---
_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'
...
---
_id: '1089'
abstract:
- lang: eng
text: We discuss properties of distributions that are multivariate totally positive
of order two (MTP2) related to conditional independence. In particular, we show
that any independence model generated by an MTP2 distribution is a compositional
semigraphoid which is upward-stable and singleton-transitive. In addition, we
prove that any MTP2 distribution satisfying an appropriate support condition is
faithful to its concentration graph. Finally, we analyze factorization properties
of MTP2 distributions and discuss ways of constructing MTP2 distributions; in
particular we give conditions on the log-linear parameters of a discrete distribution
which ensure MTP2 and characterize conditional Gaussian distributions which satisfy
MTP2.
article_processing_charge: No
arxiv: 1
author:
- first_name: Shaun
full_name: Fallat, Shaun
last_name: Fallat
- first_name: Steffen
full_name: Lauritzen, Steffen
last_name: Lauritzen
- first_name: Kayvan
full_name: Sadeghi, Kayvan
last_name: Sadeghi
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Nanny
full_name: Wermuth, Nanny
last_name: Wermuth
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
citation:
ama: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity
in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478
apa: Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik,
P. (2017). Total positivity in Markov structures. Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478
chicago: Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny
Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals
of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478.
ieee: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik,
“Total positivity in Markov structures,” Annals of Statistics, vol. 45,
no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017.
ista: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total
positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184.
mla: Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of
Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp.
1152–84, doi:10.1214/16-AOS1478.
short: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals
of Statistics 45 (2017) 1152–1184.
corr_author: '1'
date_created: 2018-12-11T11:50:05Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-06-04T08:35:37Z
day: '01'
department:
- _id: CaUh
doi: 10.1214/16-AOS1478
external_id:
arxiv:
- '1510.01290'
isi:
- '000404395900008'
intvolume: ' 45'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.01290
month: '06'
oa: 1
oa_version: Submitted Version
page: 1152 - 1184
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: Annals of Statistics
publication_identifier:
issn:
- 0090-5364
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6288'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Total positivity in Markov structures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2017'
...
---
_id: '1104'
abstract:
- lang: eng
text: In the early visual system, cells of the same type perform the same computation
in different places of the visual field. How these cells code together a complex
visual scene is unclear. A common assumption is that cells of a single-type extract
a single-stimulus feature to form a feature map, but this has rarely been observed
directly. Using large-scale recordings in the rat retina, we show that a homogeneous
population of fast OFF ganglion cells simultaneously encodes two radically different
features of a visual scene. Cells close to a moving object code quasilinearly
for its position, while distant cells remain largely invariant to the object's
position and, instead, respond nonlinearly to changes in the object's speed. We
develop a quantitative model that accounts for this effect and identify a disinhibitory
circuit that mediates it. Ganglion cells of a single type thus do not code for
one, but two features simultaneously. This richer, flexible neural map might also
be present in other sensory systems.
article_number: '1964'
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Emilie
full_name: Mace, Emilie
last_name: Mace
- first_name: Pierre
full_name: Yger, Pierre
last_name: Yger
- first_name: Romain
full_name: Caplette, Romain
last_name: Caplette
- first_name: Serge
full_name: Picaud, Serge
last_name: Picaud
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion
cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre,
O. (2017). Multiplexed computations in retinal ganglion cells of a single type.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y
chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette,
Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal
Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.
ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells
of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing
Group, 2017.
ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O.
2017. Multiplexed computations in retinal ganglion cells of a single type. Nature
Communications. 8(1), 1964.
mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells
of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing
Group, 2017, doi:10.1038/s41467-017-02159-y.
short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik,
O. Marre, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:10Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2025-07-10T11:50:05Z
day: '06'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1038/s41467-017-02159-y
ec_funded: 1
external_id:
isi:
- '000417241200004'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:06Z
date_updated: 2018-12-12T10:16:06Z
file_id: '5191'
file_name: IST-2018-921-v1+1_s41467-017-02159-y.pdf
file_size: 2872887
relation: main_file
file_date_updated: 2018-12-12T10:16:06Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25CD3DD2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '604102'
name: Localization of ion channels and receptors by two and three-dimensional immunoelectron
microscopic approaches
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '6266'
pubrep_id: '921'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiplexed computations in retinal ganglion cells of a single type
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: '11065'
abstract:
- lang: eng
text: Premature aging disorders provide an opportunity to study the mechanisms that
drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of
the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins.
We sought to investigate protein homeostasis in this disease. Here, we report
a widespread increase in protein turnover in HGPS-derived cells compared to normal
cells. We determine that global protein synthesis is elevated as a consequence
of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts.
Depleting normal lamin A or inducing mutant lamin A expression are each sufficient
to drive nucleolar expansion. We further show that nucleolar size correlates with
donor age in primary fibroblasts derived from healthy individuals and that ribosomal
RNA production increases with age, indicating that nucleolar size and activity
can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan
in several systems, we show that increased ribosome biogenesis and activity are
a hallmark of premature aging.
article_number: '328'
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z
apa: Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein
translation in premature aging. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00322-z
chicago: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated
Protein Translation in Premature Aging.” Nature Communications. Springer
Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z.
ieee: A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation
in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017.
ista: Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 8, 328.
mla: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein
Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer
Nature, 2017, doi:10.1038/s41467-017-00322-z.
short: A. Buchwalter, M. Hetzer, Nature Communications 8 (2017).
date_created: 2022-04-07T07:45:50Z
date_published: 2017-08-30T00:00:00Z
date_updated: 2024-10-14T11:20:12Z
day: '30'
doi: 10.1038/s41467-017-00322-z
extern: '1'
external_id:
pmid:
- '28855503'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-00322-z
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleolar expansion and elevated protein translation in premature aging
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '11066'
abstract:
- lang: eng
text: Recent studies have shown that a subset of nucleoporins (Nups) can detach
from the nuclear pore complex and move into the nuclear interior to regulate transcription.
One such dynamic Nup, called Nup98, has been implicated in gene activation in
healthy cells and has been shown to drive leukemogenesis when mutated in patients
with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98
binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS
(complex of proteins associated with Set1) complex, which is required for deposition
of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98
or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3
at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated
in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation
of associated genes. Our findings establish a function of Nup98 in hematopoietic
gene activation and provide mechanistic insight into which Nup98 leukemic fusion
proteins promote AML.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Asako
full_name: McCloskey, Asako
last_name: McCloskey
- first_name: Maxim Nikolaievich
full_name: Shokhirev, Maxim Nikolaievich
last_name: Shokhirev
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Annie
full_name: Rathore, Annie
last_name: Rathore
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. Nup98
recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation
in hematopoietic progenitor cells. Genes & Development. 2017;31(22):2222-2234.
doi:10.1101/gad.306753.117
apa: Franks, T. M., McCloskey, A., Shokhirev, M. N., Benner, C., Rathore, A., &
Hetzer, M. (2017). Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters
to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes &
Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.306753.117
chicago: Franks, Tobias M., Asako McCloskey, Maxim Nikolaievich Shokhirev, Chris
Benner, Annie Rathore, and Martin Hetzer. “Nup98 Recruits the Wdr82–Set1A/COMPASS
Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor
Cells.” Genes & Development. Cold Spring Harbor Laboratory, 2017. https://doi.org/10.1101/gad.306753.117.
ieee: T. M. Franks, A. McCloskey, M. N. Shokhirev, C. Benner, A. Rathore, and M.
Hetzer, “Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate
H3K4 trimethylation in hematopoietic progenitor cells,” Genes & Development,
vol. 31, no. 22. Cold Spring Harbor Laboratory, pp. 2222–2234, 2017.
ista: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. 2017.
Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation
in hematopoietic progenitor cells. Genes & Development. 31(22), 2222–2234.
mla: Franks, Tobias M., et al. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to
Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.”
Genes & Development, vol. 31, no. 22, Cold Spring Harbor Laboratory,
2017, pp. 2222–34, doi:10.1101/gad.306753.117.
short: T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer,
Genes & Development 31 (2017) 2222–2234.
date_created: 2022-04-07T07:45:59Z
date_published: 2017-12-21T00:00:00Z
date_updated: 2024-10-14T11:20:24Z
day: '21'
doi: 10.1101/gad.306753.117
extern: '1'
external_id:
pmid:
- '29269482'
intvolume: ' 31'
issue: '22'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.306753.117
month: '12'
oa: 1
oa_version: Published Version
page: 2222-2234
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4
trimethylation in hematopoietic progenitor cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2017'
...
---
_id: '11067'
abstract:
- lang: eng
text: Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that
changes during differentiation. Nucleoporins are linked with cell-type-specific
gene regulation, coupling physical changes in nuclear structure to transcriptional
output; but, whether and how they coordinate with key fate-determining transcription
factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2
in adult NeuPCs, where it is indispensable for their maintenance and controls
neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind
and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional
end sites correlates with increased or decreased gene expression, respectively,
and inhibiting Nup153 expression alters open chromatin configurations at its target
genes, disrupts genomic localization of Sox2, and promotes differentiation in
vitro and a gliogenic fate switch in vivo. Together, these findings reveal that
nuclear structural proteins may exert bimodal transcriptional effects to control
cell fate.
article_processing_charge: No
article_type: original
author:
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
- first_name: Jonathan Y.
full_name: Hsu, Jonathan Y.
last_name: Hsu
- first_name: Sara B.
full_name: Linker, Sara B.
last_name: Linker
- first_name: Lauren
full_name: Hu, Lauren
last_name: Hu
- first_name: Simon T.
full_name: Schafer, Simon T.
last_name: Schafer
- first_name: Jerome
full_name: Mertens, Jerome
last_name: Mertens
- first_name: Filipe V.
full_name: Jacinto, Filipe V.
last_name: Jacinto
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
citation:
ama: Toda T, Hsu JY, Linker SB, et al. Nup153 interacts with Sox2 to enable bimodal
gene regulation and maintenance of neural progenitor cells. Cell Stem Cell.
2017;21(5):618-634.e7. doi:10.1016/j.stem.2017.08.012
apa: Toda, T., Hsu, J. Y., Linker, S. B., Hu, L., Schafer, S. T., Mertens, J., …
Gage, F. H. (2017). Nup153 interacts with Sox2 to enable bimodal gene regulation
and maintenance of neural progenitor cells. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2017.08.012
chicago: Toda, Tomohisa, Jonathan Y. Hsu, Sara B. Linker, Lauren Hu, Simon T. Schafer,
Jerome Mertens, Filipe V. Jacinto, Martin Hetzer, and Fred H. Gage. “Nup153 Interacts
with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor
Cells.” Cell Stem Cell. Elsevier, 2017. https://doi.org/10.1016/j.stem.2017.08.012.
ieee: T. Toda et al., “Nup153 interacts with Sox2 to enable bimodal gene
regulation and maintenance of neural progenitor cells,” Cell Stem Cell,
vol. 21, no. 5. Elsevier, p. 618–634.e7, 2017.
ista: Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer
M, Gage FH. 2017. Nup153 interacts with Sox2 to enable bimodal gene regulation
and maintenance of neural progenitor cells. Cell Stem Cell. 21(5), 618–634.e7.
mla: Toda, Tomohisa, et al. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation
and Maintenance of Neural Progenitor Cells.” Cell Stem Cell, vol. 21, no.
5, Elsevier, 2017, p. 618–634.e7, doi:10.1016/j.stem.2017.08.012.
short: T. Toda, J.Y. Hsu, S.B. Linker, L. Hu, S.T. Schafer, J. Mertens, F.V. Jacinto,
M. Hetzer, F.H. Gage, Cell Stem Cell 21 (2017) 618–634.e7.
date_created: 2022-04-07T07:46:12Z
date_published: 2017-11-02T00:00:00Z
date_updated: 2022-07-18T08:33:07Z
day: '02'
doi: 10.1016/j.stem.2017.08.012
extern: '1'
external_id:
pmid:
- '28919367'
intvolume: ' 21'
issue: '5'
keyword:
- Cell Biology
- Genetics
- Molecular Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.stem.2017.08.012
month: '11'
oa: 1
oa_version: Published Version
page: 618-634.e7
pmid: 1
publication: Cell Stem Cell
publication_identifier:
issn:
- 1934-5909
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance
of neural progenitor cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 21
year: '2017'
...
---
_id: '1107'
abstract:
- lang: eng
text: The generation, migration, and differentiation of neurons requires the functional
integrity of the microtubule cytoskeleton. Mutations in the tubulin gene family
are known to cause various neurological diseases including lissencephaly, ocular
motor disorders, polymicrogyria and amyotrophic lateral sclerosis. We have previously
reported that mutations in TUBB5 cause microcephaly that is accompanied by severe
intellectual impairment and motor delay. Here we present the characterization
of a Tubb5 mouse model that allows for the conditional expression of the pathogenic
E401K mutation. Homozygous knockin animals exhibit a severe reduction in brain
size and in body weight. These animals do not show any significant impairment
in general activity, anxiety, or in the acoustic startle response, however, present
with notable defects in motor coordination. When assessed on the static rod apparatus
mice took longer to orient and often lost their balance completely. Interestingly,
mutant animals also showed defects in prepulse inhibition, a phenotype associated
with sensorimotor gating and considered an endophenotype for schizophrenia. This
study provides insight into the behavioral consequences of tubulin gene mutations.
acknowledgement: Austrian Science Fund (FWF) for funding this research [I914,P21092]
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Lukas
full_name: Landler, Lukas
last_name: Landler
- first_name: David
full_name: Keays, David
last_name: Keays
citation:
ama: Breuss M, Hansen AH, Landler L, Keays D. Brain specific knockin of the pathogenic
Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition.
Behavioural Brain Research. 2017;323:47-55. doi:10.1016/j.bbr.2017.01.029
apa: Breuss, M., Hansen, A. H., Landler, L., & Keays, D. (2017). Brain specific
knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination
and prepulse inhibition. Behavioural Brain Research. Elsevier. https://doi.org/10.1016/j.bbr.2017.01.029
chicago: Breuss, Martin, Andi H Hansen, Lukas Landler, and David Keays. “Brain Specific
Knockin of the Pathogenic Tubb5 E401K Allele Causes Defects in Motor Coordination
and Prepulse Inhibition.” Behavioural Brain Research. Elsevier, 2017. https://doi.org/10.1016/j.bbr.2017.01.029.
ieee: M. Breuss, A. H. Hansen, L. Landler, and D. Keays, “Brain specific knockin
of the pathogenic Tubb5 E401K allele causes defects in motor coordination and
prepulse inhibition,” Behavioural Brain Research, vol. 323. Elsevier, pp.
47–55, 2017.
ista: Breuss M, Hansen AH, Landler L, Keays D. 2017. Brain specific knockin of the
pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse
inhibition. Behavioural Brain Research. 323, 47–55.
mla: Breuss, Martin, et al. “Brain Specific Knockin of the Pathogenic Tubb5 E401K
Allele Causes Defects in Motor Coordination and Prepulse Inhibition.” Behavioural
Brain Research, vol. 323, Elsevier, 2017, pp. 47–55, doi:10.1016/j.bbr.2017.01.029.
short: M. Breuss, A.H. Hansen, L. Landler, D. Keays, Behavioural Brain Research
323 (2017) 47–55.
date_created: 2018-12-11T11:50:11Z
date_published: 2017-04-14T00:00:00Z
date_updated: 2023-09-20T11:37:25Z
day: '14'
ddc:
- '570'
- '571'
doi: 10.1016/j.bbr.2017.01.029
extern: '1'
external_id:
isi:
- '000397369100007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:03Z
date_updated: 2018-12-12T10:12:03Z
file_id: '4921'
file_name: IST-2017-868-v1+1_1-s2.0-S0166432816309160-main.pdf
file_size: 2291511
relation: main_file
file_date_updated: 2018-12-12T10:12:03Z
has_accepted_license: '1'
intvolume: ' 323'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 47 - 55
publication: Behavioural Brain Research
publication_identifier:
issn:
- '01664328'
publication_status: published
publisher: Elsevier
publist_id: '6262'
pubrep_id: '868'
quality_controlled: '1'
status: public
title: Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects
in motor coordination and prepulse inhibition
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 323
year: '2017'
...
---
_id: '1108'
abstract:
- lang: eng
text: In this work we study the learnability of stochastic processes with respect
to the conditional risk, i.e. the existence of a learning algorithm that improves
its next-step performance with the amount of observed data. We introduce a notion
of pairwise discrepancy between conditional distributions at different times steps
and show how certain properties of these discrepancies can be used to construct
a successful learning algorithm. Our main results are two theorems that establish
criteria for learnability for many classes of stochastic processes, including
all special cases studied previously in the literature.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Alexander
full_name: Zimin, Alexander
id: 37099E9C-F248-11E8-B48F-1D18A9856A87
last_name: Zimin
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Zimin A, Lampert C. Learning theory for conditional risk minimization. In:
Vol 54. ML Research Press; 2017:213-222.'
apa: 'Zimin, A., & Lampert, C. (2017). Learning theory for conditional risk
minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence
and Statistics, Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional
Risk Minimization,” 54:213–22. ML Research Press, 2017.
ieee: 'A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,”
presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale,
FL, United States, 2017, vol. 54, pp. 213–222.'
ista: 'Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization.
AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.'
mla: Zimin, Alexander, and Christoph Lampert. Learning Theory for Conditional
Risk Minimization. Vol. 54, ML Research Press, 2017, pp. 213–22.
short: A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2018-12-11T11:50:11Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2025-04-15T07:10:22Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
isi:
- '000509368500024'
intvolume: ' 54'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf
month: '04'
oa: 1
oa_version: Submitted Version
page: 213 - 222
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: ML Research Press
publist_id: '6261'
quality_controlled: '1'
status: public
title: Learning theory for conditional risk minimization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2017'
...
---
_id: '1109'
abstract:
- lang: eng
text: 'Rotation of molecules embedded in He nanodroplets is explored by a combination
of fs laser-induced alignment experiments and angulon quasiparticle theory. We
demonstrate that at low fluence of the fs alignment pulse, the molecule and its
solvation shell can be set into coherent collective rotation lasting long enough
to form revivals. With increasing fluence, however, the revivals disappear --
instead, rotational dynamics as rapid as for an isolated molecule is observed
during the first few picoseconds. Classical calculations trace this phenomenon
to transient decoupling of the molecule from its He shell. Our results open novel
opportunities for studying non-equilibrium solute-solvent dynamics and quantum
thermalization. '
article_number: '203203'
article_processing_charge: No
arxiv: 1
author:
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Anders
full_name: Søndergaard, Anders
last_name: Søndergaard
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Robert
full_name: Zillich, Robert
last_name: Zillich
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: 'Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation
of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical
Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203'
apa: 'Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich,
R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine
molecules in helium nanodroplets: Revivals and breaking-free. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203'
chicago: 'Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk,
Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation
of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203.'
ieee: 'B. Shepperson et al., “Laser-induced rotation of iodine molecules
in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters,
vol. 118, no. 20. American Physical Society, 2017.'
ista: 'Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko
M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets:
Revivals and breaking-free. Physical Review Letters. 118(20), 203203.'
mla: 'Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in
Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters,
vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.'
short: B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich,
M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017).
date_created: 2018-12-11T11:50:12Z
date_published: 2017-05-19T00:00:00Z
date_updated: 2025-06-04T08:36:27Z
day: '19'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.118.203203
external_id:
arxiv:
- '1702.01977'
isi:
- '000401664000005'
intvolume: ' 118'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01977
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6260'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals
and breaking-free'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '1110'
abstract:
- lang: eng
text: The phytohormone auxin is a major determinant and regulatory component important
for plant development. Auxin transport between cells is mediated by a complex
system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization
and activity is thought to be influenced by phosphatases and kinases. Flavonols
have been shown to alter auxin transport activity and changes in flavonol accumulation
in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and
seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a
regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects
of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants
show wild type-like auxin transport activity while levels of free auxin are not
affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical
shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization.
In vivo analysis of PINOID action, a kinase known to influence PIN protein localization
in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID
activity. Together, these data suggest that flavonols affect auxin transport by
modifying the antagonistic kinase/phosphatase equilibrium.
acknowledgement: European Research Council (project ERC-2011-StG-20101109-PSDP), European
Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S)
[JF].
article_number: '41906'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Kuhn, Benjamin
last_name: Kuhn
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Sanae
full_name: Errafi, Sanae
last_name: Errafi
- first_name: Rahel
full_name: Bucher, Rahel
last_name: Bucher
- first_name: Shibu
full_name: Gupta, Shibu
last_name: Gupta
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Laurent
full_name: Bigler, Laurent
last_name: Bigler
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Christoph
full_name: Ringli, Christoph
last_name: Ringli
citation:
ama: Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity
and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase
activity. Scientific Reports. 2017;7. doi:10.1038/srep41906
apa: Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli,
C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the
Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific
Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906
chicago: Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta,
Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and
Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase
Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906.
ieee: B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin
transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,”
Scientific Reports, vol. 7. Nature Publishing Group, 2017.
ista: Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler
L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes
in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant
require phosphatase activity. Scientific Reports. 7, 41906.
mla: Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin
Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.”
Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906.
short: B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev,
L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports
7 (2017).
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-06T00:00:00Z
date_updated: 2025-07-10T11:50:06Z
day: '06'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/srep41906
ec_funded: 1
external_id:
isi:
- '000393367600001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:09Z
date_updated: 2018-12-12T10:18:09Z
file_id: '5328'
file_name: IST-2017-803-v1+1_srep41906.pdf
file_size: 1654496
relation: main_file
file_date_updated: 2018-12-12T10:18:09Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Nature Publishing Group
publist_id: '6258'
pubrep_id: '803'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis
thaliana rol1-2 mutant require phosphatase activity
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: 7
year: '2017'
...
---
_id: '1111'
abstract:
- lang: eng
text: Adaptation depends critically on the effects of new mutations and their dependency
on the genetic background in which they occur. These two factors can be summarized
by the fitness landscape. However, it would require testing all mutations in all
backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible.
Instead of postulating a particular fitness landscape, we address this problem
by considering general classes of landscapes and calculating an upper limit for
the time it takes for a population to reach a fitness peak, circumventing the
need to have full knowledge about the fitness landscape. We analyze populations
in the weak-mutation regime and characterize the conditions that enable them to
quickly reach the fitness peak as a function of the number of sites under selection.
We show that for additive landscapes there is a critical selection strength enabling
populations to reach high-fitness genotypes, regardless of the distribution of
effects. This threshold scales with the number of sites under selection, effectively
setting a limit to adaptation, and results from the inevitable increase in deleterious
mutational pressure as the population adapts in a space of discrete genotypes.
Furthermore, we show that for the class of all unimodal landscapes this condition
is sufficient but not necessary for rapid adaptation, as in some highly epistatic
landscapes the critical strength does not depend on the number of sites under
selection; effectively removing this barrier to adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks
on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection
limits to adaptive walks on correlated landscapes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.116.189340
chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection
Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics
Society of America, 2017. https://doi.org/10.1534/genetics.116.189340.
ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to
adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics
Society of America, pp. 803–825, 2017.
ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive
walks on correlated landscapes. Genetics. 205(2), 803–825.
mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.”
Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25,
doi:10.1534/genetics.116.189340.
short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2025-07-10T11:50:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.189340
ec_funded: 1
external_id:
isi:
- '000394144900025'
pmid:
- '27881471'
intvolume: ' 205'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.116.189340
month: '02'
oa: 1
oa_version: Published Version
page: 803 - 825
pmid: 1
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '6256'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection limits to adaptive walks on correlated landscapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 205
year: '2017'
...
---
_id: '1112'
abstract:
- lang: eng
text: There has been renewed interest in modelling the behaviour of evolutionary
algorithms by more traditional mathematical objects, such as ordinary differential
equations or Markov chains. The advantage is that the analysis becomes greatly
facilitated due to the existence of well established methods. However, this typically
comes at the cost of disregarding information about the process. Here, we introduce
the use of stochastic differential equations (SDEs) for the study of EAs. SDEs
can produce simple analytical results for the dynamics of stochastic processes,
unlike Markov chains which can produce rigorous but unwieldy expressions about
the dynamics. On the other hand, unlike ordinary differential equations (ODEs),
they do not discard information about the stochasticity of the process. We show
that these are especially suitable for the analysis of fixed budget scenarios
and present analogs of the additive and multiplicative drift theorems for SDEs.
We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS)
on two canonical problems(OneMax and LeadingOnes).
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
citation:
ama: 'Paixao T, Pérez Heredia J. An application of stochastic differential equations
to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729'
apa: 'Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential
equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark:
ACM. https://doi.org/10.1145/3040718.3040729'
chicago: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential
Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.
ieee: T. Paixao and J. Pérez Heredia, “An application of stochastic differential
equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017,
pp. 3–11.
ista: 'Paixao T, Pérez Heredia J. 2017. An application of stochastic differential
equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms,
3–11.'
mla: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential
Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.
short: T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.
conference:
end_date: 2017-01-15
location: Copenhagen, Denmark
name: 'FOGA: Foundations of Genetic Algorithms'
start_date: 2017-01-12
date_created: 2018-12-11T11:50:12Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2021-01-12T06:48:22Z
day: '12'
department:
- _id: NiBa
doi: 10.1145/3040718.3040729
language:
- iso: eng
month: '01'
oa_version: None
page: 3 - 11
publication: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic
Algorithms
publication_identifier:
isbn:
- 978-145034651-1
publication_status: published
publisher: ACM
publist_id: '6255'
quality_controlled: '1'
scopus_import: 1
status: public
title: An application of stochastic differential equations to evolutionary algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '1113'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C 1 , . . . , C k with common center c , and edges are drawn radially
: every edge intersects every circle centered at c at most once. G is radial planar
if it has a radial embedding, that is, a crossing-free radial drawing. If the
vertices of G are ordered or partitioned into ordered levels (as they are for
leveled graphs), we require that the assignment of vertices to circles corresponds
to the given ordering or leveling. We show that a graph G is radial planar if
G has a radial drawing in which every two edges cross an even number of times;
the radial embedding has the same leveling as the radial drawing. In other words,
we establish the weak variant of the Hanani-Tutte theorem for radial planarity.
This generalizes a result by Pach and Toth.'
acknowledgement: An earlier version of the paper appeared in the proceedings of Graph
Drawing 2015. The research of the first author has received funding from the People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme
(FP7/2007-2013) under REA grant agreement no [291734].
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal
of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408
apa: Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial
planarity. Journal of Graph Algorithms and Applications. Brown University.
https://doi.org/10.7155/jgaa.00408
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown
University, 2017. https://doi.org/10.7155/jgaa.00408.
ieee: R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,”
Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University,
pp. 135–154, 2017.
ista: Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity.
Journal of Graph Algorithms and Applications. 21(1), 135–154.
mla: Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of
Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017,
pp. 135–54, doi:10.7155/jgaa.00408.
short: R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications
21 (2017) 135–154.
date_created: 2018-12-11T11:50:13Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-09-23T09:13:42Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.7155/jgaa.00408
ec_funded: 1
external_id:
arxiv:
- '1608.08662'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-10-24T10:54:37Z
date_updated: 2019-10-24T10:54:37Z
file_id: '6967'
file_name: 2017_JournalGraphAlgorithms_Fulek.pdf
file_size: 573623
relation: main_file
success: 1
file_date_updated: 2019-10-24T10:54:37Z
has_accepted_license: '1'
intvolume: ' 21'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 135 - 154
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Graph Algorithms and Applications
publication_status: published
publisher: Brown University
publist_id: '6254'
quality_controlled: '1'
related_material:
record:
- id: '1164'
relation: earlier_version
status: public
- id: '1595'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Hanani-Tutte for radial planarity
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: 21
year: '2017'
...
---
_id: '1114'
abstract:
- lang: eng
text: Nonequilibrium phase transitions exist in damped-driven open quantum systems
when the continuous tuning of an external parameter leads to a transition between
two robust steady states. In second-order transitions this change is abrupt at
a critical point, whereas in first-order transitions the two phases can coexist
in a critical hysteresis domain. Here, we report the observation of a first-order
dissipative quantum phase transition in a driven circuit quantum electrodynamics
system. It takes place when the photon blockade of the driven cavity-atom system
is broken by increasing the drive power. The observed experimental signature is
a bimodal phase space distribution with varying weights controlled by the drive
strength. Our measurements show an improved stabilization of the classical attractors
up to the millisecond range when the size of the quantum system is increased from
one to three artificial atoms. The formation of such robust pointer states could
be used for new quantum measurement schemes or to investigate multiphoton phases
of finite-size, nonlinear, open quantum systems.
article_number: '011012'
article_processing_charge: Yes
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: András
full_name: Dombi, András
last_name: Dombi
- first_name: András
full_name: Vukics, András
last_name: Vukics
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
- first_name: Peter
full_name: Domokos, Peter
last_name: Domokos
citation:
ama: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. Observation of the photon
blockade breakdown phase transition. Physical Review X. 2017;7(1). doi:10.1103/PhysRevX.7.011012
apa: Fink, J. M., Dombi, A., Vukics, A., Wallraff, A., & Domokos, P. (2017).
Observation of the photon blockade breakdown phase transition. Physical Review
X. American Physical Society. https://doi.org/10.1103/PhysRevX.7.011012
chicago: Fink, Johannes M, András Dombi, András Vukics, Andreas Wallraff, and Peter
Domokos. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical
Review X. American Physical Society, 2017. https://doi.org/10.1103/PhysRevX.7.011012.
ieee: J. M. Fink, A. Dombi, A. Vukics, A. Wallraff, and P. Domokos, “Observation
of the photon blockade breakdown phase transition,” Physical Review X,
vol. 7, no. 1. American Physical Society, 2017.
ista: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. 2017. Observation of the
photon blockade breakdown phase transition. Physical Review X. 7(1), 011012.
mla: Fink, Johannes M., et al. “Observation of the Photon Blockade Breakdown Phase
Transition.” Physical Review X, vol. 7, no. 1, 011012, American Physical
Society, 2017, doi:10.1103/PhysRevX.7.011012.
short: J.M. Fink, A. Dombi, A. Vukics, A. Wallraff, P. Domokos, Physical Review
X 7 (2017).
date_created: 2018-12-11T11:50:13Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2025-07-10T11:50:07Z
day: '31'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1103/PhysRevX.7.011012
external_id:
isi:
- '000397450500001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:52Z
date_updated: 2018-12-12T10:12:52Z
file_id: '4972'
file_name: IST-2017-753-v1+1_PhysRevX.7.011012.pdf
file_size: 1172926
relation: main_file
file_date_updated: 2018-12-12T10:12:52Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
issn:
- 2160-3308
publication_status: published
publisher: American Physical Society
publist_id: '6252'
pubrep_id: '753'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of the photon blockade breakdown phase transition
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: 7
year: '2017'
...
---
_id: '1116'
abstract:
- lang: eng
text: "Time-triggered switched networks are a deterministic communication infrastructure
used by real-time distributed embedded systems. Due to the criticality of the
applications running over them, developers need to ensure that end-to-end communication
is dependable and predictable. Traditional approaches assume static networks that
are not flexible to changes caused by reconfigurations or, more importantly, faults,
which are dealt with in the application using redundancy. We adopt the concept
of handling faults in the switches from non-real-time networks while maintaining
the required predictability. \r\n\r\nWe study a class of forwarding schemes that
can handle various types of failures. We consider probabilistic failures. We study
a class of forwarding schemes that can handle various types of failures. We consider
probabilistic failures. For a given network with a forwarding scheme and a constant
ℓ, we compute the {\\em score} of the scheme, namely the probability (induced
by faults) that at least ℓ messages arrive on time. We reduce the scoring problem
to a reachability problem on a Markov chain with a "product-like" structure.
Its special structure allows us to reason about it symbolically, and reduce the
scoring problem to #SAT. Our solution is generic and can be adapted to different
networks and other contexts. Also, we show the computational complexity of the
scoring problem is #P-complete, and we study methods to estimate the score. We
evaluate the effectiveness of our techniques with an implementation. "
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shubham
full_name: Goel, Shubham
last_name: Goel
- 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: Guillermo
full_name: Rodríguez Navas, Guillermo
last_name: Rodríguez Navas
citation:
ama: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. Computing scores of forwarding
schemes in switched networks with probabilistic faults. In: Vol 10206. Springer;
2017:169-187. doi:10.1007/978-3-662-54580-5_10'
apa: 'Avni, G., Goel, S., Henzinger, T. A., & Rodríguez Navas, G. (2017). Computing
scores of forwarding schemes in switched networks with probabilistic faults (Vol.
10206, pp. 169–187). Presented at the TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54580-5_10'
chicago: Avni, Guy, Shubham Goel, Thomas A Henzinger, and Guillermo Rodríguez Navas.
“Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic
Faults,” 10206:169–87. Springer, 2017. https://doi.org/10.1007/978-3-662-54580-5_10.
ieee: 'G. Avni, S. Goel, T. A. Henzinger, and G. Rodríguez Navas, “Computing scores
of forwarding schemes in switched networks with probabilistic faults,” presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
Uppsala, Sweden, 2017, vol. 10206, pp. 169–187.'
ista: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. 2017. Computing scores of
forwarding schemes in switched networks with probabilistic faults. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10206,
169–187.'
mla: Avni, Guy, et al. Computing Scores of Forwarding Schemes in Switched Networks
with Probabilistic Faults. Vol. 10206, Springer, 2017, pp. 169–87, doi:10.1007/978-3-662-54580-5_10.
short: G. Avni, S. Goel, T.A. Henzinger, G. Rodríguez Navas, in:, Springer, 2017,
pp. 169–187.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2017-04-22
corr_author: '1'
date_created: 2018-12-11T11:50:14Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2025-04-15T06:25:58Z
day: '31'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-54580-5_10
external_id:
isi:
- '000440733400010'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:37Z
date_updated: 2018-12-12T10:08:37Z
file_id: '4698'
file_name: IST-2017-758-v1+1_tacas-cr.pdf
file_size: 321800
relation: main_file
file_date_updated: 2018-12-12T10:08:37Z
has_accepted_license: '1'
intvolume: ' 10206'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 169 - 187
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6246'
pubrep_id: '758'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing scores of forwarding schemes in switched networks with probabilistic
faults
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10206
year: '2017'
...
---
_id: '1117'
abstract:
- lang: eng
text: 'GABAergic synapses in brain circuits generate inhibitory output signals with
submillisecond latency and temporal precision. Whether the molecular identity
of the release sensor contributes to these signaling properties remains unclear.
Here, we examined the Ca^2+ sensor of exocytosis at GABAergic basket cell (BC)
to Purkinje cell (PC) synapses in cerebellum. Immunolabeling suggested that BC
terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin
1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced
action potential-evoked release to ∼10%, identifying Syt2 as the major Ca^2+ sensor
at BC-PC synapses. Differential adenovirus-mediated rescue revealed that Syt2
triggered release with shorter latency and higher temporal precision and mediated
faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely
reduced and delayed disynaptic inhibition following parallel fiber stimulation.
Thus, the selective use of Syt2 as release sensor at BC-PC synapses ensures fast
and efficient feedforward inhibition in cerebellar microcircuits. #bioimagingfacility-author'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- first_name: Rachel
full_name: Satterield, Rachel
last_name: Satterield
- first_name: Samuel
full_name: Young, Samuel
last_name: Young
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. Synaptotagmin 2 is the
fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 2017;18(3):723-736.
doi:10.1016/j.celrep.2016.12.067
apa: Chen, C., Arai, itaru, Satterield, R., Young, S., & Jonas, P. M. (2017).
Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell
Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.12.067
chicago: Chen, Chong, itaru Arai, Rachel Satterield, Samuel Young, and Peter M Jonas.
“Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell
Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2016.12.067.
ieee: C. Chen, itaru Arai, R. Satterield, S. Young, and P. M. Jonas, “Synaptotagmin
2 is the fast Ca2+ sensor at a central inhibitory synapse,” Cell Reports,
vol. 18, no. 3. Cell Press, pp. 723–736, 2017.
ista: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. 2017. Synaptotagmin
2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 18(3),
723–736.
mla: Chen, Chong, et al. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory
Synapse.” Cell Reports, vol. 18, no. 3, Cell Press, 2017, pp. 723–36, doi:10.1016/j.celrep.2016.12.067.
short: C. Chen, itaru Arai, R. Satterield, S. Young, P.M. Jonas, Cell Reports 18
(2017) 723–736.
date_created: 2018-12-11T11:50:14Z
date_published: 2017-01-17T00:00:00Z
date_updated: 2025-07-10T11:50:09Z
day: '17'
ddc:
- '571'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2016.12.067
ec_funded: 1
external_id:
isi:
- '000396470600013'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:09Z
date_updated: 2018-12-12T10:16:09Z
file_id: '5195'
file_name: IST-2017-751-v1+1_1-s2.0-S2211124716317740-main.pdf
file_size: 4427591
relation: main_file
file_date_updated: 2018-12-12T10:16:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 723 - 736
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Cell Press
publist_id: '6245'
pubrep_id: '751'
quality_controlled: '1'
related_material:
record:
- id: '324'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse
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: 18
year: '2017'
...
---
_id: '1118'
abstract:
- lang: eng
text: Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation
during non-rapid eye movement sleep, immobility, and consummatory behavior. However,
whether temporally modulated synaptic excitation or inhibition underlies the ripples
is controversial. To address this question, we performed simultaneous recordings
of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local
field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs,
inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5.
Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with
SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated
that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly
distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons
provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition,
but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
article_processing_charge: No
author:
- first_name: Jian
full_name: Gan, Jian
id: 3614E438-F248-11E8-B48F-1D18A9856A87
last_name: Gan
- first_name: Shih-Ming
full_name: Weng, Shih-Ming
id: 2F9C5AC8-F248-11E8-B48F-1D18A9856A87
last_name: Weng
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition,
but not excitation, underlies hippocampal ripple oscillations in awake mice in
vivo. Neuron. 2017;93(2):308-314. doi:10.1016/j.neuron.2016.12.018
apa: Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., & Jonas, P.
M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal
ripple oscillations in awake mice in vivo. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.12.018
chicago: Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari,
and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal
Ripple Oscillations in Awake Mice in Vivo.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2016.12.018.
ieee: J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked
inhibition, but not excitation, underlies hippocampal ripple oscillations in awake
mice in vivo,” Neuron, vol. 93, no. 2. Elsevier, pp. 308–314, 2017.
ista: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked
inhibition, but not excitation, underlies hippocampal ripple oscillations in awake
mice in vivo. Neuron. 93(2), 308–314.
mla: Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal
Ripple Oscillations in Awake Mice in Vivo.” Neuron, vol. 93, no. 2, Elsevier,
2017, pp. 308–14, doi:10.1016/j.neuron.2016.12.018.
short: J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron
93 (2017) 308–314.
date_created: 2018-12-11T11:50:15Z
date_published: 2017-01-18T00:00:00Z
date_updated: 2025-04-15T07:20:01Z
day: '18'
ddc:
- '571'
department:
- _id: PeJo
- _id: JoCs
doi: 10.1016/j.neuron.2016.12.018
ec_funded: 1
external_id:
isi:
- '000396428200010'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:56Z
date_updated: 2018-12-12T10:08:56Z
file_id: '4719'
file_name: IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf
file_size: 2738950
relation: main_file
file_date_updated: 2018-12-12T10:08:56Z
has_accepted_license: '1'
intvolume: ' 93'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 308 - 314
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '6244'
pubrep_id: '752'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations
in awake mice in vivo
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: 93
year: '2017'
...
---
_id: '1119'
abstract:
- lang: eng
text: Understanding the behavior of molecules interacting with superfluid helium
represents a formidable challenge and, in general, requires approaches relying
on large-scale numerical simulations. Here we demonstrate that experimental data
collected over the last 20 years provide evidence that molecules immersed in superfluid
helium form recently-predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001
(2015)]. Most importantly, casting the many-body problem in terms of angulons
amounts to a drastic simplification and yields effective molecular moments of
inertia as straightforward analytic solutions of a simple microscopic Hamiltonian.
The outcome of the angulon theory is in good agreement with experiment for a broad
range of molecular impurities, from heavy to medium-mass to light species. These
results pave the way to understanding molecular rotation in liquid and crystalline
phases in terms of the angulon quasiparticle.
article_number: '095301'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Lemeshko M. Quasiparticle approach to molecules interacting with quantum solvents.
Physical Review Letters. 2017;118(9). doi:10.1103/PhysRevLett.118.095301
apa: Lemeshko, M. (2017). Quasiparticle approach to molecules interacting with quantum
solvents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.095301
chicago: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with
Quantum Solvents.” Physical Review Letters. American Physical Society,
2017. https://doi.org/10.1103/PhysRevLett.118.095301.
ieee: M. Lemeshko, “Quasiparticle approach to molecules interacting with quantum
solvents,” Physical Review Letters, vol. 118, no. 9. American Physical
Society, 2017.
ista: Lemeshko M. 2017. Quasiparticle approach to molecules interacting with quantum
solvents. Physical Review Letters. 118(9), 095301.
mla: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum
Solvents.” Physical Review Letters, vol. 118, no. 9, 095301, American Physical
Society, 2017, doi:10.1103/PhysRevLett.118.095301.
short: M. Lemeshko, Physical Review Letters 118 (2017).
date_created: 2018-12-11T11:50:15Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2025-06-04T08:36:48Z
day: '27'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.118.095301
external_id:
arxiv:
- '1610.01604'
isi:
- '000404769200006'
intvolume: ' 118'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.01604
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25636330-B435-11E9-9278-68D0E5697425
grant_number: 11-NSF-1070
name: Genome-wide Analysis of Root Traits
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
publist_id: '6243'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quasiparticle approach to molecules interacting with quantum solvents
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '1120'
abstract:
- lang: eng
text: 'The existence of a self-localization transition in the polaron problem has
been under an active debate ever since Landau suggested it 83 years ago. Here
we reveal the self-localization transition for the rotational analogue of the
polaron -- the angulon quasiparticle. We show that, unlike for the polarons, self-localization
of angulons occurs at finite impurity-bath coupling already at the mean-field
level. The transition is accompanied by the spherical-symmetry breaking of the
angulon ground state and a discontinuity in the first derivative of the ground-state
energy. Moreover, the type of the symmetry breaking is dictated by the symmetry
of the microscopic impurity-bath interaction, which leads to a number of distinct
self-localized states. The predicted effects can potentially be addressed in experiments
on cold molecules trapped in superfluid helium droplets and ultracold quantum
gases, as well as on electronic excitations in solids and Bose-Einstein condensates. '
article_number: '033608'
article_processing_charge: No
arxiv: 1
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Li X, Seiringer R, Lemeshko M. Angular self-localization of impurities rotating
in a bosonic bath. Physical Review A. 2017;95(3). doi:10.1103/PhysRevA.95.033608
apa: Li, X., Seiringer, R., & Lemeshko, M. (2017). Angular self-localization
of impurities rotating in a bosonic bath. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.95.033608
chicago: Li, Xiang, Robert Seiringer, and Mikhail Lemeshko. “Angular Self-Localization
of Impurities Rotating in a Bosonic Bath.” Physical Review A. American
Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.033608.
ieee: X. Li, R. Seiringer, and M. Lemeshko, “Angular self-localization of impurities
rotating in a bosonic bath,” Physical Review A, vol. 95, no. 3. American
Physical Society, 2017.
ista: Li X, Seiringer R, Lemeshko M. 2017. Angular self-localization of impurities
rotating in a bosonic bath. Physical Review A. 95(3), 033608.
mla: Li, Xiang, et al. “Angular Self-Localization of Impurities Rotating in a Bosonic
Bath.” Physical Review A, vol. 95, no. 3, 033608, American Physical Society,
2017, doi:10.1103/PhysRevA.95.033608.
short: X. Li, R. Seiringer, M. Lemeshko, Physical Review A 95 (2017).
date_created: 2018-12-11T11:50:15Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2025-06-04T08:37:18Z
day: '06'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/PhysRevA.95.033608
ec_funded: 1
external_id:
arxiv:
- '1610.04908'
isi:
- '000395981900009'
intvolume: ' 95'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.04908
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review A
publication_identifier:
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
publist_id: '6242'
quality_controlled: '1'
related_material:
record:
- id: '8958'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Angular self-localization of impurities rotating in a bosonic bath
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2017'
...