No
article_type: original
author:
- first_name: Tatjana
full_name: Petrov, Tatjana
last_name: Petrov
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- 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: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in
gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023
apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021).
Long lived transients in gene regulation. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023
chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin
C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.
ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived
transients in gene regulation,” Theoretical Computer Science, vol. 893.
Elsevier, pp. 1–16, 2021.
ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients
in gene regulation. Theoretical Computer Science. 893, 1–16.
mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical
Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.
short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer
Science 893 (2021) 1–16.
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2023-08-10T14:11:19Z
day: '04'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1016/j.tcs.2021.05.023
external_id:
isi:
- '000710180500002'
file:
- access_level: open_access
checksum: d3aef34cfb13e53bba4cf44d01680793
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:13:27Z
date_updated: 2022-05-12T12:13:27Z
file_id: '11364'
file_name: 2021_TheoreticalComputerScience_Petrov.pdf
file_size: 2566504
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:13:27Z
has_accepted_license: '1'
intvolume: ' 893'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1-16
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long lived transients in gene regulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 893
year: '2021'
...
---
_id: '9761'
abstract:
- lang: eng
text: 'The important roles of mitochondrial function and dysfunction in the process
of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear
to be a highly vulnerable neuronal cell type in the central nervous system with
respect to mitochondrial dysfunction but the actual reasons for this are still
incompletely understood. These cells have a unique circumstance where unmyelinated
axons must bend nearly 90° to exit the eye and then cross a translaminar pressure
gradient before becoming myelinated in the optic nerve. This region, the optic
nerve head, contains some of the highest density of mitochondria present in these
cells. Glaucoma represents a perfect storm of events occurring at this location,
with a combination of changes in the translaminar pressure gradient and reassignment
of the metabolic support functions of supporting glia, which appears to apply
increased metabolic stress to the RGC axons leading to a failure of axonal transport
mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations,
particularly in genes affecting mitochondrial dynamics and mitochondrial clearance.
These mutations, which systemically affect the mitochondria in every cell, often
lead to an optic neuropathy as the sole pathologic defect in affected patients.
This review summarizes knowledge of mitochondrial structure and function, the
known energy demands of neurons in general, and places these in the context of
normal and pathological characteristics of mitochondria attributed to RGCs. '
acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for
generously sharing some of their data for this review, and to Janis Eells for helpful
comments on the manuscript.
article_number: '1593'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole A.
full_name: Muench, Nicole A.
last_name: Muench
- first_name: Sonia
full_name: Patel, Sonia
last_name: Patel
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Ryan J.
full_name: Donahue, Ryan J.
last_name: Donahue
- first_name: Akihiro
full_name: Ikeda, Akihiro
last_name: Ikeda
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593
apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells,
R. W. (2021). The influence of mitochondrial dynamics and function on retinal
ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593
chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro
Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071593.
ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells,
“The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.
ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence
of mitochondrial dynamics and function on retinal ganglion cell susceptibility
in optic nerve disease. Cells. 10(7), 1593.
mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function
on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells,
vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.
short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells,
Cells 10 (2021).
date_created: 2021-08-01T22:01:22Z
date_published: 2021-06-25T00:00:00Z
date_updated: 2023-08-10T14:14:53Z
day: '25'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.3390/cells10071593
external_id:
isi:
- '000678193300001'
pmid:
- '34201955'
file:
- access_level: open_access
checksum: e0497ce5c77fa3b65a538c7d6e0f6c66
content_type: application/pdf
creator: cziletti
date_created: 2021-08-04T14:01:30Z
date_updated: 2021-08-04T14:01:30Z
file_id: '9768'
file_name: 2021_Cells_Muench.pdf
file_size: 4555611
relation: main_file
success: 1
file_date_updated: 2021-08-04T14:01:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
eissn:
- '20734409'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of mitochondrial dynamics and function on retinal ganglion cell
susceptibility in optic nerve disease
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9641'
abstract:
- lang: eng
text: At the encounter with a novel environment, contextual memory formation is
greatly enhanced, accompanied with increased arousal and active exploration. Although
this phenomenon has been widely observed in animal and human daily life, how the
novelty in the environment is detected and contributes to contextual memory formation
has lately started to be unveiled. The hippocampus has been studied for many decades
for its largely known roles in encoding spatial memory, and a growing body of
evidence indicates a differential involvement of dorsal and ventral hippocampal
divisions in novelty detection. In this brief review article, we discuss the recent
findings of the role of mossy cells in the ventral hippocampal moiety in novelty
detection and put them in perspective with other novelty-related pathways in the
hippocampus. We propose a mechanism for novelty-driven memory acquisition in the
dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate
granule cells. By this projection, the ventral hippocampus sends novelty signals
to the dorsal hippocampus, opening a gate for memory encoding in dentate granule
cells based on information coming from the entorhinal cortex. We conclude that,
contrary to the presently accepted functional independence, the dorsal and ventral
hippocampi cooperate to link the novelty and contextual information, and this
dorso-ventral interaction is crucial for the novelty-dependent memory formation.
acknowledgement: This work was supported by a European Research Council Advanced Grant
694539 to Ryuichi Shigemoto.
article_number: '107486'
article_processing_charge: No
article_type: original
author:
- first_name: Felipe
full_name: Fredes, Felipe
last_name: Fredes
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection.
Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486
apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells
in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486
chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021.
https://doi.org/10.1016/j.nlm.2021.107486.
ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty
detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.
ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty
detection. Neurobiology of Learning and Memory. 183, 107486.
mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells
in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486,
Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.
short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-06-30T00:00:00Z
date_updated: 2023-08-10T14:10:37Z
day: '30'
ddc:
- '610'
department:
- _id: RySh
doi: 10.1016/j.nlm.2021.107486
ec_funded: 1
external_id:
isi:
- '000677694900004'
pmid:
- '34214666'
file:
- access_level: open_access
checksum: 8e8298a9e8c7df146ad23f32c2a63929
content_type: application/pdf
creator: cziletti
date_created: 2021-07-19T13:46:06Z
date_updated: 2021-07-19T13:46:06Z
file_id: '9694'
file_name: 2021_NeurobLearnMemory_Fredes.pdf
file_size: 1994793
relation: main_file
success: 1
file_date_updated: 2021-07-19T13:46:06Z
has_accepted_license: '1'
intvolume: ' 183'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Neurobiology of Learning and Memory
publication_identifier:
eissn:
- '10959564'
issn:
- '10747427'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of hippocampal mossy cells in novelty detection
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 183
year: '2021'
...
---
_id: '9646'
abstract:
- lang: eng
text: We consider the fundamental problem of deriving quantitative bounds on the
probability that a given assertion is violated in a probabilistic program. We
provide automated algorithms that obtain both lower and upper bounds on the assertion
violation probability. The main novelty of our approach is that we prove new and
dedicated fixed-point theorems which serve as the theoretical basis of our algorithms
and enable us to reason about assertion violation bounds in terms of pre and post
fixed-point functions. To synthesize such fixed-points, we devise algorithms that
utilize a wide range of mathematical tools, including repulsing ranking supermartingales,
Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization.
On the theoretical side, we provide (i) the first automated algorithm for lower-bounds
on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds
of exponential form in affine programs, and (iii) provably and significantly tighter
upper-bounds than the previous approaches. On the practical side, we show our
algorithms can handle a wide variety of programs from the literature and synthesize
bounds that are remarkably tighter than previous results, in some cases by thousands
of orders of magnitude.
acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful
and valuable comments. The work was partially supported by the National Natural
Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research
Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and
DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).'
article_processing_charge: No
author:
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of
assertion violations in probabilistic programs. In: Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102'
apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021).
Quantitative analysis of assertion violations in probabilistic programs. In Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 1171–1186). Online: Association for Computing Machinery.
https://doi.org/10.1145/3453483.3454102'
chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.”
In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 1171–86. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454102.
ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative
analysis of assertion violations in probabilistic programs,” in Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Online, 2021, pp. 1171–1186.
ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis
of assertion violations in probabilistic programs. Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 1171–1186.'
mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic
Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on
Programming Language Design and Implementation, Association for Computing
Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.
short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:18Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:14:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454102
ec_funded: 1
external_id:
arxiv:
- '2011.14617'
isi:
- '000723661700076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.14617
month: '06'
oa: 1
oa_version: Preprint
page: 1171-1186
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative analysis of assertion violations in probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9645'
abstract:
- lang: eng
text: "We consider the fundamental problem of reachability analysis over imperative
programs with real variables. Previous works that tackle reachability are either
unable to handle programs consisting of general loops (e.g. symbolic execution),
or lack completeness guarantees (e.g. abstract interpretation), or are not automated
(e.g. incorrectness logic). In contrast, we propose a novel approach for reachability
analysis that can handle general and complex loops, is complete, and can be entirely
automated for a wide family of programs. Through the notion of Inductive Reachability
Witnesses (IRWs), our approach extends ideas from both invariant generation and
termination to reachability analysis.\r\n\r\nWe first show that our IRW-based
approach is sound and complete for reachability analysis of imperative programs.
Then, we focus on linear and polynomial programs and develop automated methods
for synthesizing linear and polynomial IRWs. In the linear case, we follow the
well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial
case, where we present a push-button semi-complete algorithm. We achieve this
using a novel combination of classical theorems in real algebraic geometry, such
as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally,
our experimental results show we can prove complex reachability objectives over
various benchmarks that were beyond the reach of previous methods."
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the
Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC
Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Mohammad
full_name: Mahdavi, Mohammad
last_name: Mahdavi
citation:
ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability
witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076'
apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021).
Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd
ACM SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076'
chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady,
and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 772–87. Association for Computing Machinery,
2021. https://doi.org/10.1145/3453483.3454076.
ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial
reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN
International Conference on Programming Language Design and Implementation,
Online, 2021, pp. 772–787.
ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability
witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 772–787.'
mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–87,
doi:10.1145/3453483.3454076.
short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 772–787.
conference:
end_date: 2021-06-26
location: Online
name: ' PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T14:13:39Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454076
ec_funded: 1
external_id:
isi:
- '000723661700050'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-03183862/
month: '06'
oa: 1
oa_version: Submitted Version
page: 772-787
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polynomial reachability witnesses via Stellensätze
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9759'
acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable
comments on an earlier version of the manuscript. We also thank the facilitators
of the 2019–2020 eLife Community Ambassador program.
article_number: e1009124
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Michael John
full_name: Bartlett, Michael John
last_name: Bartlett
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Adriana
full_name: Bankston, Adriana
last_name: Bankston
- first_name: Sarvenaz
full_name: Sarabipour, Sarvenaz
last_name: Sarabipour
citation:
ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve
academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124
apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021).
Ten simple rules to improve academic work- life balance. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124
chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz
Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS
Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.
ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple
rules to improve academic work- life balance,” PLoS Computational Biology,
vol. 17, no. 7. Public Library of Science, 2021.
ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to
improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.
mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work-
Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public
Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.
short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational
Biology 17 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-08-10T14:16:46Z
day: '15'
ddc:
- '613'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1009124
external_id:
isi:
- '000677713500008'
pmid:
- '34264932'
file:
- access_level: open_access
checksum: e56d91f0eeadb36f143a90e2c1b3ab63
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-05T12:06:49Z
date_updated: 2021-08-05T12:06:49Z
file_id: '9771'
file_name: 2021_PlosCompBio_Bartlett.pdf
file_size: 693633
relation: main_file
file_date_updated: 2021-08-05T12:06:49Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- '15537358'
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
scopus_import: '1'
status: public
title: Ten simple rules to improve academic work- life balance
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: 17
year: '2021'
...
---
_id: '9822'
abstract:
- lang: eng
text: Attachment of adhesive molecules on cell culture surfaces to restrict cell
adhesion to defined areas and shapes has been vital for the progress of in vitro
research. In currently existing patterning methods, a combination of pattern properties
such as stability, precision, specificity, high-throughput outcome, and spatiotemporal
control is highly desirable but challenging to achieve. Here, we introduce a versatile
and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent
patterning step and a subsequent functionalization of the pattern via click chemistry.
This two-step process is feasible on arbitrary surfaces and allows for generation
of sustainable patterns and gradients. The method is validated in different biological
systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining
the growth and migration of cells to the designated areas. We then implement a
sequential photopatterning approach by adding a second switchable patterning step,
allowing for spatiotemporal control over two distinct surface patterns. As a proof
of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis.
Our results show that the spatiotemporal control provided by our “sequential photopatterning”
system is essential for mimicking dynamic biological processes and that our innovative
approach has great potential for further applications in cell science.
acknowledgement: We would like to thank Charlott Leu for the production of our chromium
wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh
Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim
Rädler for his valuable scientific guidance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Miriam
full_name: Balles, Miriam
last_name: Balles
- first_name: Maibritt
full_name: Kretschmer, Maibritt
last_name: Kretschmer
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Janina
full_name: Lange, Janina
last_name: Lange
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for
studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R.
P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular
processes under spatiotemporal control. ACS Applied Materials and Interfaces.
American Chemical Society. https://doi.org/10.1021/acsami.1c09850
chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria
Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning
for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied
Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
ieee: T. Zisis et al., “Sequential and switchable patterning for studying
cellular processes under spatiotemporal control,” ACS Applied Materials and
Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.
ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild
R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning
for studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 13(30), 35545–35560.
mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying
Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and
Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560,
doi:10.1021/acsami.1c09850.
short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait,
R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials
and Interfaces 13 (2021) 35545–35560.
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-10T14:22:48Z
day: '04'
ddc:
- '620'
- '570'
department:
- _id: MiSi
- _id: GaTk
- _id: Bio
- _id: CaGu
doi: 10.1021/acsami.1c09850
ec_funded: 1
external_id:
isi:
- '000683741400026'
pmid:
- '34283577'
file:
- access_level: open_access
checksum: b043a91d9f9200e467b970b692687ed3
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:44:03Z
date_updated: 2021-08-09T09:44:03Z
file_id: '9833'
file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf
file_size: 7123293
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:44:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '30'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 35545–35560
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential and switchable patterning for studying cellular processes under
spatiotemporal control
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2021'
...
---
_id: '9819'
abstract:
- lang: eng
text: Photorealistic editing of head portraits is a challenging task as humans are
very sensitive to inconsistencies in faces. We present an approach for high-quality
intuitive editing of the camera viewpoint and scene illumination (parameterised
with an environment map) in a portrait image. This requires our method to capture
and control the full reflectance field of the person in the image. Most editing
approaches rely on supervised learning using training data captured with setups
such as light and camera stages. Such datasets are expensive to acquire, not readily
available and do not capture all the rich variations of in-the-wild portrait images.
In addition, most supervised approaches only focus on relighting, and do not allow
camera viewpoint editing. Thus, they only capture and control a subset of the
reflectance field. Recently, portrait editing has been demonstrated by operating
in the generative model space of StyleGAN. While such approaches do not require
direct supervision, there is a significant loss of quality when compared to the
supervised approaches. In this paper, we present a method which learns from limited
supervised training data. The training images only include people in a fixed neutral
expression with eyes closed, without much hair or background variations. Each
person is captured under 150 one-light-at-a-time conditions and under 8 camera
poses. Instead of training directly in the image space, we design a supervised
problem which learns transformations in the latent space of StyleGAN. This combines
the best of supervised learning and generative adversarial modeling. We show that
the StyleGAN prior allows for generalisation to different expressions, hairstyles
and backgrounds. This produces high-quality photorealistic results for in-the-wild
images and significantly outperforms existing methods. Our approach can edit the
illumination and pose simultaneously, and runs at interactive rates.
acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784).
We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng
Sun for kindly helping us with the comparisons with Sun et al. [2019].
article_number: '44'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Abdallah
full_name: Dib, Abdallah
last_name: Dib
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Louis
full_name: Chevallier, Louis
last_name: Chevallier
- first_name: Mohamed A.
full_name: Elgharib, Mohamed A.
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance
editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765'
apa: 'Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel,
H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head
portraits. ACM Transactions on Graphics. Association for Computing Machinery.
https://doi.org/10.1145/3450626.3459765'
chicago: 'Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel,
Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance
Editing of Head Portraits.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.'
ieee: 'B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing
of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association
for Computing Machinery, 2021.'
ista: 'Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister
H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic
appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.'
mla: 'Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of
Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association
for Computing Machinery, 2021, doi:10.1145/3450626.3459765.'
short: B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel,
H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:25:08Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3450626.3459765
external_id:
arxiv:
- '2103.07658'
isi:
- '000674930900011'
file:
- access_level: open_access
checksum: 51b61b7e5c175e2d7ed8fa3b35f7525a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:41:50Z
date_updated: 2021-08-09T11:41:50Z
file_id: '9834'
file_name: 2021_ACMTransactionsOnGraphics_Mallikarjun.pdf
file_size: 49840741
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:41:50Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PhotoApp: Photorealistic appearance editing of head portraits'
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: '9816'
abstract:
- lang: eng
text: "Aims: Mass antigen testing programs have been challenged because of an alleged
insufficient specificity, leading to a large number of false positives. The objective
of this study is to derive a lower bound of the specificity of the SD Biosensor
Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data
from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020
we calculate a lower confidence bound for the specificity. As positive test results
were not systematically verified by PCR tests, we base the lower bound on a worst
case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332
persons from 79 counties were tested. The lowest positivity rate was observed
in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This
implies a test specificity of at least 99.6% (97.5% one-sided lower confidence
bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests
a higher specificity compared to earlier studies in spite of the underlying worst
case assumption and the application in a mass testing setting. The actual specificity
is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible
at the time of testing. To our knowledge, this estimate constitutes the first
bound obtained from large scale practical use of an antigen test."
acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová
for very helpful comments. We also thank Matej Mišík for discussion and information
regarding the Slovak testing data and Ag-Test used.
article_number: e0255267
article_processing_charge: Yes
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Mathias
full_name: Beiglböck, Mathias
last_name: Beiglböck
- first_name: Anna Nele
full_name: Herdina, Anna Nele
last_name: Herdina
- first_name: Robert
full_name: Strassl, Robert
last_name: Strassl
- first_name: Martin
full_name: Posch, Martin
last_name: Posch
citation:
ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis
of the specificity of a COVID-19 antigen test in the Slovak mass testing program.
PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267
apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &
Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the
Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267
chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina,
Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen
Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0255267.
ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch,
“Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021.
Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program. PLoS ONE. 16(7), e0255267.
mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test
in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267,
Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.
short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2023-08-10T14:26:32Z
day: '29'
ddc:
- '610'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0255267
external_id:
isi:
- '000685248200095'
pmid:
- '34324553'
file:
- access_level: open_access
checksum: ae4df60eb62f4491278588548d0c1f93
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T11:52:14Z
date_updated: 2021-08-09T11:52:14Z
file_id: '9835'
file_name: 2021_PLoSONE_Hledík.pdf
file_size: 773921
relation: main_file
success: 1
file_date_updated: 2021-08-09T11:52:14Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
program
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: 16
year: '2021'
...
---
_id: '9821'
abstract:
- lang: eng
text: Heart rate variability (hrv) is a physiological phenomenon of the variation
in the length of the time interval between consecutive heartbeats. In many cases
it could be an indicator of the development of pathological states. The classical
approach to the analysis of hrv includes time domain methods and frequency domain
methods. However, attempts are still being made to define new and more effective
hrv assessment tools. Persistent homology is a novel data analysis tool developed
in the recent decades that is rooted at algebraic topology. The Topological Data
Analysis (TDA) approach focuses on examining the shape of the data in terms of
connectedness and holes, and has recently proved to be very effective in various
fields of research. In this paper we propose the use of persistent homology to
the hrv analysis. We recall selected topological descriptors used in the literature
and we introduce some new topological descriptors that reflect the specificity
of hrv, and we discuss their relation to the standard hrv measures. In particular,
we show that this novel approach provides a collection of indices that might be
at least as useful as the classical parameters in differentiating between series
of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering
from a stroke episode.
acknowledgement: We express our gratitude to the anonymous referees who provided constructive
comments that helped us improve the quality of the paper.
article_number: e0253851
article_processing_charge: Yes
article_type: original
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Beata
full_name: Graff, Beata
last_name: Graff
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Dariusz
full_name: Gąsecki, Dariusz
last_name: Gąsecki
- first_name: Krzysztof
full_name: Narkiewicz, Krzysztof
last_name: Narkiewicz
citation:
ama: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent
homology as a new method of the assessment of heart rate variability. PLoS
ONE. 2021;16(7). doi:10.1371/journal.pone.0253851
apa: Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz,
K. (2021). Persistent homology as a new method of the assessment of heart rate
variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851
chicago: Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz
Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the
Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0253851.
ieee: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz,
“Persistent homology as a new method of the assessment of heart rate variability,”
PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.
ista: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021.
Persistent homology as a new method of the assessment of heart rate variability.
PLoS ONE. 16(7), e0253851.
mla: Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment
of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public
Library of Science, 2021, doi:10.1371/journal.pone.0253851.
short: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz,
PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:21:42Z
day: '01'
ddc:
- '006'
department:
- _id: HeEd
doi: 10.1371/journal.pone.0253851
external_id:
isi:
- '000678124900050'
pmid:
- '34292957'
file:
- access_level: open_access
checksum: 0277aa155d5db1febd2cb384768bba5f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:25:41Z
date_updated: 2021-08-09T09:25:41Z
file_id: '9832'
file_name: 2021_PLoSONE_Graff.pdf
file_size: 2706919
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:25:41Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent homology as a new method of the assessment of heart rate variability
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: 16
year: '2021'
...
---
_id: '9820'
abstract:
- lang: eng
text: Material appearance hinges on material reflectance properties but also surface
geometry and illumination. The unlimited number of potential combinations between
these factors makes understanding and predicting material appearance a very challenging
task. In this work, we collect a large-scale dataset of perceptual ratings of
appearance attributes with more than 215,680 responses for 42,120 distinct combinations
of material, shape, and illumination. The goal of this dataset is twofold. First,
we analyze for the first time the effects of illumination and geometry in material
perception across such a large collection of varied appearances. We connect our
findings to those of the literature, discussing how previous knowledge generalizes
across very diverse materials, shapes, and illuminations. Second, we use the collected
dataset to train a deep learning architecture for predicting perceptual attributes
that correlate with human judgments. We demonstrate the consistent and robust
behavior of our predictor in various challenging scenarios, which, for the first
time, enables estimating perceived material attributes from general 2D images.
Since our predictor relies on the final appearance in an image, it can compare
appearance properties across different geometries and illumination conditions.
Finally, we demonstrate several applications that use our predictor, including
appearance reproduction using 3D printing, BRDF editing by integrating our predictor
in a differentiable renderer, illumination design, or material recommendations
for scene design.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement
Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement
Nº 804226 (PERDY).
article_number: '125'
article_processing_charge: No
article_type: original
author:
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
citation:
ama: 'Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on
material perception: Model and applications. ACM Transactions on Graphics.
2021;40(4). doi:10.1145/3450626.3459813'
apa: 'Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &
Myszkowski, K. (2021). The effect of shape and illumination on material perception:
Model and applications. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3450626.3459813'
chicago: 'Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel,
Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material
Perception: Model and Applications.” ACM Transactions on Graphics. Association
for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.'
ieee: 'A. Serrano et al., “The effect of shape and illumination on material
perception: Model and applications,” ACM Transactions on Graphics, vol.
40, no. 4. Association for Computing Machinery, 2021.'
ista: 'Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K.
2021. The effect of shape and illumination on material perception: Model and applications.
ACM Transactions on Graphics. 40(4), 125.'
mla: 'Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception:
Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4,
125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.'
short: A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski,
ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:20:10Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/3450626.3459813
external_id:
isi:
- '000674930900090'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://zaguan.unizar.es/record/110704/files/texto_completo.pdf
month: '08'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The effect of shape and illumination on material perception: Model and applications'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9818'
abstract:
- lang: eng
text: Triangle mesh-based simulations are able to produce satisfying animations
of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level
simulations. Naive texturing approaches do not consider yarn-level physics, while
full yarn-level simulations may become prohibitively expensive for large garments.
We propose a method to animate yarn-level cloth geometry on top of an underlying
deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate
precomputed yarn geometry, we are able to reproduce effects such as knit loops
tightening under stretching. In combination with precomputed mesh animation or
real-time mesh simulation, our method is able to animate yarn-level cloth in real-time
at large scales.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback. We also thank
Seddi Labs for providing the garment model with fold-over seams.\r\nThis research
was supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific\r\nComputing. This project has received funding from the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme under grant agreement No. 638176. Rahul Narain is supported
by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc."
article_number: '168'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry.
ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation
of yarn pattern geometry. ACM Transactions on Graphics. Association for
Computing Machinery. https://doi.org/10.1145/3450626.3459816
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for
Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern
geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for
Computing Machinery, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern
geometry. ACM Transactions on Graphics. 40(4), 168.
mla: Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.”
ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing
Machinery, 2021, doi:10.1145/3450626.3459816.
short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).
date_created: 2021-08-08T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
day: '01'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3450626.3459816
ec_funded: 1
external_id:
isi:
- '000674930900132'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3450626.3459816
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/knitting-virtual-yarn/
record:
- id: '12358'
relation: dissertation_contains
status: public
- id: '9327'
relation: software
status: public
scopus_import: '1'
status: public
title: Mechanics-aware deformation of yarn pattern geometry
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9828'
abstract:
- lang: eng
text: Amplitude demodulation is a classical operation used in signal processing.
For a long time, its effective applications in practice have been limited to narrowband
signals. In this work, we generalize amplitude demodulation to wideband signals.
We pose demodulation as a recovery problem of an oversampled corrupted signal
and introduce special iterative schemes belonging to the family of alternating
projection algorithms to solve it. Sensibly chosen structural assumptions on the
demodulation outputs allow us to reveal the high inferential accuracy of the method
over a rich set of relevant signals. This new approach surpasses current state-of-the-art
demodulation techniques apt to wideband signals in computational efficiency by
up to many orders of magnitude with no sacrifice in quality. Such performance
opens the door for applications of the amplitude demodulation procedure in new
contexts. In particular, the new method makes online and large-scale offline data
processing feasible, including the calculation of modulator-carrier pairs in higher
dimensions and poor sampling conditions, independent of the signal bandwidth.
We illustrate the utility and specifics of applications of the new method in practice
by using natural speech and synthetic signals.
acknowledgement: The author thanks his colleagues K. Huszár and G. Tkačik for valuable
discussions and comments on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Mantas
full_name: Gabrielaitis, Mantas
id: 4D5B0CBC-F248-11E8-B48F-1D18A9856A87
last_name: Gabrielaitis
orcid: 0000-0002-7758-2016
citation:
ama: Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals.
IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899
apa: Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899
chicago: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing. Institute of Electrical
and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.
ieee: M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,”
IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical
and Electronics Engineers, pp. 4039–4054, 2021.
ista: Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband
signals. IEEE Transactions on Signal Processing. 69, 4039–4054.
mla: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband
Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of
Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.
short: M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-10T14:19:33Z
day: '09'
department:
- _id: GaTk
doi: 10.1109/TSP.2021.3087899
external_id:
arxiv:
- '2102.04832'
isi:
- '000682123900002'
intvolume: ' 69'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.04832
month: '06'
oa: 1
oa_version: Preprint
page: 4039 - 4054
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- 1941-0476
issn:
- 1053-587X
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and accurate amplitude demodulation of wideband signals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 69
year: '2021'
...
---
_id: '9327'
abstract:
- lang: eng
text: "This archive contains the missing sweater mesh animations and displacement
models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode
Repository: https://git.ist.ac.at/gsperl/MADYPG"
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.
https://doi.org/10.15479/AT:ISTA:9327.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data).” IST Austria, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.
mla: Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.
short: G. Sperl, R. Narain, C. Wojtan, (2021).
date_created: 2021-04-16T14:26:19Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
ddc:
- '005'
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/AT:ISTA:9327
file:
- access_level: open_access
checksum: 0324cb519273371708743f3282e7c081
content_type: application/zip
creator: gsperl
date_created: 2021-04-16T14:15:12Z
date_updated: 2021-04-16T14:15:12Z
file_id: '9328'
file_name: MADYPG_extra_data.zip
file_size: 802586232
relation: main_file
success: 1
- access_level: open_access
checksum: 4c224551adf852b136ec21a4e13f0c1b
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2021-04-26T09:33:44Z
date_updated: 2021-04-26T09:33:44Z
file_id: '9353'
file_name: MADYPG.zip
file_size: 64962865
relation: main_file
file_date_updated: 2021-04-26T09:33:44Z
gitlab_commit_id: 6a77e7e22769230ae5f5edaa090fb4b828e57573
gitlab_url: https://git.ist.ac.at/gsperl/MADYPG
has_accepted_license: '1'
license: https://opensource.org/licenses/MIT
month: '05'
oa: 1
publisher: IST Austria
related_material:
record:
- id: '9818'
relation: used_for_analysis_in
status: public
status: public
title: Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model
Data)
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9770'
abstract:
- lang: eng
text: We study an effective one-dimensional quantum model that includes friction
and spin-orbit coupling (SOC), and show that the model exhibits spin polarization
when both terms are finite. Most important, strong spin polarization can be observed
even for moderate SOC, provided that the friction is strong. Our findings might
help to explain the pronounced effect of chirality on spin distribution and transport
in chiral molecules. In particular, our model implies static magnetic properties
of a chiral molecule, which lead to Shiba-like states when a molecule is placed
on a superconductor, in accordance with recent experimental data.
acknowledgement: "We thank Rafael Barfknecht for useful discussions. This work has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand
A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen
Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program.
O.M. is thankful for support through the Harry de Jur Chair in Applied Science."
article_number: '024430'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Hen
full_name: Alpern, Hen
last_name: Alpern
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Oded
full_name: Millo, Oded
last_name: Millo
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
citation:
ama: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay
between friction and spin-orbit coupling as a source of spin polarization. Physical
Review B. 2021;104(2). doi:10.1103/physrevb.104.024430
apa: Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan,
A. (2021). Interplay between friction and spin-orbit coupling as a source of spin
polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430
chicago: Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko,
and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source
of Spin Polarization.” Physical Review B. American Physical Society, 2021.
https://doi.org/10.1103/physrevb.104.024430.
ieee: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan,
“Interplay between friction and spin-orbit coupling as a source of spin polarization,”
Physical Review B, vol. 104, no. 2. American Physical Society, 2021.
ista: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021.
Interplay between friction and spin-orbit coupling as a source of spin polarization.
Physical Review B. 104(2), 024430.
mla: Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling
as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2,
024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.
short: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan,
Physical Review B 104 (2021).
date_created: 2021-08-04T15:05:32Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:27:07Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/physrevb.104.024430
ec_funded: 1
external_id:
arxiv:
- '2101.05173'
isi:
- '000678780800003'
intvolume: ' 104'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2101.05173
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay between friction and spin-orbit coupling as a source of spin polarization
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9827'
abstract:
- lang: eng
text: 'The Nearest neighbour search (NNS) is a fundamental problem in many application
domains dealing with multidimensional data. In a concurrent setting, where dynamic
modifications are allowed, a linearizable implementation of the NNS is highly
desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free
concurrent kD-tree, which implements an abstract data type (ADT) that provides
the operations Add, Remove, Contains, and NNS. Our implementation is linearizable.
The operations in the LFkD-tree use single-word read and compare-and-swap (Image
1 ) atomic primitives, which are readily supported on available multi-core processors.
We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world
and synthetic datasets. The experiments show that the presented design is scalable
and achieves significant speed-up compared to the implementations of an existing
sequential kD-tree and a recently proposed multidimensional indexing structure,
PH-tree.'
article_processing_charge: No
article_type: original
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Ivan
full_name: Walulya, Ivan
last_name: Walulya
- first_name: Philippas
full_name: Tsigas, Philippas
last_name: Tsigas
citation:
ama: Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48.
doi:10.1016/j.tcs.2021.06.041
apa: Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable
nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041
chicago: Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable
Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.
ieee: B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest
neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol.
886. Elsevier, pp. 27–48, 2021.
ista: Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.
mla: Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search
in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier,
2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041.
short: B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021)
27–48.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-08-10T14:27:43Z
day: '13'
department:
- _id: DaAl
doi: 10.1016/j.tcs.2021.06.041
external_id:
isi:
- '000694718900004'
intvolume: ' 886'
isi: 1
keyword:
- Concurrent data structure
- kD-tree
- Nearest neighbor search
- Similarity search
- Lock-free
- Linearizability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf
month: '09'
oa: 1
oa_version: Submitted Version
page: 27-48
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concurrent linearizable nearest neighbour search in LockFree-kD-tree
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 886
year: '2021'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences, vol. 118, no. 29. National
Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29),
e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118,
National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2023-08-11T10:28:10Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9874'
abstract:
- lang: eng
text: Myocardial regeneration is restricted to early postnatal life, when mammalian
cardiomyocytes still retain the ability to proliferate. The molecular cues that
induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
is higher expressed in the early postnatal myocardium and decreases in expression
towards adulthood, especially under conditions of overload, and orchestrates the
transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
heart provokes cardiomyocyte proliferation by targeting a network of negative
cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
remodeling to overload by derepression of the prohypertrophic transcription factors
Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
provokes nearly complete regeneration of the adult myocardium after ischemic injury.
Our data demonstrate that exploitation of conserved molecular programs can enhance
the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
(EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Raso, Andrea
last_name: Raso
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Vasco
full_name: Sampaio-Pinto, Vasco
last_name: Sampaio-Pinto
- first_name: Hamid
full_name: el Azzouzi, Hamid
last_name: el Azzouzi
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Daniel W.
full_name: Sorensen, Daniel W.
last_name: Sorensen
- first_name: Lara
full_name: Ottaviani, Lara
last_name: Ottaviani
- first_name: Servé
full_name: Olieslagers, Servé
last_name: Olieslagers
- first_name: Manon M.
full_name: Huibers, Manon M.
last_name: Huibers
- first_name: Roel
full_name: de Weger, Roel
last_name: de Weger
- first_name: Sailay
full_name: Siddiqi, Sailay
last_name: Siddiqi
- first_name: Silvia
full_name: Moimas, Silvia
last_name: Moimas
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Lorena
full_name: Zentillin, Lorena
last_name: Zentillin
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Diana S.
full_name: Nascimento, Diana S.
last_name: Nascimento
- first_name: Paula A.
full_name: da Costa Martins, Paula A.
last_name: da Costa Martins
- first_name: Jop H.
full_name: van Berlo, Jop H.
last_name: van Berlo
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
- first_name: Leon J.
full_name: De Windt, Leon J.
last_name: De Windt
citation:
ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4
apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4
chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.
ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
12, 4808.
mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications,
vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.
short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
isi:
- '000683910200042'
pmid:
- '34376683'
file:
- access_level: open_access
checksum: 48d8562e8229e4282f3f354b329722c5
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T12:29:59Z
date_updated: 2021-08-10T12:29:59Z
file_id: '9876'
file_name: 2021_NatureCommunications_Raso.pdf
file_size: 4364333
relation: main_file
success: 1
file_date_updated: 2021-08-10T12:29:59Z
genbank:
- GSE178867
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
and hypertrophy and stimulates cardiac regeneration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9769'
abstract:
- lang: eng
text: A few years ago, flow equations were introduced as a technique for calculating
the ground-state energies of cold Bose gases with and without impurities. In this
paper, we extend this approach to compute observables other than the energy. As
an example, we calculate the densities, and phase fluctuations of one-dimensional
Bose gases with one and two impurities. For a single mobile impurity, we use flow
equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation.
We show that the mean-field approximation is accurate for all values of the boson-impurity
interaction strength as long as the phase coherence length is much larger than
the healing length of the condensate. For two static impurities, we calculate
impurity-impurity interactions induced by the Bose gas. We find that leading order
perturbation theory fails when boson-impurity interactions are stronger than boson-boson
interactions. The mean-field approximation reproduces the flow equation results
for all values of the boson-impurity interaction strength as long as boson-boson
interactions are weak.
acknowledgement: We thank Matthias Heinz and Volker Karle for helpful comments on
the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field
calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing
with us the data for the densities presented in Ref. [14]. This work has received
funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G.
V.) and European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges
support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in
Many-Body Quantum Systems – From Atoms to Quarks". This infrastructure is part of
a project that has received funding from the European Union’s Horizon 2020 research
and innovation programme under grant agreement No 824093. H.-W.H. was supported
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID
279384907 - SFB 1245.
article_number: '008'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008'
apa: 'Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities
in a one-dimensional Bose gas: The flow equation approach. SciPost Physics.
SciPost. https://doi.org/10.21468/scipostphys.11.1.008'
chicago: 'Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev.
“Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost
Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.'
ieee: 'F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in
a one-dimensional Bose gas: The flow equation approach,” SciPost Physics,
vol. 11, no. 1. SciPost, 2021.'
ista: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.'
mla: 'Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow
Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021,
doi:10.21468/scipostphys.11.1.008.'
short: F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11
(2021).
date_created: 2021-08-04T15:00:55Z
date_published: 2021-07-13T00:00:00Z
date_updated: 2023-08-11T10:25:44Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.11.1.008
ec_funded: 1
external_id:
arxiv:
- '2101.10958'
isi:
- '000680039500013'
file:
- access_level: open_access
checksum: eaa847346b1a023d97bbb291779610ed
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T11:44:59Z
date_updated: 2021-08-10T11:44:59Z
file_id: '9875'
file_name: 2021_SciPostPhysics_Brauneis.pdf
file_size: 1085300
relation: main_file
success: 1
file_date_updated: 2021-08-10T11:44:59Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: SciPost Physics
publication_identifier:
eissn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Impurities in a one-dimensional Bose gas: The flow equation approach'
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: '9746'
abstract:
- lang: eng
text: Evolutionary adaptation is a major source of antibiotic resistance in bacterial
pathogens. Evolution-informed therapy aims to constrain resistance by accounting
for bacterial evolvability. Sequential treatments with antibiotics that target
different bacterial processes were previously shown to limit adaptation through
genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous
sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly
lead to cross-resistance. We here challenged this assumption by determining the
evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments
involving both heterogenous and homogeneous antibiotic sets. To our surprise,
we found that fast switching between only β-lactam antibiotics resulted in increased
extinction of bacterial populations. We demonstrate that extinction is favored
by low rates of spontaneous resistance emergence and low levels of spontaneous
cross-resistance among the antibiotics in sequence. The uncovered principles may
help to guide the optimized use of available antibiotics in highly potent, evolution-informed
treatment designs.
acknowledgement: We would like to thank Leif Tueffers and João Botelho for discussions
and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge
financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS,
and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the
Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS
scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus
Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further
supported by the German Science Foundation Research Infrastructure NGS_CC (project
407495230) as part of the Next Generation Sequencing Competence Network (project
423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis
Kiel (CCGA Kiel).
article_number: e68876
article_processing_charge: No
article_type: original
author:
- first_name: Aditi
full_name: Batra, Aditi
last_name: Batra
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Emilie
full_name: Rousseau, Emilie
last_name: Rousseau
- first_name: Sören
full_name: Franzenburg, Sören
last_name: Franzenburg
- first_name: Stefan
full_name: Niemann, Stefan
last_name: Niemann
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High
potency of sequential therapy with only beta-lactam antibiotics. eLife.
2021;10. doi:10.7554/elife.68876
apa: Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg,
H. (2021). High potency of sequential therapy with only beta-lactam antibiotics.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876
chicago: Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan
Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only
Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.
ieee: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg,
“High potency of sequential therapy with only beta-lactam antibiotics,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021.
High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10,
e68876.
mla: Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam
Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021,
doi:10.7554/elife.68876.
short: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg,
ELife 10 (2021).
date_created: 2021-07-28T13:36:57Z
date_published: 2021-07-28T00:00:00Z
date_updated: 2023-08-11T10:26:29Z
day: '28'
department:
- _id: CaGu
doi: 10.7554/elife.68876
external_id:
isi:
- '000692027800001'
pmid:
- '34318749'
intvolume: ' 10'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68876
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: High potency of sequential therapy with only beta-lactam antibiotics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...