---
_id: '1277'
abstract:
- lang: eng
text: "The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released
into the apoplast after cellular damage caused by pathogens or wounding to induce
innate immunity by direct binding to the membrane-localized leucine-rich repeat
receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated
signaling components and responses have been studied extensively, the contributions
of the subcellular localization and dynamics of the active PEPRs remain largely
unknown. We used live-cell imaging of the fluorescently labeled and bioactive
pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root
meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent
manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes
to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized
vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation
factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different
TGN/EE markers colocalized only rarely, implying that the intracellular route
of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression
of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits
clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization
and compromised AtPep1-mediated responses. Our results show that clathrin function
at the PM is required to induce plant defense responses, likely through CME of
cell surface-located signaling components.\r\n"
acknowledgement: "F.A.O.-M. was supported by special\r\nresearch funding from the
Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and
funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the
Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for
a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted
to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor
predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships
from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders
Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation
and the National Council\r\nfor Scientific and Technological Development (CNPq)
(D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme,
E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice
and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson,
and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych
for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line."
article_processing_charge: No
author:
- first_name: Fausto
full_name: Ortiz Morea, Fausto
last_name: Ortiz Morea
- first_name: Daniel
full_name: Savatin, Daniel
last_name: Savatin
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Rahul
full_name: Kumar, Rahul
last_name: Kumar
- first_name: Yu
full_name: Luo, Yu
last_name: Luo
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Jos
full_name: Van Begin, Jos
last_name: Van Begin
- first_name: Keini
full_name: Dressano, Keini
last_name: Dressano
- first_name: Guilherme
full_name: De Oliveira, Guilherme
last_name: De Oliveira
- first_name: Xiuyang
full_name: Zhao, Xiuyang
last_name: Zhao
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Daniel
full_name: De Moura, Daniel
last_name: De Moura
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling
in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113
apa: Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski,
M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis
requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113
chicago: Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo,
Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in
Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016.
https://doi.org/10.1073/pnas.1605588113.
ieee: F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis
requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences,
pp. 11028–11033, 2016.
ista: Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin
J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova
E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin.
PNAS. 113(39), 11028–11033.
mla: Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis
Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences,
2016, pp. 11028–33, doi:10.1073/pnas.1605588113.
short: F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski,
J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml,
D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.
date_created: 2018-12-11T11:51:06Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2025-09-22T08:37:42Z
day: '27'
department:
- _id: JiFr
doi: 10.1073/pnas.1605588113
external_id:
isi:
- '000383954700066'
intvolume: ' 113'
isi: 1
issue: '39'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/
month: '09'
oa: 1
oa_version: Preprint
page: 11028 - 11033
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6039'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Danger-associated peptide signaling in Arabidopsis requires clathrin
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 113
year: '2016'
...
---
_id: '1278'
abstract:
- lang: eng
text: Adaptations of vestibulo-ocular and optokinetic response eye movements have
been studied as an experimental model of cerebellum-dependent motor learning.
Several previous physiological and pharmacological studies have consistently suggested
that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular
nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively
maintain the memory traces of short- and long-term adaptation. To study the basic
structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy
(EM), we injected green florescence protein (GFP)-expressing lentivirus into FL
to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal
boutons were distributed in the magnocellular MVN and in the border region of
parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the
FL-P cell axons mainly terminated on somata and proximal dendrites. On the other
hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly
terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN
neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH
neurons were determined to be glutamatergic by immunocytochemistry and in-situ
hybridization of GFP expressing transgenic mice. To further examine the spatial
relationship between the synapses of FL P-cells and those of vestibular nerve
on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated
dextran amine into the semicircular canal and anterogradely labeled vestibular
nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic
boutons often closely apposed vestibular nerve synaptic boutons in both LM and
EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with
those of vestibular nerve axons in the distal dendrites of MVN neurons suggests
that inhibitory synapses of FL P-cells may influence the function of neighboring
excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons.
acknowledgement: This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan
Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112
to SN].
article_number: e0164037
article_processing_charge: No
article_type: original
author:
- first_name: Hitomi
full_name: Matsuno, Hitomi
last_name: Matsuno
- first_name: Moeko
full_name: Kudoh, Moeko
last_name: Kudoh
- first_name: Akiya
full_name: Watakabe, Akiya
last_name: Watakabe
- first_name: Tetsuo
full_name: Yamamori, Tetsuo
last_name: Yamamori
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Soichi
full_name: Nagao, Soichi
last_name: Nagao
citation:
ama: 'Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution
and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar
flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy
studies. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164037'
apa: 'Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., & Nagao,
S. (2016). Distribution and structure of synapses on medial vestibular nuclear
neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in
mice: Light and electron microscopy studies. PLoS One. Public Library of
Science. https://doi.org/10.1371/journal.pone.0164037'
chicago: 'Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi
Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial
Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and
Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One.
Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164037.'
ieee: 'H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao,
“Distribution and structure of synapses on medial vestibular nuclear neurons targeted
by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and
electron microscopy studies,” PLoS One, vol. 11, no. 10. Public Library
of Science, 2016.'
ista: 'Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution
and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar
flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy
studies. PLoS One. 11(10), e0164037.'
mla: 'Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial
Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and
Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One,
vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:10.1371/journal.pone.0164037.'
short: H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS
One 11 (2016).
date_created: 2018-12-11T11:51:06Z
date_published: 2016-10-06T00:00:00Z
date_updated: 2025-09-22T08:37:04Z
day: '06'
ddc:
- '570'
- '571'
department:
- _id: RySh
doi: 10.1371/journal.pone.0164037
external_id:
isi:
- '000385697600069'
file:
- access_level: open_access
checksum: 7c0ba0ca6d79844059158059d2a38d25
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:16Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5269'
file_name: IST-2016-689-v1+1_journal.pone.0164037.PDF
file_size: 3657084
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6038'
pubrep_id: '689'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Distribution and structure of synapses on medial vestibular nuclear neurons
targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light
and electron microscopy studies'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2016'
...
---
_id: '1279'
abstract:
- lang: eng
text: During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory
inputdriven neuronal firing patterns are replayed. Such replay is thought to be
important for plasticity- related processes and consolidation of memory traces.
It has previously been shown that the electrical stimulation-induced disruption
of SWR events interferes with learning in rodents in different experimental paradigms.
On the other hand, the cognitive map theory posits that the plastic changes of
the firing of hippocampal place cells constitute the electrophysiological counterpart
of the spatial learning, observable at the behavioral level. Therefore, we tested
whether intact SWR events occurring during the sleep/rest session after the first
exploration of a novel environment are needed for the stabilization of the CA1
code, which process requires plasticity. We found that the newly-formed representation
in the CA1 has the same level of stability with optogenetic SWR blockade as with
a control manipulation that delivered the same amount of light into the brain.
Therefore our results suggest that at least in the case of passive exploratory
behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles.
acknowledgement: 'The research leading to these results 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 n° [291734] via the IST FELLOWSHIP
awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant
(acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We
thank Lauri Viljanto for technical help in building the ripple detector.'
article_number: e0164675
article_processing_charge: No
author:
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Markku
full_name: Penttonen, Markku
last_name: Penttonen
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari
JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere
with the formation of stable spatial representation in the CA1 area of the hippocampus.
PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164675
apa: Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero,
D. K., & Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple
events in sleep does not interfere with the formation of stable spatial representation
in the CA1 area of the hippocampus. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0164675
chicago: Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen,
Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp
Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial
Representation in the CA1 Area of the Hippocampus.” PLoS One. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pone.0164675.
ieee: K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero,
and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep
does not interfere with the formation of stable spatial representation in the
CA1 area of the hippocampus,” PLoS One, vol. 11, no. 10. Public Library
of Science, 2016.
ista: Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari
JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not
interfere with the formation of stable spatial representation in the CA1 area
of the hippocampus. PLoS One. 11(10), e0164675.
mla: Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events
in Sleep Does Not Interfere with the Formation of Stable Spatial Representation
in the CA1 Area of the Hippocampus.” PLoS One, vol. 11, no. 10, e0164675,
Public Library of Science, 2016, doi:10.1371/journal.pone.0164675.
short: K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero,
J.L. Csicsvari, PLoS One 11 (2016).
corr_author: '1'
date_created: 2018-12-11T11:51:06Z
date_published: 2016-10-19T00:00:00Z
date_updated: 2025-09-22T08:36:27Z
day: '19'
ddc:
- '570'
- '571'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0164675
ec_funded: 1
external_id:
isi:
- '000386204000043'
file:
- access_level: open_access
checksum: 395895ecb2216e9c39135abaa56b28b3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:26Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5009'
file_name: IST-2016-690-v1+1_journal.pone.0164675.PDF
file_size: 4353592
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
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: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6037'
pubrep_id: '690'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optogenetically blocking sharp wave ripple events in sleep does not interfere
with the formation of stable spatial representation in the CA1 area of the hippocampus
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2016'
...
---
_id: '1280'
abstract:
- lang: eng
text: We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of
the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous
results concerning the universality of random matrices either require an averaging
in the energy parameter or they hold only for Hermitian matrices if the energy
parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion
and show that microscopic universality follows from mesoscopic statistics.
acknowledgement: "The work of P.B. was partially supported by National Sci-\r\nence
Foundation Grant DMS-1208859. The work of L.E. was partially supported\r\nby ERC
Advanced Grant RANMAT 338804. The work of H.-T. Y. was partially\r\nsupported by
National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award.
\ The work of J.Y. was partially supported by National Science\r\nFoundation Grant
DMS-1207961. The major part of this research was conducted\r\nwhen all authors
were visiting IAS and were also supported by National Science\r\nFoundation Grant
DMS-1128255."
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
full_name: Bourgade, Paul
last_name: Bourgade
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horngtzer
full_name: Yau, Horngtzer
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized
wigner matrices. Communications on Pure and Applied Mathematics. 2016;69(10):1815-1881.
doi:10.1002/cpa.21624
apa: Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2016). Fixed energy universality
for generalized wigner matrices. Communications on Pure and Applied Mathematics.
Wiley-Blackwell. https://doi.org/10.1002/cpa.21624
chicago: Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy
Universality for Generalized Wigner Matrices.” Communications on Pure and Applied
Mathematics. Wiley-Blackwell, 2016. https://doi.org/10.1002/cpa.21624.
ieee: P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for
generalized wigner matrices,” Communications on Pure and Applied Mathematics,
vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.
ista: Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized
wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881.
mla: Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.”
Communications on Pure and Applied Mathematics, vol. 69, no. 10, Wiley-Blackwell,
2016, pp. 1815–81, doi:10.1002/cpa.21624.
short: P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied
Mathematics 69 (2016) 1815–1881.
corr_author: '1'
date_created: 2018-12-11T11:51:07Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2025-09-22T08:35:52Z
day: '01'
department:
- _id: LaEr
doi: 10.1002/cpa.21624
ec_funded: 1
external_id:
arxiv:
- '1407.5606'
isi:
- '000382932900001'
intvolume: ' 69'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1407.5606
month: '10'
oa: 1
oa_version: Preprint
page: 1815 - 1881
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6036'
scopus_import: '1'
status: public
title: Fixed energy universality for generalized wigner matrices
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 69
year: '2016'
...
---
_id: '1281'
abstract:
- lang: eng
text: Plants are able to modulate root growth and development to optimize their
nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response
to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses
emergence of lateral root primordia (LRPs) at low concentration or absence of
NO3 - through its auxin transport activity that lowers auxin accumulation in LR.
However, these functional data strongly contrast with the known transcriptional
regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3
-. To explain this discrepancy, we investigated in detail the spatiotemporal expression
pattern of the NRT1.1 protein during LRP development and combined local transcript
analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our
results show that although NO3 - stimulates NRT1.1 transcription and probably
mRNA stability both in primary root tissues and in LRPs, it acts differentially
on protein accumulation, depending on the tissues considered with stimulation
in cortex and epidermis of the primary root and a strong repression in LRPs and
to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly
regulated at the posttranscriptional level by tissue-specific mechanisms. These
mechanisms are crucial for controlling the large palette of adaptive responses
to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the
proper tissue under the specific conditions where it plays a signaling role in
this particular tissue.
acknowledgement: "This work was supported by the Agropolis Foundation (RHIZOPOLIS
project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge
Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement
to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G.,
and P.N.). We thank Carine Alcon for the help with analysis of confocal images,
Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members
of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance
with biological\r\nmaterial culture, and students and trainees for assistance with
laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging
facility."
article_processing_charge: No
author:
- first_name: Eléonore
full_name: Bouguyon, Eléonore
last_name: Bouguyon
- first_name: Francine
full_name: Perrine Walker, Francine
last_name: Perrine Walker
- first_name: Marjorie
full_name: Pervent, Marjorie
last_name: Pervent
- first_name: Juliette
full_name: Rochette, Juliette
last_name: Rochette
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Lien
full_name: Bach, Lien
last_name: Bach
- first_name: Gabriel
full_name: Krouk, Gabriel
last_name: Krouk
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Philippe
full_name: Nacry, Philippe
last_name: Nacry
citation:
ama: Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development
through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor.
Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047
apa: Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková,
E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional
regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American
Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047
chicago: Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette
Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls
Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter
Sensor.” Plant Physiology. American Society of Plant Biologists, 2016.
https://doi.org/10.1104/pp.16.01047.
ieee: E. Bouguyon et al., “Nitrate controls root development through posttranscriptional
regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology,
vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.
ista: Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E,
Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development
through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor.
Plant Physiology. 172(2), 1237–1248.
mla: Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional
Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology,
vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047.
short: E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková,
A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016)
1237–1248.
date_created: 2018-12-11T11:51:07Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2025-09-22T08:35:21Z
day: '01'
department:
- _id: EvBe
doi: 10.1104/pp.16.01047
external_id:
isi:
- '000391147700046'
intvolume: ' 172'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/
month: '10'
oa: 1
oa_version: Preprint
page: 1237 - 1248
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6035'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nitrate controls root development through posttranscriptional regulation of
the NRT1.1/NPF6.3 transporter sensor
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 172
year: '2016'
...
---
_id: '1282'
abstract:
- lang: eng
text: 'We consider higher-dimensional generalizations of the normalized Laplacian
and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam
model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We
show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s.
concentrated around two values. The main tool, which goes back to the work of
Garland, are arguments that relate the eigenvalues of these matrices to those
of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns
the Laplacian; we develop an analogous result for the adjacency matrix. The same
arguments apply to other models of random complexes which allow for dependencies
between the choices of k-dimensional simplices. In the second part of the paper,
we apply this to the question of possible higher-dimensional analogues of the
discrete Cheeger inequality, which in the classical case of graphs relates the
eigenvalues of a graph and its edge expansion. It is very natural to ask whether
this generalizes to higher dimensions and, in particular, whether the eigenvalues
of the higher-dimensional Laplacian capture the notion of coboundary expansion—a
higher-dimensional generalization of edge expansion that arose in recent work
of Linial and Meshulam and of Gromov; this question was raised, for instance,
by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional
discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and
n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral
expansion properties (all nontrivial eigenvalues of the normalised k-dimensional
Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion
is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn
k can be taken to have vanishing integer homology in dimension less than k.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
full_name: Gundert, Anna
last_name: Gundert
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Gundert A, Wagner U. On eigenvalues of random complexes. Israel Journal
of Mathematics. 2016;216(2):545-582. doi:10.1007/s11856-016-1419-1
apa: Gundert, A., & Wagner, U. (2016). On eigenvalues of random complexes. Israel
Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1419-1
chicago: Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel
Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1419-1.
ieee: A. Gundert and U. Wagner, “On eigenvalues of random complexes,” Israel
Journal of Mathematics, vol. 216, no. 2. Springer, pp. 545–582, 2016.
ista: Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal
of Mathematics. 216(2), 545–582.
mla: Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel
Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:10.1007/s11856-016-1419-1.
short: A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.
date_created: 2018-12-11T11:51:07Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2025-09-22T08:34:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s11856-016-1419-1
external_id:
arxiv:
- '1411.4906'
isi:
- '000386356400002'
intvolume: ' 216'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.4906
month: '10'
oa: 1
oa_version: Preprint
page: 545 - 582
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '6034'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On eigenvalues of random complexes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 216
year: '2016'
...
---
OA_place: repository
OA_type: green
_id: '1283'
abstract:
- lang: eng
text: The impact of the plant hormone ethylene on seedling development has long
been recognized; however, its ecophysiological relevance is unexplored. Three
recent studies demonstrate that ethylene is a critical endogenous integrator of
various environmental signals including mechanical stress, light, and oxygen availability
during seedling germination and growth through the soil.
acknowledgement: 'This work was supported by the Austrian Science Fund (FWF01_I1774S)
to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the
Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of
Crops (FJ 2011 Program, No 2015-75) to Q.Z. The authors thank Israel Ausin and Xu
Chen for critical reading of the manuscript. '
article_processing_charge: No
article_type: original
author:
- first_name: Qiang
full_name: Zhu, Qiang
id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
last_name: Zhu
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. Trends
in Plant Science. 2016;21(10):809-811. doi:10.1016/j.tplants.2016.08.003
apa: Zhu, Q., & Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier.
Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2016.08.003
chicago: Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.”
Trends in Plant Science. Cell Press, 2016. https://doi.org/10.1016/j.tplants.2016.08.003.
ieee: Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” Trends
in Plant Science, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.
ista: Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends
in Plant Science. 21(10), 809–811.
mla: Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.”
Trends in Plant Science, vol. 21, no. 10, Cell Press, 2016, pp. 809–11,
doi:10.1016/j.tplants.2016.08.003.
short: Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811.
corr_author: '1'
date_created: 2018-12-11T11:51:08Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2025-09-22T08:34:15Z
day: '01'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1016/j.tplants.2016.08.003
external_id:
isi:
- '000384958300003'
pmid:
- '27553704'
file:
- access_level: open_access
checksum: 4d569977fad7a7f22b7e3424003d2ab1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:19Z
date_updated: 2025-06-25T11:40:02Z
file_id: '4679'
file_name: IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf
file_size: 229094
relation: main_file
file_date_updated: 2025-06-25T11:40:02Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 809 - 811
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '6033'
pubrep_id: '1018'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Seedlings’ strategy to overcome a soil barrier
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2016'
...
---
_id: '1284'
abstract:
- lang: eng
text: Brassinosteroids (BRs) are growth-promoting plant hormones that play a role
in abiotic stress responses, but molecular modes that enable this activity remain
largely unknown. Here we show that BRs participate in the regulation of freezing
tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive
to freezing before and after cold acclimation. The constitutive activation of
BR signaling, in contrast, enhanced freezing resistance. Evidence is provided
that the BR-controlled basic helix-loop-helix transcription factor CESTA (CES)
can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE
ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive
(COR) gene expression. In addition, CBF-independent classes of BR-regulated COR
genes are identified that are regulated in a BR- and CES-dependent manner during
cold acclimation. A model is presented in which BRs govern different cold-responsive
transcriptional cascades through the post-translational modification of CES and
redundantly acting factors. This contributes to the basal resistance against freezing
stress, but also to the further improvement of this resistance through cold acclimation.
acknowledgement: 'We thank Joanne Chory for seeds of the bee1 bee2 bee3, bes1-D, and
bzr1-1D mutants and the 35S:BRI1-GFP line; Irene Ziegler, Clarissa Fahrig, and Renata
Milcevicova for technical assistance; and the horticultural staff of the TUMs Gewächshauslaborzentrum
Dürnast for plant care. This work was supported by funds from the Austrian Science
Fund (Project P22734 to B.P.), the Deutsche Forschungsgemeinschaft (Project PO1640/4
to B.P. and SFB924 to B.P. and K.F.X.M.), and a TUM doctoral fellowship (to M.E.).
M.E. and S.J.U. were members of the TUM graduate school. '
article_processing_charge: No
author:
- first_name: Marina
full_name: Eremina, Marina
last_name: Eremina
- first_name: Simon
full_name: Unterholzner, Simon
last_name: Unterholzner
- first_name: Ajith
full_name: Rathnayake, Ajith
last_name: Rathnayake
- first_name: Marcos
full_name: Castellanos, Marcos
last_name: Castellanos
- first_name: Mamoona
full_name: Khan-Djamei, Mamoona
id: 391B5BBC-F248-11E8-B48F-1D18A9856A87
last_name: Khan-Djamei
- first_name: Karl
full_name: Kügler, Karl
last_name: Kügler
- first_name: Sean
full_name: May, Sean
last_name: May
- first_name: Klaus
full_name: Mayer, Klaus
last_name: Mayer
- first_name: Wilfried
full_name: Rozhon, Wilfried
last_name: Rozhon
- first_name: Brigitte
full_name: Poppenberger, Brigitte
last_name: Poppenberger
citation:
ama: Eremina M, Unterholzner S, Rathnayake A, et al. Brassinosteroids participate
in the control of basal and acquired freezing tolerance of plants. PNAS.
2016;113(40):E5982-E5991. doi:10.1073/pnas.1611477113
apa: Eremina, M., Unterholzner, S., Rathnayake, A., Castellanos, M., Khan-Djamei,
M., Kügler, K., … Poppenberger, B. (2016). Brassinosteroids participate in the
control of basal and acquired freezing tolerance of plants. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1611477113
chicago: Eremina, Marina, Simon Unterholzner, Ajith Rathnayake, Marcos Castellanos,
Mamoona Khan-Djamei, Karl Kügler, Sean May, Klaus Mayer, Wilfried Rozhon, and
Brigitte Poppenberger. “Brassinosteroids Participate in the Control of Basal and
Acquired Freezing Tolerance of Plants.” PNAS. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1611477113.
ieee: M. Eremina et al., “Brassinosteroids participate in the control of
basal and acquired freezing tolerance of plants,” PNAS, vol. 113, no. 40.
National Academy of Sciences, pp. E5982–E5991, 2016.
ista: Eremina M, Unterholzner S, Rathnayake A, Castellanos M, Khan-Djamei M, Kügler
K, May S, Mayer K, Rozhon W, Poppenberger B. 2016. Brassinosteroids participate
in the control of basal and acquired freezing tolerance of plants. PNAS. 113(40),
E5982–E5991.
mla: Eremina, Marina, et al. “Brassinosteroids Participate in the Control of Basal
and Acquired Freezing Tolerance of Plants.” PNAS, vol. 113, no. 40, National
Academy of Sciences, 2016, pp. E5982–91, doi:10.1073/pnas.1611477113.
short: M. Eremina, S. Unterholzner, A. Rathnayake, M. Castellanos, M. Khan-Djamei,
K. Kügler, S. May, K. Mayer, W. Rozhon, B. Poppenberger, PNAS 113 (2016) E5982–E5991.
date_created: 2018-12-11T11:51:08Z
date_published: 2016-10-04T00:00:00Z
date_updated: 2022-02-18T13:41:37Z
day: '04'
doi: 10.1073/pnas.1611477113
extern: '1'
external_id:
pmid:
- '27489342'
intvolume: ' 113'
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056081/
month: '10'
oa: 1
oa_version: Submitted Version
page: E5982 - E5991
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6032'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Brassinosteroids participate in the control of basal and acquired freezing
tolerance of plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1285'
abstract:
- lang: eng
text: Cell migration is central to a multitude of physiological processes, including
embryonic development, immune surveillance, and wound healing, and deregulated
migration is key to cancer dissemination. Decades of investigations have uncovered
many of the molecular and physical mechanisms underlying cell migration. Together
with protrusion extension and cell body retraction, adhesion to the substrate
via specific focal adhesion points has long been considered an essential step
in cell migration. Although this is true for cells moving on two-dimensional substrates,
recent studies have demonstrated that focal adhesions are not required for cells
moving in three dimensions, in which confinement is sufficient to maintain a cell
in contact with its substrate. Here, we review the investigations that have led
to challenging the requirement of specific adhesions for migration, discuss the
physical mechanisms proposed for cell body translocation during focal adhesion-independent
migration, and highlight the remaining open questions for the future.
acknowledgement: We would like to thank Dani Bodor for critical comments on the manuscript
and Guillaume Salbreux for discussions. The authors are supported by the United
Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the
MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC
GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian
Science Foundation (M.S.).
article_processing_charge: No
author:
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Irene
full_name: Aspalter, Irene
last_name: Aspalter
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. Annual
Review of Cell and Developmental Biology. 2016;32:469-490. doi:10.1146/annurev-cellbio-111315-125341
apa: Paluch, E., Aspalter, I., & Sixt, M. K. (2016). Focal adhesion-independent
cell migration. Annual Review of Cell and Developmental Biology. Annual
Reviews. https://doi.org/10.1146/annurev-cellbio-111315-125341
chicago: Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent
Cell Migration.” Annual Review of Cell and Developmental Biology. Annual
Reviews, 2016. https://doi.org/10.1146/annurev-cellbio-111315-125341.
ieee: E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,”
Annual Review of Cell and Developmental Biology, vol. 32. Annual Reviews,
pp. 469–490, 2016.
ista: Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration.
Annual Review of Cell and Developmental Biology. 32, 469–490.
mla: Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” Annual
Review of Cell and Developmental Biology, vol. 32, Annual Reviews, 2016, pp.
469–90, doi:10.1146/annurev-cellbio-111315-125341.
short: E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental
Biology 32 (2016) 469–490.
date_created: 2018-12-11T11:51:08Z
date_published: 2016-10-06T00:00:00Z
date_updated: 2025-09-22T08:33:40Z
day: '06'
department:
- _id: MiSi
doi: 10.1146/annurev-cellbio-111315-125341
ec_funded: 1
external_id:
isi:
- '000389576900019'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 469 - 490
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and force transduction of migrating leukocytes
publication: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '6031'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Focal adhesion-independent cell migration
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2016'
...
---
_id: '1286'
abstract:
- lang: eng
text: We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys.
Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to
study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein
condensates of rubidium and strontium. Based on ab initio potential energy surfaces,
we provide a detailed study of the rotational Lamb shift and many-body-induced
fine structure which arise due to dressing of molecular rotation by a field of
phonon excitations. We demonstrate that the magnitude of these effects is large
enough in order to be observed in modern experiments on cold molecular ions. Furthermore,
we introduce a novel method to construct pseudopotentials starting from the ab
initio potential energy surfaces, which provides a means to obtain effective coupling
constants for low-energy polaron models.
acknowledgement: The work was supported by the NSF through a grant for the Institute
for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and
the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges
support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG
OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P)
and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex,
the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.
article_number: '041601'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Michał
full_name: Tomza, Michał
last_name: Tomza
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside
a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical
Physics. 2016;94(4). doi:10.1103/PhysRevA.94.041601
apa: Midya, B., Tomza, M., Schmidt, R., & Lemeshko, M. (2016). Rotation of cold
molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.94.041601
chicago: Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko.
“Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical
Review A - Atomic, Molecular, and Optical Physics. American Physical Society,
2016. https://doi.org/10.1103/PhysRevA.94.041601.
ieee: B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular
ions inside a Bose-Einstein condensate,” Physical Review A - Atomic, Molecular,
and Optical Physics, vol. 94, no. 4. American Physical Society, 2016.
ista: Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular
ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular,
and Optical Physics. 94(4), 041601.
mla: Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein
Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 94, no. 4, 041601, American Physical Society, 2016, doi:10.1103/PhysRevA.94.041601.
short: B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic,
Molecular, and Optical Physics 94 (2016).
corr_author: '1'
date_created: 2018-12-11T11:51:09Z
date_published: 2016-10-13T00:00:00Z
date_updated: 2025-09-22T08:33:08Z
day: '13'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.94.041601
ec_funded: 1
external_id:
arxiv:
- '1607.06092'
isi:
- '000385618500001'
intvolume: ' 94'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.06092
month: '10'
oa: 1
oa_version: Preprint
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_status: published
publisher: American Physical Society
publist_id: '6030'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rotation of cold molecular ions inside a Bose-Einstein condensate
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 94
year: '2016'
...
---
_id: '1287'
abstract:
- lang: eng
text: A planar waveguide with an impedance boundary, composed of nonperfect metallic
plates, and with passive or active dielectric filling, is considered. We show
the possibility of selective mode guiding and amplification when a homogeneous
pump is added to the dielectric and analyze differences in TE and TM mode propagation.
Such a non-conservative system is also shown to feature exceptional points for
specific and experimentally tunable parameters, which are described for a particular
case of transparent dielectric.
acknowledgement: The research of B.M. is supported by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant No. [291734].
article_processing_charge: No
arxiv: 1
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Vladimir
full_name: Konotop, Vladimir
last_name: Konotop
citation:
ama: Midya B, Konotop V. Modes and exceptional points in waveguides with impedance
boundary conditions. Optics Letters. 2016;41(20):4621-4624. doi:10.1364/OL.41.004621
apa: Midya, B., & Konotop, V. (2016). Modes and exceptional points in waveguides
with impedance boundary conditions. Optics Letters. Optica Publishing Group.
https://doi.org/10.1364/OL.41.004621
chicago: Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points
in Waveguides with Impedance Boundary Conditions.” Optics Letters. Optica
Publishing Group, 2016. https://doi.org/10.1364/OL.41.004621.
ieee: B. Midya and V. Konotop, “Modes and exceptional points in waveguides with
impedance boundary conditions,” Optics Letters, vol. 41, no. 20. Optica
Publishing Group, pp. 4621–4624, 2016.
ista: Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with
impedance boundary conditions. Optics Letters. 41(20), 4621–4624.
mla: Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides
with Impedance Boundary Conditions.” Optics Letters, vol. 41, no. 20, Optica
Publishing Group, 2016, pp. 4621–24, doi:10.1364/OL.41.004621.
short: B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.
corr_author: '1'
date_created: 2018-12-11T11:51:09Z
date_published: 2016-10-15T00:00:00Z
date_updated: 2025-09-22T08:32:34Z
day: '15'
department:
- _id: MiLe
doi: 10.1364/OL.41.004621
ec_funded: 1
external_id:
arxiv:
- '1609.02863'
isi:
- '000386854500005'
intvolume: ' 41'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.02863
month: '10'
oa: 1
oa_version: Preprint
page: 4621 - 4624
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Optics Letters
publication_status: published
publisher: Optica Publishing Group
publist_id: '6029'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modes and exceptional points in waveguides with impedance boundary conditions
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 41
year: '2016'
...
---
_id: '1288'
abstract:
- lang: eng
text: Respiratory complex I transfers electrons from NADH to quinone, utilizing
the reaction energy to translocate protons across the membrane. It is a key enzyme
of the respiratory chain of many prokaryotic and most eukaryotic organisms. The
reversible NADH oxidation reaction is facilitated in complex I by non-covalently
bound flavin mononucleotide (FMN). Here we report that the catalytic activity
of E. coli complex I with artificial electron acceptors potassium ferricyanide
(FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced
by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation
of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar
range in oxidized complex I to the nanomolar range in the NADH reduced enzyme,
with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex
I, rather than that of FMN, proved critical to the dissociation. Such dissociation
is not observed with the T. thermophilus enzyme and our analysis suggests that
the difference may be due to the unusually high redox potential of Fe-S cluster
N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo
by releasing FMN under highly reducing conditions.
acknowledgement: This work was funded by the UK Medical Research Council.
article_processing_charge: No
author:
- first_name: Peter
full_name: Holt, Peter
last_name: Holt
- first_name: Rouslan
full_name: Efremov, Rouslan
last_name: Efremov
- first_name: Eiko
full_name: Nakamaru Ogiso, Eiko
last_name: Nakamaru Ogiso
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation
from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta
- Bioenergetics. 2016;1857(11):1777-1785. doi:10.1016/j.bbabio.2016.08.008
apa: Holt, P., Efremov, R., Nakamaru Ogiso, E., & Sazanov, L. A. (2016). Reversible
FMN dissociation from Escherichia coli respiratory complex I. Biochimica et
Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2016.08.008
chicago: Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov.
“Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” Biochimica
et Biophysica Acta - Bioenergetics. Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.08.008.
ieee: P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN
dissociation from Escherichia coli respiratory complex I,” Biochimica et Biophysica
Acta - Bioenergetics, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016.
ista: Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation
from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics.
1857(11), 1777–1785.
mla: Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory
Complex I.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no.
11, Elsevier, 2016, pp. 1777–85, doi:10.1016/j.bbabio.2016.08.008.
short: P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica
Acta - Bioenergetics 1857 (2016) 1777–1785.
corr_author: '1'
date_created: 2018-12-11T11:51:09Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T08:32:00Z
day: '01'
department:
- _id: LeSa
doi: 10.1016/j.bbabio.2016.08.008
external_id:
isi:
- '000384867400007'
intvolume: ' 1857'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1777 - 1785
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '6028'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible FMN dissociation from Escherichia coli respiratory complex I
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1857
year: '2016'
...
---
_id: '1289'
abstract:
- lang: eng
text: 'Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI)
magnifying endoscopic (ME) images of the stomach, we combine methods from image
processing, topology, geometry, and machine learning to classify patterns into
three classes: oval, tubular and irregular. Training the algorithm on a small
number of images of each type, we achieve a high rate of correct classifications.
The analysis of the learning algorithm reveals that a handful of geometric and
topological features are responsible for the overwhelming majority of decisions.'
article_processing_charge: No
author:
- first_name: Olga
full_name: Dunaeva, Olga
last_name: Dunaeva
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Lukyanov, Anton
last_name: Lukyanov
- first_name: Michael
full_name: Machin, Michael
last_name: Machin
- first_name: Daria
full_name: Malkova, Daria
last_name: Malkova
- first_name: Roman
full_name: Kuvaev, Roman
last_name: Kuvaev
- first_name: Sergey
full_name: Kashin, Sergey
last_name: Kashin
citation:
ama: Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy
images with persistent homology. Pattern Recognition Letters. 2016;83(1):13-22.
doi:10.1016/j.patrec.2015.12.012
apa: Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev,
R., & Kashin, S. (2016). The classification of endoscopy images with persistent
homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2015.12.012
chicago: Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria
Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images
with Persistent Homology.” Pattern Recognition Letters. Elsevier, 2016.
https://doi.org/10.1016/j.patrec.2015.12.012.
ieee: O. Dunaeva et al., “The classification of endoscopy images with persistent
homology,” Pattern Recognition Letters, vol. 83, no. 1. Elsevier, pp. 13–22,
2016.
ista: Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin
S. 2016. The classification of endoscopy images with persistent homology. Pattern
Recognition Letters. 83(1), 13–22.
mla: Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent
Homology.” Pattern Recognition Letters, vol. 83, no. 1, Elsevier, 2016,
pp. 13–22, doi:10.1016/j.patrec.2015.12.012.
short: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev,
S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.
date_created: 2018-12-11T11:51:10Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-23T13:44:16Z
day: '01'
ddc:
- '004'
- '514'
department:
- _id: HeEd
doi: 10.1016/j.patrec.2015.12.012
external_id:
isi:
- '000386874700003'
file:
- access_level: open_access
checksum: 33458bbb8c32a339e1adeca6d5a1112d
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:55:51Z
date_updated: 2020-07-14T12:44:42Z
file_id: '6334'
file_name: 2016-Edelsbrunner_The_classification.pdf
file_size: 1921113
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 83'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 13 - 22
publication: Pattern Recognition Letters
publication_status: published
publisher: Elsevier
publist_id: '6027'
pubrep_id: '975'
quality_controlled: '1'
related_material:
record:
- id: '1568'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The classification of endoscopy images with persistent homology
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 83
year: '2016'
...
---
_id: '1290'
abstract:
- lang: eng
text: We developed a competition-based screening strategy to identify compounds
that invert the selective advantage of antibiotic resistance. Using our assay,
we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance
efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram.
Treating a tetracycline-resistant population with β-thujaplicin selects for loss
of the resistance gene, enabling an effective second-phase treatment with doxycycline.
acknowledgement: "This work was supported in part by National Institute of Allergy
and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants
R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC
grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to
L.K.S.).\r\n"
article_processing_charge: No
author:
- first_name: Laura
full_name: Stone, Laura
last_name: Stone
- first_name: Michael
full_name: Baym, Michael
last_name: Baym
- first_name: Tami
full_name: Lieberman, Tami
last_name: Lieberman
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Jon
full_name: Clardy, Jon
last_name: Clardy
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that
select against the tetracycline-resistance efflux pump. Nature Chemical Biology.
2016;12(11):902-904. doi:10.1038/nchembio.2176
apa: Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony,
R. (2016). Compounds that select against the tetracycline-resistance efflux pump.
Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176
chicago: Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and
Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux
Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.
ieee: L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds
that select against the tetracycline-resistance efflux pump,” Nature Chemical
Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.
ista: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds
that select against the tetracycline-resistance efflux pump. Nature Chemical Biology.
12(11), 902–904.
mla: Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance
Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing
Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.
short: L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature
Chemical Biology 12 (2016) 902–904.
date_created: 2018-12-11T11:51:10Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T08:30:48Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/nchembio.2176
external_id:
isi:
- '000386798800008'
intvolume: ' 12'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/
month: '11'
oa: 1
oa_version: Preprint
page: 902 - 904
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6026'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Compounds that select against the tetracycline-resistance efflux pump
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2016'
...
---
_id: '12903'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling
the human hippocampus. In: AHPC16 - Austrian HPC Meeting 2016. VSC - Vienna
Scientific Cluster; 2016:37.'
apa: 'Schlögl, A., & Stadlbauer, S. (2016). High performance computing at IST
Austria: Modelling the human hippocampus. In AHPC16 - Austrian HPC Meeting
2016 (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.'
chicago: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at
IST Austria: Modelling the Human Hippocampus.” In AHPC16 - Austrian HPC Meeting
2016, 37. VSC - Vienna Scientific Cluster, 2016.'
ieee: 'A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria:
Modelling the human hippocampus,” in AHPC16 - Austrian HPC Meeting 2016,
Grundlsee, Austria, 2016, p. 37.'
ista: 'Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria:
Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian
HPC Meeting, 37.'
mla: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST
Austria: Modelling the Human Hippocampus.” AHPC16 - Austrian HPC Meeting 2016,
VSC - Vienna Scientific Cluster, 2016, p. 37.'
short: A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC -
Vienna Scientific Cluster, 2016, p. 37.
conference:
end_date: 2016-02-24
location: Grundlsee, Austria
name: 'AHPC: Austrian HPC Meeting'
start_date: 2016-02-22
corr_author: '1'
date_created: 2023-05-05T12:54:47Z
date_published: 2016-02-24T00:00:00Z
date_updated: 2024-10-09T21:05:23Z
day: '24'
ddc:
- '000'
department:
- _id: ScienComp
- _id: PeJo
file:
- access_level: open_access
checksum: 4a7b00362e81358d568f5e216fa03c3e
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:03:56Z
date_updated: 2023-05-16T07:03:56Z
file_id: '12968'
file_name: 2016_AHPC_Schloegl.pdf
file_size: 1073523
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:03:56Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf
month: '02'
oa: 1
oa_version: Published Version
page: '37'
publication: AHPC16 - Austrian HPC Meeting 2016
publication_status: published
publisher: VSC - Vienna Scientific Cluster
quality_controlled: '1'
status: public
title: 'High performance computing at IST Austria: Modelling the human hippocampus'
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1291'
abstract:
- lang: eng
text: We consider Ising models in two and three dimensions, with short range ferromagnetic
and long range, power-law decaying, antiferromagnetic interactions. We let J be
the ratio between the strength of the ferromagnetic to antiferromagnetic interactions.
The competition between these two kinds of interactions induces the system to
form domains of minus spins in a background of plus spins, or vice versa. If the
decay exponent p of the long range interaction is larger than d + 1, with d
the space dimension, this happens for all values of J smaller than a critical
value Jc(p), beyond which the ground state is homogeneous. In this paper, we give
a characterization of the infinite volume ground states of the system, for pÂ
>Â 2d and J in a left neighborhood of Jc(p). In particular, we prove that the
quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs
(d = 3), all of the same optimal width and orientation, and alternating magnetization,
are infinite volume ground states. Our proof is based on localization bounds combined
with reflection positivity.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria). The\r\nresearch leading to these results has received funding from
the European Research Council under the European\r\nUnion’s Seventh Framework Programme
ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN
National Grant Geometric and analytic theory of Hamiltonian systems in finite and
infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27.
Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute
for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems,
random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully
acknowledged."
article_processing_charge: No
author:
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Giuliani A, Seiringer R. Periodic striped ground states in Ising models with
competing interactions. Communications in Mathematical Physics. 2016;347(3):983-1007.
doi:10.1007/s00220-016-2665-0
apa: Giuliani, A., & Seiringer, R. (2016). Periodic striped ground states in
Ising models with competing interactions. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-016-2665-0
chicago: Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States
in Ising Models with Competing Interactions.” Communications in Mathematical
Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2665-0.
ieee: A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models
with competing interactions,” Communications in Mathematical Physics, vol.
347, no. 3. Springer, pp. 983–1007, 2016.
ista: Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models
with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007.
mla: Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States
in Ising Models with Competing Interactions.” Communications in Mathematical
Physics, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:10.1007/s00220-016-2665-0.
short: A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016)
983–1007.
date_created: 2018-12-11T11:51:11Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T08:30:16Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1007/s00220-016-2665-0
external_id:
isi:
- '000385162900010'
file:
- access_level: open_access
checksum: 3c6e08c048fc462e312788be72874bb1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:02Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4725'
file_name: IST-2016-688-v1+1_s00220-016-2665-0.pdf
file_size: 794983
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 347'
isi: 1
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 983 - 1007
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
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6025'
pubrep_id: '688'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Periodic striped ground states in Ising models with competing interactions
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 347
year: '2016'
...
---
_id: '1292'
abstract:
- lang: eng
text: We give explicit formulas and algorithms for the computation of the Thurston–Bennequin
invariant of a nullhomologous Legendrian knot on a page of a contact open book
and on Heegaard surfaces in convex position. Furthermore, we extend the results
to rationally nullhomologous knots in arbitrary 3-manifolds.
acknowledgement: "The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful
discussions and advice and Christian Evers for helpful remarks on a draft version."
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastian
full_name: Durst, Sebastian
last_name: Durst
- first_name: Marc
full_name: Kegel, Marc
last_name: Kegel
- first_name: Mirko D
full_name: Klukas, Mirko D
id: 34927512-F248-11E8-B48F-1D18A9856A87
last_name: Klukas
citation:
ama: Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in
open books. Acta Mathematica Hungarica. 2016;150(2):441-455. doi:10.1007/s10474-016-0648-4
apa: Durst, S., Kegel, M., & Klukas, M. D. (2016). Computing the Thurston–Bennequin
invariant in open books. Acta Mathematica Hungarica. Springer. https://doi.org/10.1007/s10474-016-0648-4
chicago: Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin
Invariant in Open Books.” Acta Mathematica Hungarica. Springer, 2016. https://doi.org/10.1007/s10474-016-0648-4.
ieee: S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant
in open books,” Acta Mathematica Hungarica, vol. 150, no. 2. Springer,
pp. 441–455, 2016.
ista: Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant
in open books. Acta Mathematica Hungarica. 150(2), 441–455.
mla: Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open
Books.” Acta Mathematica Hungarica, vol. 150, no. 2, Springer, 2016, pp.
441–55, doi:10.1007/s10474-016-0648-4.
short: S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455.
corr_author: '1'
date_created: 2018-12-11T11:51:11Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-09-22T08:29:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10474-016-0648-4
external_id:
arxiv:
- '1605.00794'
isi:
- '000387471100014'
intvolume: ' 150'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.00794
month: '12'
oa: 1
oa_version: Preprint
page: 441 - 455
publication: Acta Mathematica Hungarica
publication_status: published
publisher: Springer
publist_id: '6023'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the Thurston–Bennequin invariant in open books
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 150
year: '2016'
...
---
_id: '1293'
abstract:
- lang: eng
text: For a graph G with p vertices the closed convex cone S⪰0(G) consists of all
real positive semidefinite p×p matrices whose sparsity pattern is given by G,
that is, those matrices with zeros in the off-diagonal entries corresponding to
nonedges of G. The extremal rays of this cone and their associated ranks have
applications to matrix completion problems, maximum likelihood estimation in Gaussian
graphical models in statistics, and Gauss elimination for sparse matrices. While
the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of
G, has been characterized for different classes of graphs, we here study all possible
extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope
of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G).
For a graph G without K5 minors, we show that appropriately chosen normal vectors
to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of
extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars
the constant term of the linear equation of each facet-supporting hyperplane is
the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show
that if G is series-parallel then this gives a complete characterization of all
possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for
series-parallel graphs can be solved in terms of polyhedral geometry.
acknowledgement: We wish to thank Alexander Engström and Bernd Sturmfels for various
valuable discussions and insights. We also thank the two anonymous referees for
their thoughtful feedback on the paper. CU was partially supported by the Austrian
Science Fund (FWF) Y 903-N35.
article_processing_charge: No
arxiv: 1
author:
- first_name: Liam T
full_name: Solus, Liam T
id: 2AADA620-F248-11E8-B48F-1D18A9856A87
last_name: Solus
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Ruriko
full_name: Yoshida, Ruriko
last_name: Yoshida
citation:
ama: Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose
sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its
Applications. 2016;509:247-275. doi:10.1016/j.laa.2016.07.026
apa: Solus, L. T., Uhler, C., & Yoshida, R. (2016). Extremal positive semidefinite
matrices whose sparsity pattern is given by graphs without K5 minors. Linear
Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2016.07.026
chicago: Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite
Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear
Algebra and Its Applications. Elsevier, 2016. https://doi.org/10.1016/j.laa.2016.07.026.
ieee: L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices
whose sparsity pattern is given by graphs without K5 minors,” Linear Algebra
and Its Applications, vol. 509. Elsevier, pp. 247–275, 2016.
ista: Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices
whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and
Its Applications. 509, 247–275.
mla: Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity
Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications,
vol. 509, Elsevier, 2016, pp. 247–75, doi:10.1016/j.laa.2016.07.026.
short: L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509
(2016) 247–275.
date_created: 2018-12-11T11:51:11Z
date_published: 2016-11-15T00:00:00Z
date_updated: 2025-09-22T08:29:45Z
day: '15'
department:
- _id: CaUh
doi: 10.1016/j.laa.2016.07.026
external_id:
arxiv:
- '1506.06702'
isi:
- '000385338000012'
intvolume: ' 509'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.06702
month: '11'
oa: 1
oa_version: Preprint
page: 247 - 275
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: Linear Algebra and Its Applications
publication_status: published
publisher: Elsevier
publist_id: '6024'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extremal positive semidefinite matrices whose sparsity pattern is given by
graphs without K5 minors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 509
year: '2016'
...
---
_id: '1295'
abstract:
- lang: eng
text: Voronoi diagrams and Delaunay triangulations have been extensively used to
represent and compute geometric features of point configurations. We introduce
a generalization to poset diagrams and poset complexes, which contain order-k
and degree-k Voronoi diagrams and their duals as special cases. Extending a result
of Aurenhammer from 1990, we show how to construct poset diagrams as weighted
Voronoi diagrams of average balls.
acknowledgement: This work is partially supported by the Toposys project FP7-ICT-318493-STREP,
and by ESF under the ACAT Research Network Programme.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages.
Electronic Notes in Discrete Mathematics. 2016;54:169-174. doi:10.1016/j.endm.2016.09.030'
apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2016). Multiple covers with balls
II: Weighted averages. Electronic Notes in Discrete Mathematics. Elsevier.
https://doi.org/10.1016/j.endm.2016.09.030'
chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
II: Weighted Averages.” Electronic Notes in Discrete Mathematics. Elsevier,
2016. https://doi.org/10.1016/j.endm.2016.09.030.'
ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted
averages,” Electronic Notes in Discrete Mathematics, vol. 54. Elsevier,
pp. 169–174, 2016.'
ista: 'Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted
averages. Electronic Notes in Discrete Mathematics. 54, 169–174.'
mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
II: Weighted Averages.” Electronic Notes in Discrete Mathematics, vol.
54, Elsevier, 2016, pp. 169–74, doi:10.1016/j.endm.2016.09.030.'
short: H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics
54 (2016) 169–174.
corr_author: '1'
date_created: 2018-12-11T11:51:12Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2024-10-09T20:57:05Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.endm.2016.09.030
ec_funded: 1
intvolume: ' 54'
language:
- iso: eng
month: '10'
oa_version: None
page: 169 - 174
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Electronic Notes in Discrete Mathematics
publication_status: published
publisher: Elsevier
publist_id: '5976'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Multiple covers with balls II: Weighted averages'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2016'
...
---
_id: '1303'
abstract:
- lang: eng
text: In bright light, cone-photoreceptors are active and colour vision derives
from a comparison of signals in cones with different visual pigments. This comparison
begins in the retina, where certain retinal ganglion cells have 'colour-opponent'
visual responses-excited by light of one colour and suppressed by another colour.
In dim light, rod-photoreceptors are active, but colour vision is impossible because
they all use the same visual pigment. Instead, the rod signals are thought to
splice into retinal circuits at various points, in synergy with the cone signals.
Here we report a new circuit for colour vision that challenges these expectations.
A genetically identified type of mouse retinal ganglion cell called JAMB (J-RGC),
was found to have colour-opponent responses, OFF to ultraviolet (UV) light and
ON to green light. Although the mouse retina contains a green-sensitive cone,
the ON response instead originates in rods. Rods and cones both contribute to
the response over several decades of light intensity. Remarkably, the rod signal
in this circuit is antagonistic to that from cones. For rodents, this UV-green
channel may play a role in social communication, as suggested by spectral measurements
from the environment. In the human retina, all of the components for this circuit
exist as well, and its function can explain certain experiences of colour in dim
lights, such as a 'blue shift' in twilight. The discovery of this genetically
defined pathway will enable new targeted studies of colour processing in the brain.
acknowledgement: This work was supported by grants to M.M. from the NIH and to M.J.
from The International Human Frontier Science Program Organization.
author:
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Markus
full_name: Meister, Markus
last_name: Meister
citation:
ama: Jösch MA, Meister M. A neuronal circuit for colour vision based on rod-cone
opponency. Nature. 2016;532(7598):236-239. doi:10.1038/nature17158
apa: Jösch, M. A., & Meister, M. (2016). A neuronal circuit for colour vision
based on rod-cone opponency. Nature. Nature Publishing Group. https://doi.org/10.1038/nature17158
chicago: Jösch, Maximilian A, and Markus Meister. “A Neuronal Circuit for Colour
Vision Based on Rod-Cone Opponency.” Nature. Nature Publishing Group, 2016.
https://doi.org/10.1038/nature17158.
ieee: M. A. Jösch and M. Meister, “A neuronal circuit for colour vision based on
rod-cone opponency,” Nature, vol. 532, no. 7598. Nature Publishing Group,
pp. 236–239, 2016.
ista: Jösch MA, Meister M. 2016. A neuronal circuit for colour vision based on rod-cone
opponency. Nature. 532(7598), 236–239.
mla: Jösch, Maximilian A., and Markus Meister. “A Neuronal Circuit for Colour Vision
Based on Rod-Cone Opponency.” Nature, vol. 532, no. 7598, Nature Publishing
Group, 2016, pp. 236–39, doi:10.1038/nature17158.
short: M.A. Jösch, M. Meister, Nature 532 (2016) 236–239.
date_created: 2018-12-11T11:51:15Z
date_published: 2016-04-14T00:00:00Z
date_updated: 2021-01-12T06:49:45Z
day: '14'
doi: 10.1038/nature17158
extern: 1
intvolume: ' 532'
issue: '7598'
month: '04'
page: 236 - 239
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5966'
quality_controlled: 0
status: public
title: A neuronal circuit for colour vision based on rod-cone opponency
type: journal_article
volume: 532
year: '2016'
...