---
_id: '822'
abstract:
- lang: eng
text: 'Polymicrobial infections constitute small ecosystems that accommodate several
bacterial species. Commonly, these bacteria are investigated in isolation. However,
it is unknown to what extent the isolates interact and whether their interactions
alter bacterial growth and ecosystem resilience in the presence and absence of
antibiotics. We quantified the complete ecological interaction network for 72
bacterial isolates collected from 23 individuals diagnosed with polymicrobial
urinary tract infections and found that most interactions cluster based on evolutionary
relatedness. Statistical network analysis revealed that competitive and cooperative
reciprocal interactions are enriched in the global network, while cooperative
interactions are depleted in the individual host community networks. A population
dynamics model parameterized by our measurements suggests that interactions restrict
community stability, explaining the observed species diversity of these communities.
We further show that the clinical isolates frequently protect each other from
clinically relevant antibiotics. Together, these results highlight that ecological
interactions are crucial for the growth and survival of bacteria in polymicrobial
infection communities and affect their assembly and resilience. '
article_processing_charge: No
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Alan
full_name: Mcnally, Alan
last_name: Mcnally
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological
stability, and collective antibiotic tolerance in polymicrobial infections. PNAS.
2017;114(40):10666-10671. doi:10.1073/pnas.1713372114
apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114
chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach.
“Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance
in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1713372114.
ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp.
10666–10671, 2017.
ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks,
ecological stability, and collective antibiotic tolerance in polymicrobial infections.
PNAS. 114(40), 10666–10671.
mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective
Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no.
40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.
short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-10-03T00:00:00Z
date_updated: 2023-09-26T16:18:48Z
day: '03'
department:
- _id: ToBo
doi: 10.1073/pnas.1713372114
ec_funded: 1
external_id:
isi:
- '000412130500061'
pmid:
- '28923953'
intvolume: ' 114'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/
month: '10'
oa: 1
oa_version: Submitted Version
page: 10666 - 10671
pmid: 1
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6827'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interaction networks, ecological stability, and collective antibiotic tolerance
in polymicrobial infections
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2017'
...
---
_id: '823'
abstract:
- lang: eng
text: The resolution of a linear system with positive integer variables is a basic
yet difficult computational problem with many applications. We consider sparse
uncorrelated random systems parametrised by the density c and the ratio α=N/M
between number of variables N and number of constraints M. By means of ensemble
calculations we show that the space of feasible solutions endows a Van-Der-Waals
phase diagram in the plane (c, α). We give numerical evidence that the associated
computational problems become more difficult across the critical point and in
particular in the coexistence region.
article_number: '093404'
article_processing_charge: No
author:
- first_name: Simona
full_name: Colabrese, Simona
last_name: Colabrese
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Luca
full_name: Leuzzi, Luca
last_name: Leuzzi
- first_name: Enzo
full_name: Marinari, Enzo
last_name: Marinari
citation:
ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer
linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017;2017(9). doi:10.1088/1742-5468/aa85c3'
apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase
transitions in integer linear problems. Journal of Statistical Mechanics:
Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3'
chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari.
“Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics:
Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.'
ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions
in integer linear problems,” Journal of Statistical Mechanics: Theory and
Experiment, vol. 2017, no. 9. IOPscience, 2017.'
ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions
in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017(9), 093404.'
mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.”
Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no.
9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.'
short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical
Mechanics: Theory and Experiment 2017 (2017).'
date_created: 2018-12-11T11:48:41Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-26T16:18:12Z
day: '26'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa85c3
ec_funded: 1
external_id:
isi:
- '000411842900001'
intvolume: ' 2017'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.06303
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOPscience
publist_id: '6826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transitions in integer linear problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '824'
abstract:
- lang: eng
text: 'In shear flows at transitional Reynolds numbers, localized patches of turbulence,
known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev.
Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic
solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds
number. Combining slicing methods for continuous symmetry reduction with Poincaré
sections for the first time in a shear flow setting, we compute and visualize
the unstable manifold of the lower-branch solution and show that it extends towards
the neighbourhood of the upper-branch solution. Surprisingly, this connection
even persists far above the bifurcation point and appears to mediate the first
stage of the puff generation: amplification of streamwise localized fluctuations.
When the state-space trajectories on the unstable manifold reach the vicinity
of the upper branch, corresponding fluctuations expand in space and eventually
take the usual shape of a puff.'
article_number: R1
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow.
Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516
apa: Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized
chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2017.516
chicago: Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press,
2017. https://doi.org/10.1017/jfm.2017.516.
ieee: N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos
in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University
Press, 2017.
ista: Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in
pipe flow. Journal of Fluid Mechanics. 827, R1.
mla: Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge
University Press, 2017, doi:10.1017/jfm.2017.516.
short: N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-18T00:00:00Z
date_updated: 2023-09-26T16:17:43Z
day: '18'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.516
external_id:
isi:
- '000408326300001'
intvolume: ' 827'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.10484
month: '08'
oa: 1
oa_version: Submitted Version
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6824'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic path to spatially localized chaos in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 827
year: '2017'
...
---
_id: '825'
abstract:
- lang: eng
text: What data is needed about data? Describing the process to answer this question
for the institutional data repository IST DataRep.
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207.
doi:10.31263/voebm.v70i2.1678
apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.
https://doi.org/10.31263/voebm.v70i2.1678
chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1678.
ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70,
no. 2. VÖB, pp. 200–207, 2017.
ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.
mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol.
70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.
short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
& Bibliothekare 70 (2017) 200–207.
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:44Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1678
file:
- access_level: open_access
checksum: 7c4544d07efa2c2add8612b489abb4e2
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:32:17Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5850'
file_name: 2017_VOEB_Petritsch.pdf
file_size: 7843975
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 200 - 207
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6823'
scopus_import: 1
status: public
title: Metadata for research data in practice
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '833'
abstract:
- lang: eng
text: We present an efficient algorithm to compute Euler characteristic curves of
gray scale images of arbitrary dimension. In various applications the Euler characteristic
curve is used as a descriptor of an image. Our algorithm is the first streaming
algorithm for Euler characteristic curves. The usage of streaming removes the
necessity to store the entire image in RAM. Experiments show that our implementation
handles terabyte scale images on commodity hardware. Due to lock-free parallelism,
it scales well with the number of processor cores. Additionally, we put the concept
of the Euler characteristic curve in the wider context of computational topology.
In particular, we explain the connection with persistence diagrams.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of
multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer;
2017:397-409. doi:10.1007/978-3-319-64689-3_32'
apa: 'Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic
curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger
(Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of
Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32'
chicago: Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden,
and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32.
ieee: 'T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves
of multidimensional images,” presented at the CAIP: Computer Analysis of Images
and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.'
ista: 'Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves
of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS,
vol. 10424, 397–409.'
mla: Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol.
10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.
short: T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer,
2017, pp. 397–409.
conference:
end_date: 2017-08-24
location: Ystad, Sweden
name: 'CAIP: Computer Analysis of Images and Patterns'
start_date: 2017-08-22
date_created: 2018-12-11T11:48:45Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2023-09-26T16:10:03Z
day: '28'
department:
- _id: HeEd
doi: 10.1007/978-3-319-64689-3_32
editor:
- first_name: Michael
full_name: Felsberg, Michael
last_name: Felsberg
- first_name: Anders
full_name: Heyden, Anders
last_name: Heyden
- first_name: Norbert
full_name: Krüger, Norbert
last_name: Krüger
external_id:
isi:
- '000432085900032'
intvolume: ' 10424'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02045
month: '07'
oa: 1
oa_version: Submitted Version
page: 397 - 409
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6815'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Streaming algorithm for Euler characteristic curves of multidimensional images
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10424
year: '2017'
...
---
_id: '834'
abstract:
- lang: eng
text: 'Thermal and many-body localized phases are separated by a dynamical phase
transition of a new kind. We analyze the distribution of off-diagonal matrix elements
of local operators across this transition in two different models of disordered
spin chains. We show that the behavior of matrix elements can be used to characterize
the breakdown of thermalization and to extract the many-body Thouless energy.
We find that upon increasing the disorder strength the system enters a critical
region around the many-body localization transition. The properties of the system
in this region are: (i) the Thouless energy becomes smaller than the level spacing,
(ii) the matrix elements show critical dependence on the energy difference, and
(iii) the matrix elements, viewed as amplitudes of a fictitious wave function,
exhibit strong multifractality. This critical region decreases with the system
size, which we interpret as evidence for a diverging correlation length at the
many-body localization transition. Our findings show that the correlation length
becomes larger than the accessible system sizes in a broad range of disorder strength
values and shed light on the critical behavior near the many-body localization
transition.'
acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover,
and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS
Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of
this work were completed (supported in part by the National Science Foundation under
Grant No. NSF PHY11-25915)
article_number: '104201'
article_processing_charge: No
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Papic
full_name: Zlatko, Papic
last_name: Zlatko
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
citation:
ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the
many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201
apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality
across the many-body localization transition. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201
chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality
across the Many-Body Localization Transition.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.
ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality
across the many-body localization transition,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 10. American Physical Society,
2017.
ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across
the many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 96(10), 104201.
mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body
Localization Transition.” Physical Review B - Condensed Matter and Materials
Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.
short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 96 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-09-06T00:00:00Z
date_updated: 2023-09-26T15:51:54Z
day: '06'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104201
external_id:
isi:
- '000409429300004'
intvolume: ' 96'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02389
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6814'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thouless energy and multifractality across the many-body localization transition
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '836'
abstract:
- lang: eng
text: Recent research has examined how to study the topological features of a continuous
self-map by means of the persistence of the eigenspaces, for given eigenvalues,
of the endomorphism induced in homology over a field. This raised the question
of how to select dynamically significant eigenvalues. The present paper aims to
answer this question, giving an algorithm that computes the persistence of eigenspaces
for every eigenvalue simultaneously, also expressing said eigenspaces as direct
sums of “finite” and “singular” subspaces.
alternative_title:
- PROMS
article_processing_charge: No
author:
- first_name: Marc
full_name: Ethier, Marc
last_name: Ethier
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Marian
full_name: Mrozek, Marian
last_name: Mrozek
citation:
ama: 'Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the
Kronecker canonical form. In: Special Sessions in Applications of Computer
Algebra. Vol 198. Springer; 2017:119-136. doi:10.1007/978-3-319-56932-1_8'
apa: 'Ethier, M., Jablonski, G., & Mrozek, M. (2017). Finding eigenvalues of
self-maps with the Kronecker canonical form. In Special Sessions in Applications
of Computer Algebra (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. https://doi.org/10.1007/978-3-319-56932-1_8'
chicago: Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues
of Self-Maps with the Kronecker Canonical Form.” In Special Sessions in Applications
of Computer Algebra, 198:119–36. Springer, 2017. https://doi.org/10.1007/978-3-319-56932-1_8.
ieee: M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps
with the Kronecker canonical form,” in Special Sessions in Applications of
Computer Algebra, Kalamata, Greece, 2017, vol. 198, pp. 119–136.
ista: 'Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with
the Kronecker canonical form. Special Sessions in Applications of Computer Algebra.
ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.'
mla: Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical
Form.” Special Sessions in Applications of Computer Algebra, vol. 198,
Springer, 2017, pp. 119–36, doi:10.1007/978-3-319-56932-1_8.
short: M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications
of Computer Algebra, Springer, 2017, pp. 119–136.
conference:
end_date: 2015-07-23
location: Kalamata, Greece
name: 'ACA: Applications of Computer Algebra'
start_date: 2015-07-20
date_created: 2018-12-11T11:48:46Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2023-09-26T15:50:52Z
day: '27'
department:
- _id: HeEd
doi: 10.1007/978-3-319-56932-1_8
ec_funded: 1
external_id:
isi:
- '000434088200008'
intvolume: ' 198'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 119 - 136
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Special Sessions in Applications of Computer Algebra
publication_identifier:
isbn:
- 978-331956930-7
publication_status: published
publisher: Springer
publist_id: '6812'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finding eigenvalues of self-maps with the Kronecker canonical form
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 198
year: '2017'
...
---
_id: '837'
abstract:
- lang: eng
text: 'The hippocampus is a key brain region for memory and notably for spatial
memory, and is needed for both spatial working and reference memories. Hippocampal
place cells selectively discharge in specific locations of the environment to
form mnemonic represen tations of space. Several behavioral protocols have been
designed to test spatial memory which requires the experimental subject to utilize
working memory and reference memory. However, less is known about how these memory
traces are presented in the hippo campus, especially considering tasks that require
both spatial working and long -term reference memory demand. The aim of my thesis
was to elucidate how spatial working memory, reference memory, and the combination
of both are represented in the hippocampus. In this thesis, using a radial eight
-arm maze, I examined how the combined demand on these memories influenced place
cell assemblies while reference memories were partially updated by changing some
of the reward- arms. This was contrasted with task varian ts requiring working
or reference memories only. Reference memory update led to gradual place field
shifts towards the rewards on the switched arms. Cells developed enhanced firing
in passes between newly -rewarded arms as compared to those containing an unchanged
reward. The working memory task did not show such gradual changes. Place assemblies
on occasions replayed trajectories of the maze; at decision points the next arm
choice was preferentially replayed in tasks needing reference memory while in
the pure working memory task the previously visited arm was replayed. Hence trajectory
replay only reflected the decision of the animal in tasks needing reference memory
update. At the reward locations, in all three tasks outbound trajectories of the
current arm were preferentially replayed, showing the animals’ next path to the
center. At reward locations trajectories were replayed preferentially in reverse
temporal order. Moreover, in the center reverse replay was seen in the working
memory task but in the other tasks forward replay was seen. Hence, the direction
of reactivation was determined by the goal locations so that part of the trajectory
which was closer to the goal was reactivated later in an HSE while places further
away from the goal were reactivated earlier. Altogether my work demonstrated that
reference memory update triggers several levels of reorganization of the hippocampal
cognitive map which are not seen in simpler working memory demand s. Moreover,
hippocampus is likely to be involved in spatial decisions through reactivating
planned trajectories when reference memory recall is required for such a decision. '
acknowledgement: 'I am very grateful for the opportunity I have had as a graduate
student to explore and incredibly interesting branch of neuroscience, and for the
people who made it possible. Firstly, I would like to offer my thanks to my supervisor
Professor Jozsef Csicsvari for his great support, guidance and patience offered
over the years. The door to his office was always open whenever I had questions.
I have learned a lot from him about carefully designing experiments, asking interesting
questions and how to integrate results into a broader picture. I also express my
gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific
role model who is always willing to teach , and advice and talk through problems
with his full attention. Many thanks to my wonderful “office mates” over the years
and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree
Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián
Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in
the lab for the many useful discussions about science and for making the laboratory
such a nice and friendly place to work in. A special thank goes to Michael LoBianco
and Jago Wallenschus for wonderful technical support. I would also like to thank
Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam
and thesi s committee members despite their busy schedule. I am also very thankful
to IST Austria for their support all throughout my PhD. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
citation:
ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks. 2017. doi:10.15479/AT:ISTA:th_858
apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858
chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.
ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks,” Institute of Science and Technology Austria, 2017.
ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria.
mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.
short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial
Tasks, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-08-23T00:00:00Z
date_updated: 2023-09-07T12:06:38Z
day: '23'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:th_858
file:
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oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6811'
pubrep_id: '858'
related_material:
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- id: '5828'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '838'
abstract:
- lang: eng
text: 'In this thesis we discuss the exact security of message authentications codes
HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length
keyed hash function f into a variable input-length function. A practical single-key
variant of NMAC called HMAC is a very popular and widely deployed message authentication
code (MAC). PMAC is a block-cipher based mode of operation, which also happens
to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti
and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF),
and thus also a MAC, under two assumptions. Unfortunately, for many instantiations
of HMAC one of them has been found to be wrong. To restore the provable guarantees
for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC
was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a
pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure
variable input-length PRF. For adversaries making q queries, each of length at
most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves
an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently
best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by
giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one
initially XORs a mask to every message block, where the mask for the i th block
is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is
the i -th codeword of the Gray code. Our attack applies more generally to any
sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As
for NMAC , our first contribution is a simpler and uniform proof: If f is an ε
-secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q
queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length
at most ` blocks each. We also show that this ε + `qδ bound is basically tight
by constructing an f for which an attack with advantage `qδ exists. Moreover,
we analyze the PRF-security of a modification of NMAC called NI by An and Bellare
that avoids the constant rekeying on multi-block messages in NMAC and allows for
an information-theoretic analysis. We carry out such an analysis, obtaining a
tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2
q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved
by using τ i ’s that are k -wise independent, for k > 1 (the original has k
= 1). We observe that the security of PMAC will not increase in general if k =
2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4.
Due to simple extension attacks, this is the best bound one can hope for, using
any distribution on the masks. Whether k = 3 is already sufficient to get this
level of security is left as an open problem. Keywords: Message authentication
codes, Pseudorandom functions, HMAC, PMAC. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828
apa: Rybar, M. (2017). (The exact security of) Message authentication codes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828
chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.
ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute
of Science and Technology Austria, 2017.
ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute
of Science and Technology Austria.
mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.
short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute
of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2023-09-07T12:02:28Z
day: '26'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:th_828
file:
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checksum: ff8639ec4bded6186f44c7bd3ee26804
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date_created: 2019-04-05T08:24:11Z
date_updated: 2020-07-14T12:48:12Z
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- iso: eng
month: '06'
oa: 1
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page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6810'
pubrep_id: '828'
related_material:
record:
- id: '2082'
relation: part_of_dissertation
status: public
- id: '6196'
relation: part_of_dissertation
status: public
status: public
title: (The exact security of) Message authentication codes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '839'
abstract:
- lang: eng
text: 'This thesis describes a brittle fracture simulation method for visual effects
applications. Building upon a symmetric Galerkin boundary element method, we first
compute stress intensity factors following the theory of linear elastic fracture
mechanics. We then use these stress intensities to simulate the motion of a propagating
crack front at a significantly higher resolution than the overall deformation
of the breaking object. Allowing for spatial variations of the material''s toughness
during crack propagation produces visually realistic, highly-detailed fracture
surfaces. Furthermore, we introduce approximations for stress intensities and
crack opening displacements, resulting in both practical speed-up and theoretically
superior runtime complexity compared to previous methods. While we choose a quasi-static
approach to fracture mechanics, ignoring dynamic deformations, we also couple
our fracture simulation framework to a standard rigid-body dynamics solver, enabling
visual effects artists to simulate both large scale motion, as well as fracturing
due to collision forces in a combined system. As fractures inside of an object
grow, their geometry must be represented both in the coarse boundary element mesh,
as well as at the desired fine output resolution. Using a boundary element method,
we avoid complicated volumetric meshing operations. Instead we describe a simple
set of surface meshing operations that allow us to progressively add cracks to
the mesh of an object and still re-use all previously computed entries of the
linear boundary element system matrix. On the high resolution level, we opt for
an implicit surface representation. We then describe how to capture fracture surfaces
during crack propagation, as well as separate the individual fragments resulting
from the fracture process, based on this implicit representation. We show results
obtained with our method, either solving the full boundary element system in every
time step, or alternatively using our fast approximations. These results demonstrate
that both of these methods perform well in basic test cases and produce realistic
fracture surfaces. Furthermore we show that our fast approximations substantially
out-perform the standard approach in more demanding scenarios. Finally, these
two methods naturally combine, using the full solution while the problem size
is manageably small and switching to the fast approximations later on. The resulting
hybrid method gives the user a direct way to choose between speed and accuracy
of the simulation. '
acknowledgement: "ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all,
let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for
supporting me throughout my PhD. Obviously, none of this work would\r\nhave been
possible without you.\r\nFurthermore, Thank You to all the people who have contributed
to this work in various\r\nways, in particular Martin Schanz and his group for providing
and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and
Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions
during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel,
and all the members – past and present – of his\r\nand Chris’ research groups at
IST Austria for always providing honest and insightful\r\nfeedback throughout many
joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang
Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs
only virtual objects have been harmed in the process of creating this work, I would\r\nlike
to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo”
models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg
for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different
ways.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
citation:
ama: Hahn D. Brittle fracture simulation with boundary elements for computer graphics.
2017. doi:10.15479/AT:ISTA:th_855
apa: Hahn, D. (2017). Brittle fracture simulation with boundary elements for
computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855
chicago: Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer
Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855.
ieee: D. Hahn, “Brittle fracture simulation with boundary elements for computer
graphics,” Institute of Science and Technology Austria, 2017.
ista: Hahn D. 2017. Brittle fracture simulation with boundary elements for computer
graphics. Institute of Science and Technology Austria.
mla: Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer
Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855.
short: D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer
Graphics, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-14T00:00:00Z
date_updated: 2024-02-21T13:48:02Z
day: '14'
ddc:
- '004'
- '005'
- '006'
- '531'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_855
ec_funded: 1
file:
- access_level: open_access
checksum: 6c1ae8c90bfaba5e089417fefbc4a272
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6809'
pubrep_id: '855'
related_material:
record:
- id: '1362'
relation: part_of_dissertation
status: public
- id: '1633'
relation: part_of_dissertation
status: public
- id: '5568'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Brittle fracture simulation with boundary elements for computer graphics
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '84'
abstract:
- lang: eng
text: The advent of high-throughput technologies and the concurrent advances in
information sciences have led to a data revolution in biology. This revolution
is most significant in molecular biology, with an increase in the number and scale
of the “omics” projects over the last decade. Genomics projects, for example,
have produced impressive advances in our knowledge of the information concealed
into genomes, from the many genes that encode for the proteins that are responsible
for most if not all cellular functions, to the noncoding regions that are now
known to provide regulatory functions. Proteomics initiatives help to decipher
the role of post-translation modifications on the protein structures and provide
maps of protein-protein interactions, while functional genomics is the field that
attempts to make use of the data produced by these projects to understand protein
functions. The biggest challenge today is to assimilate the wealth of information
provided by these initiatives into a conceptual framework that will help us decipher
life. For example, the current views of the relationship between protein structure
and function remain fragmented. We know of their sequences, more and more about
their structures, we have information on their biological activities, but we have
difficulties connecting this dotted line into an informed whole. We lack the experimental
and computational tools for directly studying protein structure, function, and
dynamics at the molecular and supra-molecular levels. In this chapter, we review
some of the current developments in building the computational tools that are
needed, focusing on the role that geometry and topology play in these efforts.
One of our goals is to raise the general awareness about the importance of geometric
methods in elucidating the mysterious foundations of our very existence. Another
goal is the broadening of what we consider a geometric algorithm. There is plenty
of valuable no-man’s-land between combinatorial and numerical algorithms, and
it seems opportune to explore this land with a computational-geometric frame of
mind.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
citation:
ama: 'Edelsbrunner H, Koehl P. Computational topology for structural molecular biology.
In: Toth C, O’Rourke J, Goodman J, eds. Handbook of Discrete and Computational
Geometry, Third Edition. Handbook of Discrete and Computational Geometry.
Taylor & Francis; 2017:1709-1735. doi:10.1201/9781315119601'
apa: Edelsbrunner, H., & Koehl, P. (2017). Computational topology for structural
molecular biology. In C. Toth, J. O’Rourke, & J. Goodman (Eds.), Handbook
of Discrete and Computational Geometry, Third Edition (pp. 1709–1735). Taylor
& Francis. https://doi.org/10.1201/9781315119601
chicago: Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural
Molecular Biology.” In Handbook of Discrete and Computational Geometry, Third
Edition, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35.
Handbook of Discrete and Computational Geometry. Taylor & Francis, 2017. https://doi.org/10.1201/9781315119601.
ieee: H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular
biology,” in Handbook of Discrete and Computational Geometry, Third Edition,
C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor & Francis, 2017, pp. 1709–1735.
ista: 'Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular
biology. In: Handbook of Discrete and Computational Geometry, Third Edition. ,
1709–1735.'
mla: Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural
Molecular Biology.” Handbook of Discrete and Computational Geometry, Third
Edition, edited by Csaba Toth et al., Taylor & Francis, 2017, pp. 1709–35,
doi:10.1201/9781315119601.
short: H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.),
Handbook of Discrete and Computational Geometry, Third Edition, Taylor & Francis,
2017, pp. 1709–1735.
date_created: 2018-12-11T11:44:32Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2023-10-16T11:15:22Z
day: '09'
department:
- _id: HeEd
doi: 10.1201/9781315119601
editor:
- first_name: Csaba
full_name: Toth, Csaba
last_name: Toth
- first_name: Joseph
full_name: O'Rourke, Joseph
last_name: O'Rourke
- first_name: Jacob
full_name: Goodman, Jacob
last_name: Goodman
language:
- iso: eng
month: '11'
oa_version: None
page: 1709 - 1735
publication: Handbook of Discrete and Computational Geometry, Third Edition
publication_identifier:
eisbn:
- '9781498711425'
publication_status: published
publisher: Taylor & Francis
publist_id: '7970'
quality_controlled: '1'
scopus_import: '1'
series_title: Handbook of Discrete and Computational Geometry
status: public
title: Computational topology for structural molecular biology
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '840'
abstract:
- lang: eng
text: Heavy holes confined in quantum dots are predicted to be promising candidates
for the realization of spin qubits with long coherence times. Here we focus on
such heavy-hole states confined in germanium hut wires. By tuning the growth density
of the latter we can realize a T-like structure between two neighboring wires.
Such a structure allows the realization of a charge sensor, which is electrostatically
and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3
e. By integrating the T-like structure into a radiofrequency reflectometry setup,
single-shot measurements allowing the extraction of hole tunneling times are performed.
The extracted tunneling times of less than 10 μs are attributed to the small effective
mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.
acknowledged_ssus:
- _id: M-Shop
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in
germanium hut wires probed by single-shot reflectometry. Nano Letters.
2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627
apa: Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole
tunneling times in germanium hut wires probed by single-shot reflectometry. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627
chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros.
“Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.
ieee: L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling
times in germanium hut wires probed by single-shot reflectometry,” Nano Letters,
vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.
ista: Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times
in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9),
5706–5710.
mla: Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed
by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical
Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.
short: L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017)
5706–5710.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-10T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '10'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.7b02627
ec_funded: 1
external_id:
isi:
- '000411043500078'
file:
- access_level: open_access
checksum: 761371a0129b2aa442424b9561450ece
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:33Z
date_updated: 2020-07-14T12:48:13Z
file_id: '4951'
file_name: IST-2017-865-v1+1_acs.nanolett.7b02627.pdf
file_size: 2449546
relation: main_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 5706 - 5710
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6808'
pubrep_id: '865'
quality_controlled: '1'
related_material:
record:
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relation: popular_science
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relation: dissertation_contains
status: public
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2017'
...
---
_id: '2016'
abstract:
- lang: eng
text: The Ising model is one of the simplest and most famous models of interacting
systems. It was originally proposed to model ferromagnetic interactions in statistical
physics and is now widely used to model spatial processes in many areas such as
ecology, sociology, and genetics, usually without testing its goodness-of-fit.
Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model.
The theory of Markov bases has been developed in algebraic statistics for exact
goodness-of-fit testing using a Monte Carlo approach. However, this beautiful
theory has fallen short of its promise for applications, because finding a Markov
basis is usually computationally intractable. We develop a Monte Carlo method
for exact goodness-of-fit testing for the Ising model which avoids computing a
Markov basis and also leads to a better connectivity of the Markov chain and hence
to a faster convergence. We show how this method can be applied to analyze the
spatial organization of receptors on the cell membrane.
article_processing_charge: No
arxiv: 1
author:
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
last_name: Martin Del Campo Sanchez
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306.
doi:10.1111/sjos.12251
apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017).
Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of
Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251
chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline
Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal
of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit
testing for the Ising model,” Scandinavian Journal of Statistics, vol.
44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for
the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell,
2017, pp. 285–306, doi:10.1111/sjos.12251.
short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian
Journal of Statistics 44 (2017) 285–306.
date_created: 2018-12-11T11:55:13Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-19T15:13:27Z
day: '01'
department:
- _id: GaTk
doi: 10.1111/sjos.12251
external_id:
arxiv:
- '1410.1242'
isi:
- '000400985000001'
intvolume: ' 44'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.1242
month: '06'
oa: 1
oa_version: Preprint
page: 285 - 306
publication: Scandinavian Journal of Statistics
publication_identifier:
issn:
- '03036898'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5060'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Exact goodness-of-fit testing for the Ising model
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2017'
...
---
_id: '202'
abstract:
- lang: eng
text: 'Restriction-modification (RM) represents the simplest and possibly the most
widespread mechanism of self/non-self discrimination in nature. In order to provide
bacteria with immunity against bacteriophages and other parasitic genetic elements,
RM systems rely on a balance between two enzymes: the restriction enzyme, which
cleaves non-self DNA at specific restriction sites, and the modification enzyme,
which tags the host’s DNA as self and thus protects it from cleavage. In this
thesis, I use population and single-cell level experiments in combination with
mathematical modeling to study different aspects of the interplay between RM systems,
bacteria and bacteriophages. First, I analyze how mutations in phage restriction
sites affect the probability of phage escape – an inherently stochastic process,
during which phages accidently get modified instead of restricted. Next, I use
single-cell experiments to show that RM systems can, with a low probability, attack
the genome of their bacterial host and that this primitive form of autoimmunity
leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally,
I investigate the nature of interactions between bacteria, RM systems and temperate
bacteriophages to find that, as a consequence of phage escape and its impact on
population dynamics, RM systems can promote acquisition of symbiotic bacteriophages,
rather than limit it. The results presented here uncover new fundamental biological
properties of RM systems and highlight their importance in the ecology and evolution
of bacteria, bacteriophages and their interactions.'
acknowledgement: "During my PhD studies, I received help from many people, all of
which unfortunately cannot be listed here. I thank them deeply and hope that I never
made them regret their kindness.\r\nI would like to express my deepest gratitude
to Călin Guet, who went far beyond his responsibilities as an advisor and was to
me also a great mentor and a friend. Călin never questioned my potential or lacked
compassion and I cannot thank him enough for cultivating in me an independent scientist.
I was amazed by his ability to recognize the most fascinating scientific problems
in objects of study that others would find mundane. I hope I adopted at least a
fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his
support and especially for giving me the best possible example of how one can practice
excellent science with humor and style. Working with Bruce was a true privilege.\r\nI
thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the
Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI
thank all our lab members: Tobias Bergmiller for his guidance, especially in the
first years of my research, and for being a good friend throughout; Remy Chait for
staying in the lab at unreasonable hours and for the good laughs at bad jokes we
shared; Anna Staron for supportively listening to my whines whenever I had to run
a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for
keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek
for always being nice to me, no matter how much bench space I took from her.\r\nI
thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing
the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics
analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical
modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally,
I would like to thank my family and especially my wife Edita, who sacrificed a lot
so that I can pursue my goals and dreams.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
citation:
ama: Pleska M. Biology of restriction-modification systems at the single-cell and
population level. 2017. doi:10.15479/AT:ISTA:th_916
apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916
chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell
and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.
ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell
and population level,” Institute of Science and Technology Austria, 2017.
ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria.
mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell
and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.
short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell
and Population Level, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:45:10Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-15T12:04:56Z
day: '01'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th_916
file:
- access_level: open_access
checksum: 33cfb59674e91f82e3738396d3fb3776
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:48Z
date_updated: 2020-07-14T12:45:24Z
file_id: '4710'
file_name: IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf
file_size: 18569590
relation: main_file
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checksum: dcc239968decb233e7f98cf1083d8c26
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:33:14Z
date_updated: 2020-07-14T12:45:24Z
file_id: '6204'
file_name: 2017_Pleska_Maros_Thesis.docx
file_size: 2801649
relation: source_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '126'
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7711'
pubrep_id: '916'
related_material:
record:
- id: '1243'
relation: part_of_dissertation
status: public
- id: '561'
relation: part_of_dissertation
status: public
- id: '457'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Biology of restriction-modification systems at the single-cell and population
level
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '662'
abstract:
- lang: eng
text: 'We report a direct-numerical-simulation study of the Taylor-Couette flow
in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian
rotating flow has been investigated for decades as a simplified model system to
study the origin of turbulence in accretion disks that is not fully understood.
The flow in this study is axially periodic and thus the experimental end-wall
effects on the stability of the flow are avoided. Using optimal linear perturbations
as initial conditions, our simulations find no sustained turbulence: the strong
initial perturbations distort the velocity profile and trigger turbulence that
eventually decays.'
article_number: '044107'
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Markus
full_name: Rampp, Markus
last_name: Rampp
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian
rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525
apa: Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence
in quasi Keplerian rotating flows. Physics of Fluids. American Institute
of Physics. https://doi.org/10.1063/1.4981525
chicago: Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence
in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute
of Physics, 2017. https://doi.org/10.1063/1.4981525.
ieee: L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi
Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American
Institute of Physics, 2017.
ista: Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian
rotating flows. Physics of Fluids. 29(4), 044107.
mla: Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.”
Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics,
2017, doi:10.1063/1.4981525.
short: L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:08:15Z
day: '01'
department:
- _id: BjHo
doi: 10.1063/1.4981525
intvolume: ' 29'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.01714
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Physics of Fluids
publication_identifier:
issn:
- '10706631'
publication_status: published
publisher: American Institute of Physics
publist_id: '7072'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hydrodynamic turbulence in quasi Keplerian rotating flows
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2017'
...
---
_id: '663'
abstract:
- lang: eng
text: 'In this paper, we propose an approach to automatically compute invariant
clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for
an ordinary differential equation (ODE) is a multivariate polynomial invariant
g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete
invariants by assigning different values to u→ so that every trajectory of the
system can be overapproximated precisely by the intersection of a group of concrete
invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial
right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant
cluster can be obtained by first computing the remainder of the Lie derivative
of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations
obtained from the coefficients of the remainder. Based on invariant clusters and
sum-of-squares (SOS) programming, we present a new method for the safety verification
of hybrid systems. Experiments on nonlinear benchmark systems from biology and
control theory show that our approach is efficient. '
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Sergiy
full_name: Bogomolov, Sergiy
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification
of nonlinear hybrid systems based on invariant clusters. In: Proceedings of
the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814'
apa: 'Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A.
(2017). Safety verification of nonlinear hybrid systems based on invariant clusters.
In Proceedings of the 20th International Conference on Hybrid Systems (pp.
163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814'
chicago: Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas
A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant
Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems,
163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814.
ieee: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety
verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings
of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United
States, 2017, pp. 163–172.
ista: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification
of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th
International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and
Control , 163–172.'
mla: Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on
Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid
Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.
short: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings
of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.
conference:
end_date: 2017-04-20
location: Pittsburgh, PA, United States
name: 'HSCC: Hybrid Systems Computation and Control '
start_date: 2017-04-18
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:08:17Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3049797.3049814
file:
- access_level: open_access
checksum: b7667434cbf5b5f0ade3bea1dbe5bf63
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:20Z
date_updated: 2020-07-14T12:47:34Z
file_id: '4873'
file_name: IST-2017-817-v1+1_p163-kong.pdf
file_size: 1650530
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 163 - 172
publication: Proceedings of the 20th International Conference on Hybrid Systems
publication_identifier:
isbn:
- 978-145034590-3
publication_status: published
publisher: ACM
publist_id: '7067'
pubrep_id: '817'
quality_controlled: '1'
scopus_import: 1
status: public
title: Safety verification of nonlinear hybrid systems based on invariant clusters
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '664'
abstract:
- lang: eng
text: Immune cells communicate using cytokine signals, but the quantitative rules
of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et
al. (2017) suggest that the distribution of a cytokine within a lymphatic organ
is primarily governed by the local density of cells consuming it.
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520.
doi:10.1016/j.immuni.2017.04.006
apa: Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity.
Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006
chicago: Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity.
Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.
ieee: F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity,
vol. 46, no. 4. Cell Press, pp. 519–520, 2017.
ista: Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.
mla: Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity,
vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.
short: F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-18T00:00:00Z
date_updated: 2024-03-25T23:30:05Z
day: '18'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2017.04.006
intvolume: ' 46'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 519 - 520
publication: Immunity
publication_identifier:
issn:
- '10747613'
publication_status: published
publisher: Cell Press
publist_id: '7065'
quality_controlled: '1'
related_material:
record:
- id: '6947'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The dynamic cytokine niche
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2017'
...
---
_id: '665'
abstract:
- lang: eng
text: The molecular mechanisms underlying phenotypic variation in isogenic bacterial
populations remain poorly understood.We report that AcrAB-TolC, the main multidrug
efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell
poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex
formation. Mother cells inheriting old poles are phenotypically distinct and display
increased drug efflux activity relative to daughters. Consequently, we find systematic
and long-lived growth differences between mother and daughter cells in the presence
of subinhibitory drug concentrations. A simple model for biased partitioning predicts
a population structure of long-lived and highly heterogeneous phenotypes. This
straightforward mechanism of generating sustained growth rate differences at subinhibitory
antibiotic concentrations has implications for understanding the emergence of
multidrug resistance in bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M
full_name: Andersson, Anna M
id: 2B8A40DA-F248-11E8-B48F-1D18A9856A87
last_name: Andersson
orcid: 0000-0003-2912-6769
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Enrique
full_name: Balleza, Enrique
last_name: Balleza
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- 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: Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug
efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science.
2017;356(6335):311-315. doi:10.1126/science.aaf4762
apa: Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild,
R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB
TolC underlies long lived phenotypic heterogeneity. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.aaf4762
chicago: Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza,
Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning
of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
ieee: T. Bergmiller et al., “Biased partitioning of the multidrug efflux
pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science,
vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315,
2017.
ista: Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik
G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC
underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
mla: Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump
AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol.
356, no. 6335, American Association for the Advancement of Science, 2017, pp.
311–15, doi:10.1126/science.aaf4762.
short: T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild,
G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-21T00:00:00Z
date_updated: 2024-02-21T13:49:00Z
day: '21'
department:
- _id: CaGu
- _id: GaTk
- _id: Bio
doi: 10.1126/science.aaf4762
intvolume: ' 356'
issue: '6335'
language:
- iso: eng
month: '04'
oa_version: None
page: 311 - 315
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7064'
quality_controlled: '1'
related_material:
record:
- id: '5560'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long
lived phenotypic heterogeneity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2017'
...
---
_id: '666'
abstract:
- lang: eng
text: Antibiotics elicit drastic changes in microbial gene expression, including
the induction of stress response genes. While certain stress responses are known
to “cross-protect” bacteria from other stressors, it is unclear whether cellular
responses to antibiotics have a similar protective role. By measuring the genome-wide
transcriptional response dynamics of Escherichia coli to four antibiotics, we
found that trimethoprim induces a rapid acid stress response that protects bacteria
from subsequent exposure to acid. Combining microfluidics with time-lapse imaging
to monitor survival and acid stress response in single cells revealed that the
noisy expression of the acid resistance operon gadBC correlates with single-cell
survival. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. The seemingly random single-cell
survival under acid stress can therefore be predicted from gadBC expression and
rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap
for identifying the molecular mechanisms of single-cell cross-protection between
antibiotics and other stressors.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts
subsequent single cell survival in an acidic environment. Cell Systems.
2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to
antibiotic stress predicts subsequent single cell survival in an acidic environment.
Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response
to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.”
Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic
stress predicts subsequent single cell survival in an acidic environment,” Cell
Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress
predicts subsequent single cell survival in an acidic environment. Cell Systems.
4(4), 393–403.
mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent
Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no.
4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-07T12:00:25Z
day: '26'
ddc:
- '576'
- '610'
department:
- _id: ToBo
- _id: GaTk
doi: 10.1016/j.cels.2017.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 04ff20011c3d9a601c514aa999a5fe1a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:54Z
date_updated: 2020-07-14T12:47:35Z
file_id: '5041'
file_name: IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf
file_size: 2438660
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 393 - 403
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Cell Systems
publication_identifier:
issn:
- '24054712'
publication_status: published
publisher: Cell Press
publist_id: '7061'
pubrep_id: '901'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Noisy response to antibiotic stress predicts subsequent single cell survival
in an acidic environment
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2017'
...
---
_id: '667'
abstract:
- lang: eng
text: Perinatal exposure to penicillin may result in longlasting gut and behavioral
changes.
article_number: '2786'
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. The antisocial side of antibiotics. Science Translational Medicine.
2017;9(387). doi:10.1126/scitranslmed.aan2786
apa: Novarino, G. (2017). The antisocial side of antibiotics. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786
chicago: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786.
ieee: G. Novarino, “The antisocial side of antibiotics,” Science Translational
Medicine, vol. 9, no. 387. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. The antisocial side of antibiotics. Science Translational
Medicine. 9(387), 2786.
mla: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational
Medicine, vol. 9, no. 387, 2786, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aan2786.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2021-01-12T08:08:30Z
day: '26'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aan2786
intvolume: ' 9'
issue: '387'
language:
- iso: eng
month: '04'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7060'
quality_controlled: '1'
scopus_import: 1
status: public
title: The antisocial side of antibiotics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...