---
_id: '15243'
abstract:
- lang: eng
text: High-energy (>250 keV) emission has been detected persisting for several tens
of seconds after the initial spike of magnetar giant flares (GFs). It has been
conjectured that this emission might arise via inverse Compton scattering in a
highly extended corona generated by super-Eddington outflows high up in the magnetosphere.
In this paper, we undertake a detailed examination of this model. We investigate
the properties of the required scatterers, and whether the mechanism is consistent
with the degree of pulsed emission observed in the tail of the GF. We conclude
that the mechanism is consistent with current data, although the origin of the
scattering population remains an open question. We propose an alternative picture
in which the emission is closer to that star and is dominated by synchrotron radiation.
The Reuven Ramaty High Energy Solar Spectroscopic Imager observations of the 2004
December flare modestly favour this latter picture. We assess the prospects for
the Fermi Gamma-ray Space Telescope to detect and characterize a similar high-energy
component in a future GF. Such a detection should help to resolve some of the
outstanding issues.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: C.
full_name: Elenbaas, C.
last_name: Elenbaas
- first_name: D.
full_name: Huppenkothen, D.
last_name: Huppenkothen
- first_name: C.
full_name: Omand, C.
last_name: Omand
- first_name: A. L.
full_name: Watts, A. L.
last_name: Watts
- first_name: E.
full_name: Bissaldi, E.
last_name: Bissaldi
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: J.
full_name: Heyl, J.
last_name: Heyl
citation:
ama: Elenbaas C, Huppenkothen D, Omand C, et al. Magnetar giant flare high-energy
emission. Monthly Notices of the Royal Astronomical Society. 2017;471(2):1856-1872.
doi:10.1093/mnras/stx1727
apa: Elenbaas, C., Huppenkothen, D., Omand, C., Watts, A. L., Bissaldi, E., Caiazzo,
I., & Heyl, J. (2017). Magnetar giant flare high-energy emission. Monthly
Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1727
chicago: Elenbaas, C., D. Huppenkothen, C. Omand, A. L. Watts, E. Bissaldi, Ilaria
Caiazzo, and J. Heyl. “Magnetar Giant Flare High-Energy Emission.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2017.
https://doi.org/10.1093/mnras/stx1727.
ieee: C. Elenbaas et al., “Magnetar giant flare high-energy emission,” Monthly
Notices of the Royal Astronomical Society, vol. 471, no. 2. Oxford University
Press, pp. 1856–1872, 2017.
ista: Elenbaas C, Huppenkothen D, Omand C, Watts AL, Bissaldi E, Caiazzo I, Heyl
J. 2017. Magnetar giant flare high-energy emission. Monthly Notices of the Royal
Astronomical Society. 471(2), 1856–1872.
mla: Elenbaas, C., et al. “Magnetar Giant Flare High-Energy Emission.” Monthly
Notices of the Royal Astronomical Society, vol. 471, no. 2, Oxford University
Press, 2017, pp. 1856–72, doi:10.1093/mnras/stx1727.
short: C. Elenbaas, D. Huppenkothen, C. Omand, A.L. Watts, E. Bissaldi, I. Caiazzo,
J. Heyl, Monthly Notices of the Royal Astronomical Society 471 (2017) 1856–1872.
date_created: 2024-03-26T10:41:24Z
date_published: 2017-07-13T00:00:00Z
date_updated: 2024-04-08T07:05:47Z
day: '13'
doi: 10.1093/mnras/stx1727
extern: '1'
external_id:
arxiv:
- '1707.02922'
intvolume: ' 471'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1707.02922
month: '07'
oa: 1
oa_version: Preprint
page: 1856-1872
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetar giant flare high-energy emission
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 471
year: '2017'
...
---
_id: '1061'
abstract:
- lang: eng
text: 'Background: Metabolic engineering and synthetic biology of cyanobacteria
offer a promising sustainable alternative approach for fossil-based ethylene production,
by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly
into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis
sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce
ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae
pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the
ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene.
Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene
production through the integration of a codon-optimized version of the efe gene
under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\''-AGGAGG-3\'')
as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased
ethylene production twofold by RBS screening and further investigated improving
ethylene production from a single gene copy of efe, using multiple tandem promoters
and by putting our best construct on an RSF1010-based broad-host-self-replicating
plasmid, which has a higher copy number than the genome. Moreover, to raise the
intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene
is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced
the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the
glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however,
surprisingly, ethylene production was lower in this strain than in the wild-type
background. Conclusion: Making use of different RBS sequences, production of ethylene
ranging over a 20-fold difference has been achieved. However, a further increase
of production through multiple tandem promoters and a broad-host plasmid was not
achieved speculating that the transcription strength and the gene copy number
are not the limiting factors in our system.'
article_number: '34'
article_processing_charge: No
author:
- first_name: Vinod
full_name: Veetil, Vinod
last_name: Veetil
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
citation:
ama: Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis
sp PCC 6803 strains. Microbial Cell Factories. 2017;16(1). doi:10.1186/s12934-017-0645-5
apa: Veetil, V., Angermayr, A., & Hellingwerf, K. (2017). Ethylene production
with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories.
BioMed Central. https://doi.org/10.1186/s12934-017-0645-5
chicago: Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production
with Engineered Synechocystis Sp PCC 6803 Strains.” Microbial Cell Factories.
BioMed Central, 2017. https://doi.org/10.1186/s12934-017-0645-5.
ieee: V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered
Synechocystis sp PCC 6803 strains,” Microbial Cell Factories, vol. 16,
no. 1. BioMed Central, 2017.
ista: Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered
Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.
mla: Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp
PCC 6803 Strains.” Microbial Cell Factories, vol. 16, no. 1, 34, BioMed
Central, 2017, doi:10.1186/s12934-017-0645-5.
short: V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).
date_created: 2018-12-11T11:49:56Z
date_published: 2017-02-23T00:00:00Z
date_updated: 2023-09-20T12:09:21Z
day: '23'
ddc:
- '579'
doi: 10.1186/s12934-017-0645-5
extern: '1'
external_id:
isi:
- '000397733000001'
pmid:
- '28231787'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:50Z
date_updated: 2018-12-12T10:16:50Z
file_id: '5240'
file_name: IST-2017-792-v1+1_s12934-017-0645-5.pdf
file_size: 1361313
relation: main_file
file_date_updated: 2018-12-12T10:16:50Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Microbial Cell Factories
publication_identifier:
issn:
- '14752859'
publication_status: published
publisher: BioMed Central
publist_id: '6325'
pubrep_id: '792'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ethylene production with engineered Synechocystis sp PCC 6803 strains
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: 16
year: '2017'
...
---
_id: '1062'
abstract:
- lang: eng
text: Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates
the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that
MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’
to the less frequent ‘burst’ firing. This latter is evident in a small fraction
of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available
or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted.
Burst firing causes large increases of Ca2+‐entry and potentiates CA release by
∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the
aim to uncover a physiological role for burst‐firing we investigated the effects
of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0
and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts.
Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase
of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive
TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo
7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that
support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures
of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could
be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of
the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold),
showing that the action of protons on vesicle release is mainly a result of the
ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide
direct evidence suggesting that MCCs respond to low pHo with sustained depolarization,
burst firing and enhanced CA‐secretion, thus mimicking the physiological response
of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and
muscle fatigue.
article_processing_charge: No
author:
- first_name: Laura
full_name: Guarina, Laura
last_name: Guarina
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing
and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 2017;595(8):2587-2609.
doi:10.1113/JP273735
apa: Guarina, L., Vandael, D. H., Carabelli, V., & Carbone, E. (2017). Low pH
inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK
channels while preserving Cav1 channels in mouse chromaffin cells. Journal
of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP273735
chicago: Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone.
“Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1
and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” Journal
of Physiology. Wiley-Blackwell, 2017. https://doi.org/10.1113/JP273735.
ieee: L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts
burst firing and catecholamine release by blocking TASK-1 and BK channels while
preserving Cav1 channels in mouse chromaffin cells,” Journal of Physiology,
vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.
ista: Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst
firing and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.
mla: Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine
Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse
Chromaffin Cells.” Journal of Physiology, vol. 595, no. 8, Wiley-Blackwell,
2017, pp. 2587–609, doi:10.1113/JP273735.
short: L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology
595 (2017) 2587–2609.
date_created: 2018-12-11T11:49:56Z
date_published: 2017-04-15T00:00:00Z
date_updated: 2023-09-20T12:09:47Z
day: '15'
doi: 10.1113/JP273735
extern: '1'
external_id:
isi:
- '000399430300022'
intvolume: ' 595'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: '2587 - 2609 '
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6326'
quality_controlled: '1'
status: public
title: Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1
and BK channels while preserving Cav1 channels in mouse chromaffin cells
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 595
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2025-07-10T11:49:52Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2017'
...
---
_id: '1065'
abstract:
- lang: eng
text: 'We consider the problem of reachability in pushdown graphs. We study the
problem for pushdown graphs with constant treewidth. Even for pushdown graphs
with treewidth 1, for the reachability problem we establish the following: (i)
the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem
would contradict the k-clique conjecture and imply faster combinatorial algorithms
for cliques in graphs.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information
Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003
apa: Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant
treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003
chicago: Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with
Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.
ieee: K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,”
Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.
ista: Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth.
Information Processing Letters. 122, 25–29.
mla: Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant
Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp.
25–29, doi:10.1016/j.ipl.2017.02.003.
short: K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-07-10T11:49:53Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: HeEd
doi: 10.1016/j.ipl.2017.02.003
ec_funded: 1
external_id:
isi:
- '000399506600005'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2019-10-15T07:44:51Z
file_id: '4998'
file_name: IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf
file_size: 247657
relation: main_file
file_date_updated: 2019-10-15T07:44:51Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 25 - 29
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Information Processing Letters
publication_identifier:
issn:
- 0020-0190
publication_status: published
publisher: Elsevier
publist_id: '6323'
pubrep_id: '991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pushdown reachability with constant treewidth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2017'
...
---
OA_place: publisher
OA_type: free access
_id: '1066'
abstract:
- lang: eng
text: "Simulation is an attractive alternative to language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. Simulation has also been extended in two orthogonal directions, namely,
(1) fair simulation, for simulation over specified set of infinite runs; and (2)
quantitative simulation, for simulation between weighted automata. While fair
trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial
time. For weighted automata, the (quantitative) language inclusion problem is
undecidable in general, whereas the (quantitative) simulation reduces to quantitative
games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we
study (quantitative) simulation for weighted automata with Büchi acceptance conditions,
i.e., we generalize fair simulation from non-weighted automata to weighted automata.
We show that imposing Büchi acceptance conditions on weighted automata changes
many fundamental properties of the simulation games, yet they still admit pseudo-polynomial
time algorithms."
acknowledgement: This research was funded in part by the European Research Council
(ERC) under grant agreements 267989 (QUAREM), 279307 (Graph Games), by the Austrian
Science Fund (FWF) projects S11402-N23 (RiSE), S11407-N23 (RiSE), P23499-N23, and
Microsoft faculty fellows award.
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation
games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative
fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
“Quantitative Fair Simulation Games.” Information and Computation. Elsevier,
2017. https://doi.org/10.1016/j.ic.2016.10.006.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair
simulation games,” Information and Computation, vol. 254, no. 2. Elsevier,
pp. 143–166, 2017.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation
games. Information and Computation. 254(2), 143–166.
mla: Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information
and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation
254 (2017) 143–166.
corr_author: '1'
date_created: 2018-12-11T11:49:58Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-06-25T11:18:09Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2016.10.006
ec_funded: 1
external_id:
isi:
- '000402025600002'
intvolume: ' 254'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ic.2016.10.006
month: '06'
oa: 1
oa_version: Published Version
page: 143 - 166
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '6322'
quality_controlled: '1'
related_material:
record:
- id: '5428'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Quantitative fair simulation games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 254
year: '2017'
...
---
_id: '10663'
abstract:
- lang: eng
text: 'The superconducting state of matter enables one to observe quantum effects
on the macroscopic scale and hosts many fascinating phenomena. Topological defects
of the superconducting order parameter, such as vortices and fluxoid states in
multiply connected structures, are often the key ingredients of these phenomena.
This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for
investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures.
The technique relies on the magneto-mechanical coupling of a MFM cantilever to
the motion of fluxons. The novelty of the technique is that a magnetic particle
attached to the cantilever is used not only to sense the state of a SC structure,
but also as a primary source of the inhomogeneous magnetic field which induces
that state. Φ0-MFM enables us to map the transitions between tip-induced states
during a scan: at the positions of the tip, where the two lowest energy states
become degenerate, small oscillations of the tip drive the transitions between
these states, which causes a significant shift in the resonant frequency and dissipation
of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions
form concentric contours on a scan. We show that the changes in the cantilever
resonant frequency and dissipation are well-described by a stochastic resonance
(SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model
allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin
(LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR
model to qualitatively study the effects of a locally applied magnetic field on
the phase slip rate in rings containing constrictions. The states with multiple
vortices or winding numbers could be useful for the development of novel superconducting
devices, or the study of vortex interactions and interference effects. Using Φ0-MFM
allows us to induce, probe and control fluxoid states in thin wall structures
comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions
allow us to identify the underlying states and to investigate their energetics
and dynamics even in complicated structures.'
alternative_title:
- Graduate Dissertations and Theses at Illinois
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
citation:
ama: Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting
structures. 2017.
apa: Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting
structures. University of Illinois at Urbana-Champaign.
chicago: Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting
Structures.” University of Illinois at Urbana-Champaign, 2017.
ieee: H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting
structures,” University of Illinois at Urbana-Champaign, 2017.
ista: Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting
structures. University of Illinois at Urbana-Champaign.
mla: Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting
Structures. University of Illinois at Urbana-Champaign, 2017.
short: H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting
Structures, University of Illinois at Urbana-Champaign, 2017.
date_created: 2022-01-25T14:54:14Z
date_published: 2017-09-18T00:00:00Z
date_updated: 2024-10-14T11:13:43Z
day: '18'
degree_awarded: PhD
extern: '1'
keyword:
- physics
- superconductivity
- magnetic force microscopy
- phase slips
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hdl.handle.net/2142/99178
month: '09'
oa: 1
oa_version: Published Version
page: '103'
publication_status: published
publisher: University of Illinois at Urbana-Champaign
status: public
supervisor:
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
title: Magnetic force microscopy studies of mesoscopic superconducting structures
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '1067'
abstract:
- lang: eng
text: Embryo morphogenesis relies on highly coordinated movements of different tissues.
However, remarkably little is known about how tissues coordinate their movements
to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements
first become apparent during “doming,” when the blastoderm begins to spread over
the yolk sac, a process involving coordinated epithelial surface cell layer expansion
and mesenchymal deep cell intercalations. Here, we find that active surface cell
expansion represents the key process coordinating tissue movements during doming.
By using a combination of theory and experiments, we show that epithelial surface
cells not only trigger blastoderm expansion by reducing tissue surface tension,
but also drive blastoderm thinning by inducing tissue contraction through radial
deep cell intercalations. Thus, coordinated tissue expansion and thinning during
doming relies on surface cells simultaneously controlling tissue surface tension
and radial tissue contraction.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Martin
full_name: Bock, Martin
last_name: Bock
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical
basis of coordinated tissue spreading in zebrafish gastrulation. Developmental
Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010
apa: Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg,
C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish
gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010
chicago: Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume
Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue
Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017.
https://doi.org/10.1016/j.devcel.2017.01.010.
ieee: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg,
“The physical basis of coordinated tissue spreading in zebrafish gastrulation,”
Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.
ista: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017.
The physical basis of coordinated tissue spreading in zebrafish gastrulation.
Developmental Cell. 40(4), 354–366.
mla: Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading
in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press,
2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.
short: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg,
Developmental Cell 40 (2017) 354–366.
corr_author: '1'
date_created: 2018-12-11T11:49:58Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2025-07-10T11:49:55Z
day: '27'
ddc:
- '572'
- '597'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2017.01.010
ec_funded: 1
external_id:
isi:
- '000395368300007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:57Z
date_updated: 2018-12-12T10:10:57Z
file_id: '4849'
file_name: IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf
file_size: 6866187
relation: main_file
file_date_updated: 2018-12-12T10:10:57Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 354 - 366
project:
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Cell Press
publist_id: '6320'
pubrep_id: '869'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The physical basis of coordinated tissue spreading in zebrafish gastrulation
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: 40
year: '2017'
...
---
_id: '1072'
abstract:
- lang: eng
text: Given a finite set of points in Rn and a radius parameter, we study the Čech,
Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized
discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel
sets of generalized discrete Morse functions, we prove that the four complexes
are simple-homotopy equivalent by a sequence of simplicial collapses, which are
explicitly described by a single discrete gradient field.
acknowledgement: This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP),
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR
109 “Discretization in Geometry and Dynamics”.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions
of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991
apa: Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay
complexes. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/6991
chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and
Delaunay Complexes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.
ieee: U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,”
Transactions of the American Mathematical Society, vol. 369, no. 5. American
Mathematical Society, pp. 3741–3762, 2017.
ista: Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes.
Transactions of the American Mathematical Society. 369(5), 3741–3762.
mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay
Complexes.” Transactions of the American Mathematical Society, vol. 369,
no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.
short: U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society
369 (2017) 3741–3762.
date_created: 2018-12-11T11:49:59Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2025-04-15T08:37:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/6991
ec_funded: 1
external_id:
arxiv:
- '1312.1231'
isi:
- '000398030400024'
intvolume: ' 369'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.1231
month: '05'
oa: 1
oa_version: Preprint
page: 3741 - 3762
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '6311'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Morse theory of Čech and delaunay complexes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 369
year: '2017'
...
---
_id: '1073'
abstract:
- lang: eng
text: Let X and Y be finite simplicial sets (e.g. finite simplicial complexes),
both equipped with a free simplicial action of a finite group G. Assuming that
Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes
the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|;
the existence of such a map can be decided even for dimX≤2d+1. This yields the
first algorithm for deciding topological embeddability of a k-dimensional finite
simplicial complex into Rn under the condition k≤23n−1. More generally, we present
an algorithm that, given a lifting-extension problem satisfying an appropriate
stability assumption, computes the set of all homotopy classes of solutions. This
result is new even in the non-equivariant situation.
article_processing_charge: No
arxiv: 1
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
citation:
ama: Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension
problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6
apa: Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of
the lifting extension problem. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-016-9855-6
chicago: Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability
of the Lifting Extension Problem.” Discrete & Computational Geometry.
Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.
ieee: M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting
extension problem,” Discrete & Computational Geometry, vol. 54, no.
4. Springer, pp. 915–965, 2017.
ista: Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting
extension problem. Discrete & Computational Geometry. 54(4), 915–965.
mla: Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.”
Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017,
pp. 915–65, doi:10.1007/s00454-016-9855-6.
short: M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54
(2017) 915–965.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-06-04T08:11:10Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-016-9855-6
external_id:
arxiv:
- '1307.6444'
isi:
- '000400072700008'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1307.6444
month: '06'
oa: 1
oa_version: Submitted Version
page: 915 - 965
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6309'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic solvability of the lifting extension problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2017'
...
---
_id: '10745'
abstract:
- lang: eng
text: New ways to investigate and manipulate fluxoid and vortex states of mesoscopic
superconducting structures are of great interest. The states with multiple vortices
or winding numbers could be useful for the study of vortex interactions and interference
effects, the braiding of Majorana bound states by winding vortices, and the development
of novel superconducting devices. We demonstrate a methodology based on magnetic
force microscopy that allows us to induce, probe and control fluxoid states in
thin wall structures comprised of multiple loops. By using micro-magnet as a source
of inhomogeneous magnetic field, we can efficiently explore the configuration
space of fluxoid states. Scanning over the structure reveals the energy crossing
points of the lowest laying fluxoid states. This is due the strong interaction
of cantilever with thermally activated fluxoid transitions at points of degeneracy.
We show that measured patterns of fluxoid transitions allow to identify the states,
investigate their energetics, and manipulate them. Further, we show that the dynamics
of driven fluxoid transitions can be described by stochastic resonance model,
which provides a unique way of measuring fluxoid transition rate and related energy
barrier for chosen transitions even in complicated structures
alternative_title:
- Bulletin of the American Physical Society
article_number: P39.00011
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tyler
full_name: Naibert, Tyler
last_name: Naibert
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Polshyn H, Naibert T, Budakian R. Probing and controlling fluxoid states
in multiply-connected mesoscopic superconducting structures. In: APS March
Meeting 2017. Vol 62. American Physical Society; 2017.'
apa: 'Polshyn, H., Naibert, T., & Budakian, R. (2017). Probing and controlling
fluxoid states in multiply-connected mesoscopic superconducting structures. In
APS March Meeting 2017 (Vol. 62). New Orleans, LA, United States: American
Physical Society.'
chicago: Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling
Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In
APS March Meeting 2017, Vol. 62. American Physical Society, 2017.
ieee: H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid
states in multiply-connected mesoscopic superconducting structures,” in APS
March Meeting 2017, New Orleans, LA, United States, 2017, vol. 62, no. 4.
ista: 'Polshyn H, Naibert T, Budakian R. 2017. Probing and controlling fluxoid
states in multiply-connected mesoscopic superconducting structures. APS March
Meeting 2017. APS: American Physical Society, Bulletin of the American Physical
Society, vol. 62, P39.00011.'
mla: Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected
Mesoscopic Superconducting Structures.” APS March Meeting 2017, vol. 62,
no. 4, P39.00011, American Physical Society, 2017.
short: H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American
Physical Society, 2017.
conference:
end_date: 2017-03-17
location: New Orleans, LA, United States
name: 'APS: American Physical Society'
start_date: 2017-03-13
date_created: 2022-02-08T09:49:17Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2022-02-08T10:44:35Z
day: '01'
extern: '1'
intvolume: ' 62'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR17/Session/P39.11
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2017
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: ' Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting
structures'
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 62
year: '2017'
...
---
_id: '1075'
alternative_title:
- American Studies in Austria
author:
- first_name: Bernhard
full_name: Wenzl, Bernhard
id: 479E9046-F248-11E8-B48F-1D18A9856A87
last_name: Wenzl
citation:
ama: 'Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on
"The Vienna Frontier" In: Parker J, Poole R, eds. Austria
and America: 20th-Century Cross-Cultural Encounters. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London;
2017:73-80.'
apa: 'Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos
Reports on "The Vienna Frontier" In J. Parker & R. Poole
(Eds.), Austria and America: 20th-Century Cross-Cultural Encounters (Vol.
15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.'
chicago: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos
Reports on "The Vienna Frontier"” In Austria and America:
20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph
Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.'
ieee: 'B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports
on "The Vienna Frontier",” in Austria and America: 20th-Century
Cross-Cultural Encounters, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag
Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.'
ista: 'Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports
on "The Vienna Frontier" In: Austria and America: 20th-Century
Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.'
mla: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos
Reports on "The Vienna Frontier"” Austria and America: 20th-Century
Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, vol. 15,
LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.'
short: 'B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century
Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017,
pp. 73–80.'
date_created: 2018-12-11T11:50:00Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2021-01-12T06:48:06Z
day: '01'
ddc:
- '001'
editor:
- first_name: Joshua
full_name: Parker, Joshua
last_name: Parker
- first_name: Ralph
full_name: Poole, Ralph
last_name: Poole
extern: '1'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:06Z
date_updated: 2018-12-12T10:08:06Z
file_id: '4666'
file_name: IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf
file_size: 380624
relation: main_file
file_date_updated: 2018-12-12T10:08:06Z
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '02'
oa: 1
oa_version: None
page: 73 - 80
publication: 'Austria and America: 20th-Century Cross-Cultural Encounters'
publication_identifier:
isbn:
- 978-3643908124
publication_status: published
publisher: LIT Verlag Berlin-Münster-Wien-Zürich-London
publist_id: '6306'
status: public
title: 'An American in Allied-occupied Austria: John Dos Passos Reports on "The
Vienna Frontier"'
type: book_chapter
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2017'
...
---
_id: '1076'
abstract:
- lang: eng
text: Signatures of the Coulomb corrections in the photoelectron momentum distribution
during laser-induced ionization of atoms or ions in tunneling and multiphoton
regimes are investigated analytically in the case of a one-dimensional problem.
A high-order Coulomb-corrected strong-field approximation is applied, where the
exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov
state including the second-order corrections to the eikonal. Although without
high-order corrections our theory coincides with the known analytical R-matrix
(ARM) theory, we propose a simplified procedure for the matrix element derivation.
Rather than matching the eikonal Coulomb-Volkov wave function with the bound state
as in the ARM theory to remove the Coulomb singularity, we calculate the matrix
element via the saddle-point integration method by time as well as by coordinate,
and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron
momentum distribution with respect to the ARM theory due to high-order corrections
is analyzed for tunneling and multiphoton regimes. The relation of the quantum
corrections to the tunneling delay time is discussed.
article_number: '023403'
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Jiří
full_name: Daněk, Jiří
last_name: Daněk
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Karen
full_name: Hatsagortsyan, Karen
last_name: Hatsagortsyan
- first_name: Christoph
full_name: Keitel, Christoph
last_name: Keitel
citation:
ama: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization
via a high-order Coulomb-corrected strong-field approximation. Physical Review
A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403
apa: Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C.
(2017). Strong-field ionization via a high-order Coulomb-corrected strong-field
approximation. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403
chicago: Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan,
and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.
ieee: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation,”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2.
American Physical Society, 2017.
ista: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation. Physical
Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.
mla: Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.
short: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical
Review A - Atomic, Molecular, and Optical Physics 95 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2025-06-04T08:11:30Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.95.023403
ec_funded: 1
external_id:
arxiv:
- '1609.07018'
isi:
- '000400571700011'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.07018
month: '02'
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: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_identifier:
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
publist_id: '6305'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong-field ionization via a high-order Coulomb-corrected strong-field approximation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2017'
...
---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2025-07-10T11:49:59Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- 1742-5689
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2017'
...
---
_id: '1078'
abstract:
- lang: eng
text: 'One of the key questions in understanding plant development is how single
cells behave in a larger context of the tissue. Therefore, it requires the observation
of the whole organ with a high spatial- as well as temporal resolution over prolonged
periods of time, which may cause photo-toxic effects. This protocol shows a plant
sample preparation method for light-sheet microscopy, which is characterized by
mounting the plant vertically on the surface of a gel. The plant is mounted in
such a way that the roots are submerged in a liquid medium while the leaves remain
in the air. In order to ensure photosynthetic activity of the plant, a custom-made
lighting system illuminates the leaves. To keep the roots in darkness the water
surface is covered with sheets of black plastic foil. This method allows long-term
imaging of plant organ development in standardized conditions. '
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
article_number: e55044
article_processing_charge: No
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel. Journal of visualized experiments
JoVE. 2017;2017(119). doi:10.3791/55044
apa: von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence
microscopy of plant roots growing on the surface of a gel. Journal of Visualized
Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044
chicago: Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet
Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal
of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.
ieee: D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel,” Journal of visualized experiments
JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.
ista: von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel. Journal of visualized experiments
JoVE. 2017(119), e55044.
mla: von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant
Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE,
vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.
short: D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments
JoVE 2017 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-18T00:00:00Z
date_updated: 2025-04-15T06:50:23Z
day: '18'
ddc:
- '580'
department:
- _id: JiFr
- _id: Bio
doi: 10.3791/55044
ec_funded: 1
external_id:
isi:
- '000397847200041'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:31Z
date_updated: 2018-12-12T10:16:31Z
file_id: '5219'
file_name: IST-2017-808-v1+1_2017_VWangenheim_list.pdf
file_size: 57678
relation: main_file
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:32Z
date_updated: 2018-12-12T10:16:32Z
file_id: '5220'
file_name: IST-2017-808-v1+2_2017_VWangenheim_article.pdf
file_size: 1317820
relation: main_file
file_date_updated: 2018-12-12T10:16:32Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
issue: '119'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of visualized experiments JoVE
publication_status: published
publisher: Journal of Visualized Experiments
publist_id: '6302'
pubrep_id: '808'
related_material:
record:
- id: '5565'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Light sheet fluorescence microscopy of plant roots growing on the surface of
a gel
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '1079'
abstract:
- lang: eng
text: We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory
for atoms and molecules. We prove the nonexistence of minimizers for the energy
functional when the number of electrons is large and the total nuclear charge
is small. This nonexistence result also applies to external potentials decaying
faster than the Coulomb potential. In the case of arbitrary nuclear charges, we
obtain the nonexistence of stable minimizers and radial minimizers.
article_number: '6'
article_processing_charge: No
arxiv: 1
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Hanne
full_name: Van Den Bosch, Hanne
last_name: Van Den Bosch
citation:
ama: Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory
with small nuclear charges. Mathematical Physics, Analysis and Geometry.
2017;20(2). doi:10.1007/s11040-017-9238-0
apa: Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis
and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0
chicago: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis
and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0.
ieee: P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker
theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry,
vol. 20, no. 2. Springer, 2017.
ista: Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker
theory with small nuclear charges. Mathematical Physics, Analysis and Geometry.
20(2), 6.
mla: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis
and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.
short: P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20
(2017).
date_created: 2018-12-11T11:50:02Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-06-04T08:11:50Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s11040-017-9238-0
external_id:
arxiv:
- '1603.07368'
isi:
- '000401270000004'
intvolume: ' 20'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.07368
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Mathematical Physics, Analysis and Geometry
publication_identifier:
issn:
- 1385-0172
publication_status: published
publisher: Springer
publist_id: '6300'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear
charges
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2017'
...
---
_id: '1080'
abstract:
- lang: eng
text: Reconstructing the evolutionary history of metastases is critical for understanding
their basic biological principles and has profound clinical implications. Genome-wide
sequencing data has enabled modern phylogenomic methods to accurately dissect
subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented
depth. However, existing methods are not designed to infer metastatic seeding
patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny
of metastases and map subclones to their anatomic locations. Treeomics infers
comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers.
Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing
artifacts; 7% of variants were misclassified by conventional statistical methods.
These artifacts can skew phylogenies by creating illusory tumour heterogeneity
among distinct samples. In silico benchmarking on simulated tumour phylogenies
across a wide range of sample purities (15–95%) and sequencing depths (25-800
× ) demonstrates the accuracy of Treeomics compared with existing methods.
article_number: '14114'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Alvin
full_name: Makohon Moore, Alvin
last_name: Makohon Moore
- first_name: Jeffrey
full_name: Gerold, Jeffrey
last_name: Gerold
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christine
full_name: Iacobuzio Donahue, Christine
last_name: Iacobuzio Donahue
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding
patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114
apa: Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio
Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of
human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114
chicago: Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu
Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing
Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature
Publishing Group, 2017. https://doi.org/10.1038/ncomms14114.
ieee: J. Reiter et al., “Reconstructing metastatic seeding patterns of human
cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017.
ista: Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue
C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of
human cancers. Nature Communications. 8, 14114.
mla: Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human
Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group,
2017, doi:10.1038/ncomms14114.
short: J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio
Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:02Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2025-07-10T11:50:00Z
day: '31'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1038/ncomms14114
ec_funded: 1
external_id:
isi:
- '000393096600001'
file:
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content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:15Z
date_updated: 2018-12-12T10:15:15Z
file_id: '5133'
file_name: IST-2017-786-v1+1_ncomms14114.pdf
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file_date_updated: 2018-12-12T10:15:15Z
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intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '6301'
pubrep_id: '786'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstructing metastatic seeding patterns of human cancers
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: 8
year: '2017'
...
---
_id: '1085'
abstract:
- lang: eng
text: Sex chromosomes evolve once recombination is halted between a homologous pair
of chromosomes. The dominant model of sex chromosome evolution posits that recombination
is suppressed between emerging X and Y chromosomes in order to resolve sexual
conflict. Here we test this model using whole genome and transcriptome resequencing
data in the guppy, a model for sexual selection with many Y-linked colour traits.
We show that although the nascent Y chromosome encompasses nearly half of the
linkage group, there has been no perceptible degradation of Y chromosome gene
content or activity. Using replicate wild populations with differing levels of
sexually antagonistic selection for colour, we also show that sexual selection
leads to greater expansion of the non-recombining region and increased Y chromosome
divergence. These results provide empirical support for longstanding models of
sex chromosome catalysis, and suggest an important role for sexual selection and
sexual conflict in genome evolution.
article_number: '14251'
article_processing_charge: No
author:
- first_name: Alison
full_name: Wright, Alison
last_name: Wright
- first_name: Iulia
full_name: Darolti, Iulia
last_name: Darolti
- first_name: Natasha
full_name: Bloch, Natasha
last_name: Bloch
- first_name: Vicencio
full_name: Oostra, Vicencio
last_name: Oostra
- first_name: Benjamin
full_name: Sandkam, Benjamin
last_name: Sandkam
- first_name: Séverine
full_name: Buechel, Séverine
last_name: Buechel
- first_name: Niclas
full_name: Kolm, Niclas
last_name: Kolm
- first_name: Felix
full_name: Breden, Felix
last_name: Breden
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Judith
full_name: Mank, Judith
last_name: Mank
citation:
ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests
role of sexual selection in guppy sex chromosome formation. Nature Communications.
2017;8. doi:10.1038/ncomms14251
apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., …
Mank, J. (2017). Convergent recombination suppression suggests role of sexual
selection in guppy sex chromosome formation. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms14251
chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin
Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith
Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection
in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/ncomms14251.
ieee: A. Wright et al., “Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden
F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation. Nature Communications.
8, 14251.
mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role
of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications,
vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251.
short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm,
F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:04Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2025-07-10T11:50:01Z
day: '31'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1038/ncomms14251
external_id:
isi:
- '000392953700001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:22Z
date_updated: 2018-12-12T10:15:22Z
file_id: '5141'
file_name: IST-2017-791-v1+1_ncomms14251.pdf
file_size: 955256
relation: main_file
file_date_updated: 2018-12-12T10:15:22Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '6292'
pubrep_id: '791'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergent recombination suppression suggests role of sexual selection in guppy
sex chromosome formation
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: 8
year: '2017'
...
---
_id: '1086'
abstract:
- lang: eng
text: 'Characterisation of G protein-coupled receptors (GPCR) relies on the availability
of a toolbox of ligands that selectively modulate different functional states
of the receptors. To uncover such molecules, we explored a unique strategy for
ligand discovery that takes advantage of the evolutionary conservation of the
600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect
oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger),
identified and cloned its cognate receptor and determined its pharmacological
properties on the insect and human oxytocin/vasopressin receptors. Subsequently,
we identified a functional dichotomy: inotocin activated the insect inotocin and
the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement
of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist
([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over
the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further
investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor
interaction, which led to the identification of key residues of the receptors
that are important for ligand functionality and selectivity. These observations
could play an important role for development of oxytocin/vasopressin receptor
modulators that would enable clear distinction of the physiological and pathological
responses of the individual receptor subtypes.'
article_processing_charge: No
author:
- first_name: Maria
full_name: Di Giglio, Maria
last_name: Di Giglio
- first_name: Markus
full_name: Muttenthaler, Markus
last_name: Muttenthaler
- first_name: Kasper
full_name: Harpsøe, Kasper
last_name: Harpsøe
- first_name: Zita
full_name: Liutkeviciute, Zita
last_name: Liutkeviciute
- first_name: Peter
full_name: Keov, Peter
last_name: Keov
- first_name: Thomas
full_name: Eder, Thomas
last_name: Eder
- first_name: Thomas
full_name: Rattei, Thomas
last_name: Rattei
- first_name: Sarah
full_name: Arrowsmith, Sarah
last_name: Arrowsmith
- first_name: Susan
full_name: Wray, Susan
last_name: Wray
- first_name: Ales
full_name: Marek, Ales
last_name: Marek
- first_name: Tomas
full_name: Elbert, Tomas
last_name: Elbert
- first_name: Paul
full_name: Alewood, Paul
last_name: Alewood
- first_name: David
full_name: Gloriam, David
last_name: Gloriam
- first_name: Christian
full_name: Gruber, Christian
last_name: Gruber
citation:
ama: Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin
V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific
Reports. 2017;7:41002. doi:10.1038/srep41002
apa: Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P.,
Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor
antagonist from an evolutionary-related insect neuropeptide. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep41002
chicago: Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute,
Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin
V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific
Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41002.
ieee: M. Di Giglio et al., “Development of a human vasopressin V1a-receptor
antagonist from an evolutionary-related insect neuropeptide,” Scientific Reports,
vol. 7. Nature Publishing Group, p. 41002, 2017.
ista: Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei
T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017.
Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related
insect neuropeptide. Scientific Reports. 7, 41002.
mla: Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist
from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports,
vol. 7, Nature Publishing Group, 2017, p. 41002, doi:10.1038/srep41002.
short: M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T.
Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam,
C. Gruber, Scientific Reports 7 (2017) 41002.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:47:47Z
day: '01'
ddc:
- '570'
- '590'
doi: 10.1038/srep41002
external_id:
isi:
- '000393163800001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:59Z
date_updated: 2018-12-12T10:14:59Z
file_id: '5115'
file_name: IST-2017-790-v1+1_srep41002_1_.pdf
file_size: 1994139
relation: main_file
file_date_updated: 2018-12-12T10:14:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '41002'
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6291'
pubrep_id: '790'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related
insect neuropeptide
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: 7
year: '2017'
...
---
_id: '1087'
abstract:
- lang: eng
text: Using extensive direct numerical simulations, the dynamics of laminar-turbulent
fronts in pipe flow is investigated for Reynolds numbers between and 5500. We
here investigate the physical distinction between the fronts of weak and strong
slugs both by analysing the turbulent kinetic energy budget and by comparing the
downstream front motion to the advection speed of bulk turbulent structures. Our
study shows that weak downstream fronts travel slower than turbulent structures
in the bulk and correspond to decaying turbulence at the front. At the downstream
front speed becomes faster than the advection speed, marking the onset of strong
fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts
by feeding on the downstream laminar flow. Our study also suggests that temporal
fluctuations of production and dissipation at the downstream laminar-turbulent
front drive the dynamical switches between the two types of front observed up
to.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
arxiv: 1
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts
in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14
apa: Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure
of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge
University Press. https://doi.org/10.1017/jfm.2017.14
chicago: Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure
of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge
University Press, 2017. https://doi.org/10.1017/jfm.2017.14.
ieee: B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent
fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University
Press, pp. 1045–1059, 2017.
ista: Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent
fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.
mla: Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.”
Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017,
pp. 1045–59, doi:10.1017/jfm.2017.14.
short: B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017)
1045–1059.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-25T00:00:00Z
date_updated: 2025-06-04T08:35:11Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.14
ec_funded: 1
external_id:
arxiv:
- '1603.04077'
isi:
- '000394376400044'
intvolume: ' 813'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.04077
month: '02'
oa: 1
oa_version: Submitted Version
page: 1045 - 1059
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
publist_id: '6290'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Speed and structure of turbulent fronts in pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 813
year: '2017'
...