---
_id: '5385'
abstract:
- lang: eng
text: There is recently a significant effort to add quantitative objectives to formal
verification and synthesis. We introduce and investigate the extension of temporal
logics with quantitative atomic assertions, aiming for a general and flexible
framework for quantitative-oriented specifications. In the heart of quantitative
objectives lies the accumulation of values along a computation. It is either the
accumulated summation, as with the energy objectives, or the accumulated average,
as with the mean-payoff objectives. We investigate the extension of temporal logics
with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is
a numeric variable of the system, c is a constant rational number, and Sum(v)
and Avg(v) denote the accumulated sum and average of the values of v from the
beginning of the computation up to the current point of time. We also allow the
path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring
to the average value along an entire computation. We study the border of decidability
for extensions of various temporal logics. In particular, we show that extending
the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by
prefix-accumulation assertions and extending LTL with path-accumulation assertions,
result in temporal logics whose model-checking problem is decidable. The extended
logics allow to significantly extend the currently known energy and mean-payoff
objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”,
allowing, for example, to specify constraints on the average waiting time between
a request and a grant. On the negative side, we show that the fragment we point
to is, in a sense, the maximal logic whose extension with prefix-accumulation
assertions permits a decidable model-checking procedure. Extending a temporal
logic that has the EG or EU modalities, and in particular CTL and LTL, makes the
problem undecidable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal Specifications
with Accumulative Values. IST Austria; 2011. doi:10.15479/AT:IST-2011-0003
apa: Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2011). Temporal
specifications with accumulative values. IST Austria. https://doi.org/10.15479/AT:IST-2011-0003
chicago: Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman.
Temporal Specifications with Accumulative Values. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0003.
ieee: U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, Temporal specifications
with accumulative values. IST Austria, 2011.
ista: Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications
with accumulative values, IST Austria, 14p.
mla: Boker, Udi, et al. Temporal Specifications with Accumulative Values.
IST Austria, 2011, doi:10.15479/AT:IST-2011-0003.
short: U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications
with Accumulative Values, IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-04-04T00:00:00Z
date_updated: 2023-02-23T11:23:41Z
day: '04'
ddc:
- '000'
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.15479/AT:IST-2011-0003
ec_funded: 1
file:
- access_level: open_access
checksum: 8491d0d48c4911620ecd5350b413c11e
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:00Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5461'
file_name: IST-2011-0003_IST-2011-0003.pdf
file_size: 366281
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '14'
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '21'
related_material:
record:
- id: '2038'
relation: later_version
status: public
- id: '3356'
relation: later_version
status: public
status: public
title: Temporal specifications with accumulative values
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5386'
abstract:
- lang: eng
text: 'We introduce TopoCut: a new way to integrate knowledge about topological
properties (TPs) into random field image segmentation model. Instead of including
TPs as additional constraints during minimization of the energy function, we devise
an efficient algorithm for modifying the unary potentials such that the resulting
segmentation is guaranteed with the desired properties. Our method is more flexible
in the sense that it handles more topology constraints than previous methods,
which were only able to enforce pairwise or global connectivity. In particular,
our method is very fast, making it for the first time possible to enforce global
topological properties in practical image segmentation tasks.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Chen C, Freedman D, Lampert C. Enforcing Topological Constraints in Random
Field Image Segmentation. IST Austria; 2011. doi:10.15479/AT:IST-2011-0002
apa: Chen, C., Freedman, D., & Lampert, C. (2011). Enforcing topological
constraints in random field image segmentation. IST Austria. https://doi.org/10.15479/AT:IST-2011-0002
chicago: Chen, Chao, Daniel Freedman, and Christoph Lampert. Enforcing Topological
Constraints in Random Field Image Segmentation. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0002.
ieee: C. Chen, D. Freedman, and C. Lampert, Enforcing topological constraints
in random field image segmentation. IST Austria, 2011.
ista: Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in
random field image segmentation, IST Austria, 69p.
mla: Chen, Chao, et al. Enforcing Topological Constraints in Random Field Image
Segmentation. IST Austria, 2011, doi:10.15479/AT:IST-2011-0002.
short: C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random
Field Image Segmentation, IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-03-28T00:00:00Z
date_updated: 2023-02-23T11:22:48Z
day: '28'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.15479/AT:IST-2011-0002
file:
- access_level: open_access
checksum: ad64c2add5fe2ad10e9d5c669f3f9526
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:34Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5495'
file_name: IST-2011-0002_IST-2011-0002.pdf
file_size: 26390601
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '69'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '22'
related_material:
record:
- id: '3336'
relation: later_version
status: public
status: public
title: Enforcing topological constraints in random field image segmentation
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5387'
abstract:
- lang: eng
text: We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy
parity objectives. In system design, the parity objective is used to encode ω-regular
specifications, and the mean-payoff and energy objectives can be used to model
quantitative resource constraints. The energy condition re- quires that the resource
level never drops below 0, and the mean-payoff condi- tion requires that the limit-average
value of the resource consumption is within a threshold. While these two (energy
and mean-payoff) classical conditions are equivalent for two-player games, we
show that they differ for MDPs. We show that the problem of deciding whether a
state is almost-sure winning (i.e., winning with probability 1) in energy parity
MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable
in polynomial time, improving a recent PSPACE bound.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Energy and Mean-Payoff Parity Markov Decision Processes.
IST Austria; 2011. doi:10.15479/AT:IST-2011-0001
apa: Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov
decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2011-0001
chicago: Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity
Markov Decision Processes. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0001.
ieee: K. Chatterjee and L. Doyen, Energy and mean-payoff parity Markov decision
processes. IST Austria, 2011.
ista: Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision
processes, IST Austria, 20p.
mla: Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity
Markov Decision Processes. IST Austria, 2011, doi:10.15479/AT:IST-2011-0001.
short: K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes,
IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-02-16T00:00:00Z
date_updated: 2023-02-23T11:23:11Z
day: '16'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0001
file:
- access_level: open_access
checksum: 824d6c70e6d3feb3e836b009e0b3cf73
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:52:57Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5458'
file_name: IST-2011-0001_IST-2011-0001.pdf
file_size: 329976
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '23'
related_material:
record:
- id: '3345'
relation: later_version
status: public
status: public
title: Energy and mean-payoff parity Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '580'
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: 'Hosten O. Quantum physics: How to catch a wave. Nature. 2011;474(7350):170-171.
doi:10.1038/474170a'
apa: 'Hosten, O. (2011). Quantum physics: How to catch a wave. Nature. Nature
Publishing Group. https://doi.org/10.1038/474170a'
chicago: 'Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature. Nature
Publishing Group, 2011. https://doi.org/10.1038/474170a.'
ieee: 'O. Hosten, “Quantum physics: How to catch a wave,” Nature, vol. 474,
no. 7350. Nature Publishing Group, pp. 170–171, 2011.'
ista: 'Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350),
170–171.'
mla: 'Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature, vol.
474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:10.1038/474170a.'
short: O. Hosten, Nature 474 (2011) 170–171.
date_created: 2018-12-11T11:47:18Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T08:03:34Z
day: '08'
doi: 10.1038/474170a
extern: 1
intvolume: ' 474'
issue: '7350'
month: '06'
page: 170 - 171
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7224'
quality_controlled: 0
status: public
title: 'Quantum physics: How to catch a wave'
type: journal_article
volume: 474
year: '2011'
...
---
_id: '585'
abstract:
- lang: eng
text: |+
We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.
alternative_title:
- Optics InfoBase Conference Papers
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Shiraz
full_name: Hazrat, Shiraz
last_name: Hazrat
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Stephan
full_name: Quint, Stephan
last_name: Quint
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards
achieving precise birefringent focusing. In: OSA; 2011. doi:10.1364/CLEO_AT.2011.JThB130'
apa: 'Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., & Kwiat,
P. (2011). Methods towards achieving precise birefringent focusing. Presented
at the QELS: Quantum Electronics and Laser Science, OSA. https://doi.org/10.1364/CLEO_AT.2011.JThB130'
chicago: Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan
Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.”
OSA, 2011. https://doi.org/10.1364/CLEO_AT.2011.JThB130.
ieee: 'D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods
towards achieving precise birefringent focusing,” presented at the QELS: Quantum
Electronics and Laser Science, 2011.'
ista: 'Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods
towards achieving precise birefringent focusing. QELS: Quantum Electronics and
Laser Science, Optics InfoBase Conference Papers, .'
mla: Schmid, David, et al. Methods towards Achieving Precise Birefringent Focusing.
OSA, 2011, doi:10.1364/CLEO_AT.2011.JThB130.
short: D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:,
OSA, 2011.
conference:
name: 'QELS: Quantum Electronics and Laser Science'
date_created: 2018-12-11T11:47:20Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:44Z
day: '01'
doi: 10.1364/CLEO_AT.2011.JThB130
extern: 1
month: '01'
publication_status: published
publisher: OSA
publist_id: '7220'
quality_controlled: 0
status: public
title: Methods towards achieving precise birefringent focusing
type: conference
year: '2011'
...
...
---
_id: '586'
abstract:
- lang: eng
text: We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a
high-finesse optical cavity. We observe robust continuous wave lasing in the atypical
regime where single atoms can considerably affect the cavity field. Consequently,
we discover unusual lasing threshold behavior in the system causing jumps in lasing
power, and propose a model to explain the effect. We also measure the intermode
laser linewidth, and observe values as low as 80Hz. The tunable gain properties
of this laser suggest multiple directions for future research.
author:
- first_name: Geert
full_name: Vrijsen, Geert
last_name: Vrijsen
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Jongmin
full_name: Lee, Jongmin
last_name: Lee
- first_name: Simon
full_name: Bernon, Simon
last_name: Bernon
- first_name: Mark
full_name: Kasevich, Mark A
last_name: Kasevich
citation:
ama: Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold
atom gain medium in a high-finesse optical cavity. Physical Review Letters.
2011;107(6). doi:10.1103/PhysRevLett.107.063904
apa: Vrijsen, G., Hosten, O., Lee, J., Bernon, S., & Kasevich, M. (2011). Raman
lasing with a cold atom gain medium in a high-finesse optical cavity. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.063904
chicago: Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich.
“Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.”
Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.063904.
ieee: G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with
a cold atom gain medium in a high-finesse optical cavity,” Physical Review
Letters, vol. 107, no. 6. American Physical Society, 2011.
ista: Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with
a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters.
107(6).
mla: Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse
Optical Cavity.” Physical Review Letters, vol. 107, no. 6, American Physical
Society, 2011, doi:10.1103/PhysRevLett.107.063904.
short: G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters
107 (2011).
date_created: 2018-12-11T11:47:20Z
date_published: 2011-08-04T00:00:00Z
date_updated: 2021-01-12T08:05:05Z
day: '04'
doi: 10.1103/PhysRevLett.107.063904
extern: 1
intvolume: ' 107'
issue: '6'
month: '08'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7223'
quality_controlled: 0
status: public
title: Raman lasing with a cold atom gain medium in a high-finesse optical cavity
type: journal_article
volume: 107
year: '2011'
...
---
_id: '597'
abstract:
- lang: eng
text: The macromolecular assembly required to initiate transcription of protein-coding
genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein
complexes and is approximately 3.5 MDa in size. At the heart of this assembly
is the Mediator complex, which helps regulate PIC activity and interacts with
the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol
II interface is not well-characterized, whereas attempts to structurally define
the Mediator-pol II interaction in yeast have relied on incomplete assemblies
of Mediator and/or pol II and have yielded inconsistent interpretations. We have
assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified
components and have characterized its structural organization using cryo-electron
microscopy and single-particle reconstruction techniques. The orientation of pol
II within this assembly was determined by crystal structure docking and further
validated with projection matching experiments, allowing the structural organization
of the entire human PIC to be envisioned. Significantly, pol II orientation within
the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined
the location of other PIC components relative to pol II itself. Pol II surfaces
required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II
cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered
along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding
additional factors; and no major structural re-organization is necessary to accommodate
the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol
II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural
basis for Mediator-dependent control of PIC assembly and function. Finally, parallel
structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF
plays a key role in stabilizing pol II orientation within the assembly.
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patricia
full_name: Grob, Patricia
last_name: Grob
- first_name: Christopher
full_name: Ebmeier, Christopher
last_name: Ebmeier
- first_name: Eva
full_name: Nogales, Eva
last_name: Nogales
- first_name: Dylan
full_name: Taatjes, Dylan
last_name: Taatjes
citation:
ama: Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 2011;9(3).
doi:10.1371/journal.pbio.1000603
apa: Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., & Taatjes, D. (2011).
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000603
chicago: Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and
Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF
Assembly.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000603.
ieee: C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly,” PLoS Biology,
vol. 9, no. 3. Public Library of Science, 2011.
ista: Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).
mla: Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA
Polymerase II-TFIIF Assembly.” PLoS Biology, vol. 9, no. 3, Public Library
of Science, 2011, doi:10.1371/journal.pbio.1000603.
short: C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9
(2011).
date_created: 2018-12-11T11:47:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T08:05:25Z
day: '01'
doi: 10.1371/journal.pbio.1000603
extern: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7209'
status: public
title: Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2011'
...
---
_id: '6137'
abstract:
- lang: eng
text: Variation in food quality and abundance requires animals to decide whether
to stay on a poor food patch or leave in search of better food. An important question
in behavioral ecology asks when is it optimal for an animal to leave a food patch
it is depleting. Although optimal foraging is central to evolutionary success,
the neural and molecular mechanisms underlying it are poorly understood. Here
we investigate the neuronal basis for adaptive food-leaving behavior in response
to resource depletion in Caenorhabditis elegans, and identify several of the signaling
pathways involved. The ASE neurons, previously implicated in salt chemoattraction,
promote food-leaving behavior via a cGMP pathway as food becomes limited. High
ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX.
Ectopic activation of these neurons using channelrhodopsin is sufficient to induce
high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which
regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH
neurons, and in the RMG interneuron to repress food-leaving. Finally, we show
that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are
necessary for adaptive food-leaving behavior. We suggest that animals integrate
information about their nutritional state with ambient oxygen and gustatory stimuli
to formulate optimal foraging strategies.
author:
- first_name: K.
full_name: Milward, K.
last_name: Milward
- first_name: K. E.
full_name: Busch, K. E.
last_name: Busch
- first_name: R. J.
full_name: Murphy, R. J.
last_name: Murphy
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: B.
full_name: Olofsson, B.
last_name: Olofsson
citation:
ama: Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular
substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the
National Academy of Sciences. 2011;108(51):20672-20677. doi:10.1073/pnas.1106134109
apa: Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., & Olofsson, B. (2011).
Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1106134109
chicago: Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson.
“Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2011. https://doi.org/10.1073/pnas.1106134109.
ieee: K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal
and molecular substrates for optimal foraging in Caenorhabditis elegans,” Proceedings
of the National Academy of Sciences, vol. 108, no. 51. National Academy of
Sciences, pp. 20672–20677, 2011.
ista: Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and
molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings
of the National Academy of Sciences. 108(51), 20672–20677.
mla: Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging
in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences,
vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:10.1073/pnas.1106134109.
short: K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings
of the National Academy of Sciences 108 (2011) 20672–20677.
date_created: 2019-03-20T14:30:06Z
date_published: 2011-12-20T00:00:00Z
date_updated: 2021-01-12T08:06:18Z
day: '20'
doi: 10.1073/pnas.1106134109
extern: '1'
external_id:
pmid:
- '22135454'
intvolume: ' 108'
issue: '51'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/
month: '12'
oa: 1
oa_version: Submitted Version
page: 20672-20677
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '6138'
author:
- first_name: Andrew Jonathan
full_name: Bretscher, Andrew Jonathan
last_name: Bretscher
- first_name: Eiji
full_name: Kodama-Namba, Eiji
last_name: Kodama-Namba
- first_name: Karl Emanuel
full_name: Busch, Karl Emanuel
last_name: Busch
- first_name: Robin Joseph
full_name: Murphy, Robin Joseph
last_name: Murphy
- first_name: Zoltan
full_name: Soltesz, Zoltan
last_name: Soltesz
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Bretscher AJ, Kodama-Namba E, Busch KE, et al. Temperature, oxygen, and salt-sensing
neurons in C. elegans are carbon dioxide sensors that control avoidance behavior.
Neuron. 2011;69(6):1099-1113. doi:10.1016/j.neuron.2011.02.023
apa: Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z.,
Laurent, P., & de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons
in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron.
Elsevier BV. https://doi.org/10.1016/j.neuron.2011.02.023
chicago: Bretscher, Andrew Jonathan, Eiji Kodama-Namba, Karl Emanuel Busch, Robin Joseph
Murphy, Zoltan Soltesz, Patrick Laurent, and Mario de Bono. “Temperature, Oxygen,
and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control
Avoidance Behavior.” Neuron. Elsevier BV, 2011. https://doi.org/10.1016/j.neuron.2011.02.023.
ieee: A. J. Bretscher et al., “Temperature, oxygen, and salt-sensing neurons
in C. elegans are carbon dioxide sensors that control avoidance behavior,” Neuron,
vol. 69, no. 6. Elsevier BV, pp. 1099–1113, 2011.
ista: Bretscher AJ, Kodama-Namba E, Busch KE, Murphy RJ, Soltesz Z, Laurent P, de
Bono M. 2011. Temperature, oxygen, and salt-sensing neurons in C. elegans are
carbon dioxide sensors that control avoidance behavior. Neuron. 69(6), 1099–1113.
mla: Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons
in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” Neuron,
vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:10.1016/j.neuron.2011.02.023.
short: A.J. Bretscher, E. Kodama-Namba, K.E. Busch, R.J. Murphy, Z. Soltesz, P.
Laurent, M. de Bono, Neuron 69 (2011) 1099–1113.
date_created: 2019-03-20T15:01:41Z
date_published: 2011-03-24T00:00:00Z
date_updated: 2021-01-12T08:06:18Z
day: '24'
ddc:
- '570'
doi: 10.1016/j.neuron.2011.02.023
extern: '1'
external_id:
pmid:
- '21435556'
file:
- access_level: open_access
checksum: 547cffd123f4c508ae927c9244b8f92a
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T15:06:32Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6139'
file_name: 2011_Cell_Bretscher.pdf
file_size: 2448332
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 69'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1099-1113
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
status: public
title: Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide
sensors that control avoidance behavior
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2011'
...
---
_id: '6140'
abstract:
- lang: eng
text: 'Genome sequence comparisons have highlighted many novel gene families that
are conserved across animal phyla but whose biological function is unknown. Here,
we functionally characterize a member of one such family, the macoilins. Macoilins
are characterized by several highly conserved predicted transmembrane domains
towards the N-terminus and by coiled-coil regions C-terminally. They are found
throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis
elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including
defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed
broadly and specifically in the nervous system and localizes to the rough endoplasmic
reticulum; it is excluded from dendrites and axons. Apart from subtle synapse
defects, nervous system development appears wild-type in maco-1 mutants. However,
maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive
to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show
that macoilin is required to evoke Ca2+ transients, at least in some neurons:
in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response
to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic
input is not necessary for PQR to respond to O2, indicating that the response
is mediated by cell-intrinsic sensory transduction and amplification. Disrupting
the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+
channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli.
By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans
L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect
we see in maco-1 mutants, although we do not see defects in localization of EGL-19.
Together, our data suggest that macoilin acts in the ER to regulate assembly or
traffic of ion channels or ion channel regulators.'
article_number: e1001341
author:
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Luis
full_name: Briseño-Roa, Luis
last_name: Briseño-Roa
- first_name: Africa
full_name: Couto, Africa
last_name: Couto
- first_name: Benny H. H.
full_name: Cheung, Benny H. H.
last_name: Cheung
- first_name: Michel
full_name: Labouesse, Michel
last_name: Labouesse
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono
M. Macoilin, a conserved nervous system–specific ER membrane protein that regulates
neuronal excitability. PLoS Genetics. 2011;7(3). doi:10.1371/journal.pgen.1001341
apa: Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse,
M., & de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER
membrane protein that regulates neuronal excitability. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1001341
chicago: Arellano-Carbajal, Fausto, Luis Briseño-Roa, Africa Couto, Benny H. H.
Cheung, Michel Labouesse, and Mario de Bono. “Macoilin, a Conserved Nervous System–Specific
ER Membrane Protein That Regulates Neuronal Excitability.” PLoS Genetics.
Public Library of Science, 2011. https://doi.org/10.1371/journal.pgen.1001341.
ieee: F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B. H. H. Cheung, M. Labouesse,
and M. de Bono, “Macoilin, a conserved nervous system–specific ER membrane protein
that regulates neuronal excitability,” PLoS Genetics, vol. 7, no. 3. Public
Library of Science, 2011.
ista: Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono
M. 2011. Macoilin, a conserved nervous system–specific ER membrane protein that
regulates neuronal excitability. PLoS Genetics. 7(3), e1001341.
mla: Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific
ER Membrane Protein That Regulates Neuronal Excitability.” PLoS Genetics,
vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:10.1371/journal.pgen.1001341.
short: F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse,
M. de Bono, PLoS Genetics 7 (2011).
date_created: 2019-03-20T15:08:23Z
date_published: 2011-03-17T00:00:00Z
date_updated: 2021-01-12T08:06:19Z
day: '17'
ddc:
- '570'
doi: 10.1371/journal.pgen.1001341
extern: '1'
external_id:
pmid:
- '21437263'
file:
- access_level: open_access
checksum: c609b2ce616d7dafbb617ec5d022f1ea
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T15:18:11Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6141'
file_name: 2011_PLOS_Arellano-Carbajal.PDF
file_size: 5625063
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Macoilin, a conserved nervous system–specific ER membrane protein that regulates
neuronal excitability
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2011'
...
---
_id: '6298'
abstract:
- lang: eng
text: Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding
protein that plays important roles ininflammation and ovulation. TSG-6-mediated
cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating
leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know
very little about its impact on HA ultra-structure. Here we used films of polymeric
and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive
biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate
binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced
positive cooperativity and demonstrate that it cancross-link HA at physiologically
relevant concentrations. Ourdata indicate that cooperative binding of full-length
TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers
act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module)
alone binds withoutpositive cooperativity and weaker than the full-length protein.Both
the Link module and full-length TSG-6 condensed andrigidified HA films, and the
degree of condensation scaled withthe affinity between the TSG-6 constructs and
HA. We proposethat condensation is the result of protein-mediated HA cross-linking.
Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and
might hence have important implica-tions for the mechanistic understanding of
the biological func-tion of TSG-6 (e.g.in inflammation).
author:
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Erik
full_name: Nilebäck, Erik
last_name: Nilebäck
- first_name: F. Michael
full_name: Haller, F. Michael
last_name: Haller
- first_name: David C.
full_name: Briggs, David C.
last_name: Briggs
- first_name: Sofia
full_name: Svedhem, Sofia
last_name: Svedhem
- first_name: Anthony J.
full_name: Day, Anthony J.
last_name: Day
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
citation:
ama: Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein
TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal
of Biological Chemistry. 2011;286(29):25675-25686. doi:10.1074/jbc.m111.247395
apa: Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day,
A. J., & Richter, R. P. (2011). The inflammation-associated protein TSG-6
cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological
Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.m111.247395
chicago: Baranova, Natalia S., Erik Nilebäck, F. Michael Haller, David C. Briggs,
Sofia Svedhem, Anthony J. Day, and Ralf P. Richter. “The Inflammation-Associated
Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.”
Journal of Biological Chemistry. American Society for Biochemistry &
Molecular Biology, 2011. https://doi.org/10.1074/jbc.m111.247395.
ieee: N. S. Baranova et al., “The inflammation-associated protein TSG-6 cross-links
hyaluronan via hyaluronan-induced TSG-6 oligomers,” Journal of Biological Chemistry,
vol. 286, no. 29. American Society for Biochemistry & Molecular Biology, pp.
25675–25686, 2011.
ista: Baranova NS, Nilebäck E, Haller FM, Briggs DC, Svedhem S, Day AJ, Richter
RP. 2011. The inflammation-associated protein TSG-6 cross-links hyaluronan via
hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 286(29),
25675–25686.
mla: Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links
Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” Journal of Biological Chemistry,
vol. 286, no. 29, American Society for Biochemistry & Molecular Biology, 2011,
pp. 25675–86, doi:10.1074/jbc.m111.247395.
short: N.S. Baranova, E. Nilebäck, F.M. Haller, D.C. Briggs, S. Svedhem, A.J. Day,
R.P. Richter, Journal of Biological Chemistry 286 (2011) 25675–25686.
date_created: 2019-04-11T20:57:43Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T08:06:58Z
day: '22'
doi: 10.1074/jbc.m111.247395
extern: '1'
intvolume: ' 286'
issue: '29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.jbc.org/content/286/29/25675.full.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 25675-25686
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced
TSG-6 oligomers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 286
year: '2011'
...
---
_id: '6496'
abstract:
- lang: eng
text: We report the switching behavior of the full bacterial flagellum system that
includes the filament and the motor in wild-type Escherichia coli cells. In sorting
the motor behavior by the clockwise bias, we find that the distributions of the
clockwise (CW) and counterclockwise (CCW) intervals are either exponential or
nonexponential with long tails. At low bias, CW intervals are exponentially distributed
and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and
CCW intervals are mainly exponentially distributed. A simple model suggests that
these two distinct switching behaviors are governed by the presence of signaling
noise within the chemotaxis network. Low noise yields exponentially distributed
intervals, whereas large noise yields nonexponential behavior with long tails.
These drastically different motor statistics may play a role in optimizing bacterial
behavior for a wide range of environmental conditions.
article_processing_charge: No
author:
- first_name: Heungwon
full_name: Park, Heungwon
last_name: Park
- first_name: Panos
full_name: Oikonomou, Panos
last_name: Oikonomou
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Philippe
full_name: Cluzel, Philippe
last_name: Cluzel
citation:
ama: Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior
of the bacterial flagellum. Biophysical Journal. 2011;101(10):2336-2340.
doi:10.1016/j.bpj.2011.09.040
apa: Park, H., Oikonomou, P., Guet, C. C., & Cluzel, P. (2011). Noise underlies
switching behavior of the bacterial flagellum. Biophysical Journal. Elsevier.
https://doi.org/10.1016/j.bpj.2011.09.040
chicago: Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise
Underlies Switching Behavior of the Bacterial Flagellum.” Biophysical Journal.
Elsevier, 2011. https://doi.org/10.1016/j.bpj.2011.09.040.
ieee: H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching
behavior of the bacterial flagellum,” Biophysical Journal, vol. 101, no.
10. Elsevier, pp. 2336–2340, 2011.
ista: Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior
of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.
mla: Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial
Flagellum.” Biophysical Journal, vol. 101, no. 10, Elsevier, 2011, pp.
2336–40, doi:10.1016/j.bpj.2011.09.040.
short: H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011)
2336–2340.
date_created: 2019-05-28T11:54:29Z
date_published: 2011-11-16T00:00:00Z
date_updated: 2021-04-16T11:54:49Z
day: '16'
department:
- _id: CaGu
doi: 10.1016/j.bpj.2011.09.040
external_id:
pmid:
- '22098731'
intvolume: ' 101'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/
month: '11'
oa: 1
oa_version: Published Version
page: 2336-2340
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Noise underlies switching behavior of the bacterial flagellum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2011'
...
---
_id: '1467'
abstract:
- lang: eng
text: We propose a general conjecture for the mixed Hodge polynomial of the generic
character varieties of representations of the fundamental group of a Riemann surface
of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures.
This conjecture generalizes the Cauchy identity for Macdonald polynomials and
is a common generalization of two formulas that we prove in this paper. The first
is a formula for the E-polynomial of these character varieties which we obtain
using the character table of GLn(Fq). We use this formula to compute the Euler
characteristic of character varieties. The second formula gives the Poincaré polynomial
of certain associated quiver varieties which we obtain using the character table
of gln(Fq). In the last main result we prove that the Poincaré polynomials of
the quiver varieties equal certain multiplicities in the tensor product of irreducible
characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody
algebras associated with comet-shaped, and typically wild, quivers and the representation
theory of GLn(Fq).
acknowledgement: |-
Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.
Rodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Emmanuel
full_name: Letellier, Emmanuel
last_name: Letellier
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on
character and quiver varieties. Duke Mathematical Journal. 2011;160(2):323-400.
doi:10.1215/00127094-1444258
apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2011). Arithmetic
harmonic analysis on character and quiver varieties. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-1444258
chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic
Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal.
Duke University Press, 2011. https://doi.org/10.1215/00127094-1444258.
ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis
on character and quiver varieties,” Duke Mathematical Journal, vol. 160,
no. 2. Duke University Press, pp. 323–400, 2011.
ista: Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis
on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.
mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver
Varieties.” Duke Mathematical Journal, vol. 160, no. 2, Duke University
Press, 2011, pp. 323–400, doi:10.1215/00127094-1444258.
short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal
160 (2011) 323–400.
date_created: 2018-12-11T11:52:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:56Z
day: '01'
doi: 10.1215/00127094-1444258
extern: 1
intvolume: ' 160'
issue: '2'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0810.2076
month: '01'
oa: 1
page: 323 - 400
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5728'
quality_controlled: 0
status: public
title: Arithmetic harmonic analysis on character and quiver varieties
type: journal_article
volume: 160
year: '2011'
...
---
_id: '14305'
abstract:
- lang: eng
text: Understanding the mechanism of protein folding requires a detailed knowledge
of the structural properties of the barriers separating unfolded from native conformations.
The S-peptide from ribonuclease S forms its α-helical structure only upon binding
to the folded S-protein. We characterized the transition state for this binding-induced
folding reaction at high resolution by determining the effect of site-specific
backbone thioxylation and side-chain modifications on the kinetics and thermodynamics
of the reaction, which allows us to monitor formation of backbone hydrogen bonds
and side-chain interactions in the transition state. The experiments reveal that
α-helical structure in the S-peptide is absent in the transition state of binding.
Recognition between the unfolded S-peptide and the S-protein is mediated by loosely
packed hydrophobic side-chain interactions in two well defined regions on the
S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing
hydrophobic residues at positions outside the recognition region can drastically
slow down association.
article_processing_charge: No
article_type: original
author:
- first_name: Annett
full_name: Bachmann, Annett
last_name: Bachmann
- first_name: Dirk
full_name: Wildemann, Dirk
last_name: Wildemann
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Gunter
full_name: Fischer, Gunter
last_name: Fischer
- first_name: Thomas
full_name: Kiefhaber, Thomas
last_name: Kiefhaber
citation:
ama: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone
and side-chain interactions in the transition state of a coupled protein folding
and binding reaction. PNAS. 2011;108(10):3952-3957. doi:10.1073/pnas.1012668108
apa: Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., & Kiefhaber,
T. (2011). Mapping backbone and side-chain interactions in the transition state
of a coupled protein folding and binding reaction. PNAS. Proceedings of
the National Academy of Sciences. https://doi.org/10.1073/pnas.1012668108
chicago: Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer,
and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition
State of a Coupled Protein Folding and Binding Reaction.” PNAS. Proceedings
of the National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1012668108.
ieee: A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber,
“Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction,” PNAS, vol. 108, no. 10. Proceedings
of the National Academy of Sciences, pp. 3952–3957, 2011.
ista: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping
backbone and side-chain interactions in the transition state of a coupled protein
folding and binding reaction. PNAS. 108(10), 3952–3957.
mla: Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the
Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS,
vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57,
doi:10.1073/pnas.1012668108.
short: A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS
108 (2011) 3952–3957.
date_created: 2023-09-06T12:54:36Z
date_published: 2011-01-12T00:00:00Z
date_updated: 2023-11-07T11:50:29Z
day: '12'
doi: 10.1073/pnas.1012668108
extern: '1'
external_id:
pmid:
- '21325613'
intvolume: ' 108'
issue: '10'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1012668108
month: '01'
oa: 1
oa_version: Published Version
page: 3952-3957
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '9143'
abstract:
- lang: eng
text: Understanding and predicting the response of the hydrological cycle to climate
change is a major challenge with important societal implications. Much progress
has been made in understanding the response of global average precipitation by
considering the energy balances of the atmosphere and the surface1,2,3,4,5,6.
This energetic perspective reveals that changes in temperature, greenhouse gases,
aerosols, solar forcing and cloud feedbacks can all affect the global average
rate of precipitation5,7,8,9,10,11. Local precipitation changes have conventionally
been analysed using the water vapour budget, but here we show that the energetic
approach can be extended to local changes in precipitation by including changes
in horizontal energy transport. In simulations of twenty-first century climate
change, this energy transport accounts for much of the spatial variability in
precipitation change. We show that changes in radiative and surface sensible heat
fluxes are a guide to the local precipitation response over land and at large
scales, but not at small scales over the ocean, where cloud and water vapour radiative
feedbacks dampen the response. The energetic approach described here helps bridge
the gap between our understanding of global and regional precipitation changes.
It could be applied to better understand the response of regional precipitation
to different radiative forcings, including geo-engineering schemes, as well as
to understand the differences between the fast and slow responses of regional
precipitation to such forcings.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: P. A.
full_name: O’Gorman, P. A.
last_name: O’Gorman
citation:
ama: Muller CJ, O’Gorman PA. An energetic perspective on the regional response of
precipitation to climate change. Nature Climate Change. 2011;1(5):266-271.
doi:10.1038/nclimate1169
apa: Muller, C. J., & O’Gorman, P. A. (2011). An energetic perspective on the
regional response of precipitation to climate change. Nature Climate Change.
Springer Nature. https://doi.org/10.1038/nclimate1169
chicago: Muller, Caroline J, and P. A. O’Gorman. “An Energetic Perspective on the
Regional Response of Precipitation to Climate Change.” Nature Climate Change.
Springer Nature, 2011. https://doi.org/10.1038/nclimate1169.
ieee: C. J. Muller and P. A. O’Gorman, “An energetic perspective on the regional
response of precipitation to climate change,” Nature Climate Change, vol.
1, no. 5. Springer Nature, pp. 266–271, 2011.
ista: Muller CJ, O’Gorman PA. 2011. An energetic perspective on the regional response
of precipitation to climate change. Nature Climate Change. 1(5), 266–271.
mla: Muller, Caroline J., and P. A. O’Gorman. “An Energetic Perspective on the Regional
Response of Precipitation to Climate Change.” Nature Climate Change, vol.
1, no. 5, Springer Nature, 2011, pp. 266–71, doi:10.1038/nclimate1169.
short: C.J. Muller, P.A. O’Gorman, Nature Climate Change 1 (2011) 266–271.
date_created: 2021-02-15T14:39:29Z
date_published: 2011-07-24T00:00:00Z
date_updated: 2022-01-24T13:52:11Z
day: '24'
doi: 10.1038/nclimate1169
extern: '1'
intvolume: ' 1'
issue: '5'
language:
- iso: eng
month: '07'
oa_version: None
page: 266-271
publication: Nature Climate Change
publication_identifier:
issn:
- 1758-678X
- 1758-6798
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: An energetic perspective on the regional response of precipitation to climate
change
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 1
year: '2011'
...
---
_id: '9144'
abstract:
- lang: eng
text: "A cloud-resolving model is used to investigate the effect of warming on high
percentiles of precipitation (precipitation extremes) in the idealized setting
of radiative-convective equilibrium. While this idealized setting does not allow
for several factors that influence precipitation in the tropics, it does allow
for an evaluation of the response of precipitation extremes to warming in simulations
with resolved rather than parameterized convection. The methodology developed
should also be applicable to less idealized simulations.\r\n\r\nModeled precipitation
extremes are found to increase in magnitude in response to an increase in sea
surface temperature. A dry static energy budget is used to relate the changes
in precipitation extremes to changes in atmospheric temperature, vertical velocity,
and precipitation efficiency. To first order, the changes in precipitation extremes
are captured by changes in the mean temperature structure of the atmosphere. Changes
in vertical velocities play a secondary role and tend to weaken the strength of
precipitation extremes, despite an intensification of updraft velocities in the
upper troposphere. The influence of changes in condensate transports on precipitation
extremes is quantified in terms of a precipitation efficiency; it does not change
greatly with warming.\r\n\r\nTropical precipitation extremes have previously been
found to increase at a greater fractional rate than the amount of atmospheric
water vapor in observations of present-day variability and in some climate model
simulations with parameterized convection. But the fractional increases in precipitation
extremes in the cloud-resolving simulations are comparable in magnitude to those
in surface water vapor concentrations (owing to a partial cancellation between
dynamical and thermodynamical changes), and are substantially less than the fractional
increases in column water vapor."
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Paul A.
full_name: O’Gorman, Paul A.
last_name: O’Gorman
- first_name: Larissa E.
full_name: Back, Larissa E.
last_name: Back
citation:
ama: Muller CJ, O’Gorman PA, Back LE. Intensification of precipitation extremes
with warming in a cloud-resolving model. Journal of Climate. 2011;24(11):2784-2800.
doi:10.1175/2011jcli3876.1
apa: Muller, C. J., O’Gorman, P. A., & Back, L. E. (2011). Intensification of
precipitation extremes with warming in a cloud-resolving model. Journal of
Climate. American Meteorological Society. https://doi.org/10.1175/2011jcli3876.1
chicago: Muller, Caroline J, Paul A. O’Gorman, and Larissa E. Back. “Intensification
of Precipitation Extremes with Warming in a Cloud-Resolving Model.” Journal
of Climate. American Meteorological Society, 2011. https://doi.org/10.1175/2011jcli3876.1.
ieee: C. J. Muller, P. A. O’Gorman, and L. E. Back, “Intensification of precipitation
extremes with warming in a cloud-resolving model,” Journal of Climate,
vol. 24, no. 11. American Meteorological Society, pp. 2784–2800, 2011.
ista: Muller CJ, O’Gorman PA, Back LE. 2011. Intensification of precipitation extremes
with warming in a cloud-resolving model. Journal of Climate. 24(11), 2784–2800.
mla: Muller, Caroline J., et al. “Intensification of Precipitation Extremes with
Warming in a Cloud-Resolving Model.” Journal of Climate, vol. 24, no. 11,
American Meteorological Society, 2011, pp. 2784–800, doi:10.1175/2011jcli3876.1.
short: C.J. Muller, P.A. O’Gorman, L.E. Back, Journal of Climate 24 (2011) 2784–2800.
date_created: 2021-02-15T14:39:57Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2022-01-24T13:52:46Z
day: '01'
doi: 10.1175/2011jcli3876.1
extern: '1'
intvolume: ' 24'
issue: '11'
keyword:
- Atmospheric Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/2011JCLI3876.1
month: '06'
oa: 1
oa_version: Published Version
page: 2784-2800
publication: Journal of Climate
publication_identifier:
eissn:
- 1520-0442
issn:
- 0894-8755
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Intensification of precipitation extremes with warming in a cloud-resolving
model
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 24
year: '2011'
...
---
_id: '918'
abstract:
- lang: eng
text: We study theoretically the shapes of a dividing epithelial monolayer of cells
lying on top of an elastic stroma. The negative tension created by cell division
provokes a buckling instability at a finite wave vector leading to the formation
of periodic arrays of villi and crypts. The instability is similar to the buckling
of a metallic plate under compression. We use the results to rationalize the various
structures of the intestinal lining observed in vivo. Taking into account the
coupling between cell division and local curvature, we obtain different patterns
of villi and crypts, which could explain the different morphologies of the small
intestine and the colon.
acknowledgement: We thank S. Fre and M. Huygue for discussion and for showing us in
vivo samples and A. Bergès for help with the manuscript.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape
and structure of villi and crypts. Physical Review Letters. 2011;107(7).
doi:10.1103/PhysRevLett.107.078104
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2011). Instabilities of monolayered
epithelia Shape and structure of villi and crypts. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.107.078104
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered
Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters.
American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.078104.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia
Shape and structure of villi and crypts,” Physical Review Letters, vol.
107, no. 7. American Physical Society, 2011.
ista: Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia
Shape and structure of villi and crypts. Physical Review Letters. 107(7).
mla: Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and
Structure of Villi and Crypts.” Physical Review Letters, vol. 107, no.
7, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.078104.
short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011).
date_created: 2018-12-11T11:49:11Z
date_published: 2011-08-11T00:00:00Z
date_updated: 2021-01-12T08:21:54Z
day: '11'
doi: 10.1103/PhysRevLett.107.078104
extern: '1'
intvolume: ' 107'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6521'
status: public
title: Instabilities of monolayered epithelia Shape and structure of villi and crypts
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2011'
...
---
_id: '919'
abstract:
- lang: eng
text: Collective cell migration in tissues occurs throughout embryonic development,
during wound healing, and in cancerous tumor invasion, yet most detailed knowledge
of cell migration comes from single-cell studies. As single cells migrate, the
shape of the cell body fluctuates dramatically through cyclic processes of extension,
adhesion, and retraction, accompanied by erratic changes in migration direction.
Within confluent cell layers, such subcellular motions must be coupled between
neighbors, yet the influence of these subcellular motions on collective migration
is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously
measuring collective migration and subcellular motions, covering a broad range
of length scales, time scales, and cell densities. At large length scales and
time scales collective migration slows as cell density rises, yet the fastest
cells move in large, multicell groups whose scale grows with increasing cell density.
This behavior has an intriguing analogy to dynamic heterogeneities found in particulate
systems as they become more crowded and approach a glass transition. In addition
we find a diminishing self-diffusivity of short-wavelength motions within the
cell layer, and growing peaks in the vibrational density of states associated
with cooperative cell-shape fluctuations. Both of these observations are also
intriguingly reminiscent of a glass transition. Thus, these results provide a
broad and suggestive analogy between cell motion within a confluent layer and
the dynamics of supercooled colloidal and molecular fluids approaching a glass
transition.
author:
- first_name: Thomas
full_name: Angelini, Thomas
last_name: Angelini
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Xavier
full_name: Trepatc, Xavier
last_name: Trepatc
- first_name: Manuel
full_name: Marquez, Manuel
last_name: Marquez
- first_name: Jeffrey
full_name: Fredberg, Jeffrey
last_name: Fredberg
- first_name: David
full_name: Weitz, David
last_name: Weitz
citation:
ama: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like
dynamics of collective cell migration. Proceedings of the National Academy
of Sciences of the United States of America. 2011;108(12):4714-4719. doi:10.1073/pnas.1010059108
apa: Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., &
Weitz, D. (2011). Glass-like dynamics of collective cell migration. Proceedings
of the National Academy of Sciences of the United States of America. PNAS.
https://doi.org/10.1073/pnas.1010059108
chicago: Angelini, Thomas, Edouard B Hannezo, Xavier Trepatc, Manuel Marquez, Jeffrey
Fredberg, and David Weitz. “Glass-like Dynamics of Collective Cell Migration.”
Proceedings of the National Academy of Sciences of the United States of America.
PNAS, 2011. https://doi.org/10.1073/pnas.1010059108.
ieee: T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz,
“Glass-like dynamics of collective cell migration,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 108, no. 12. PNAS,
pp. 4714–4719, 2011.
ista: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. 2011. Glass-like
dynamics of collective cell migration. Proceedings of the National Academy of
Sciences of the United States of America. 108(12), 4714–4719.
mla: Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:10.1073/pnas.1010059108.
short: T. Angelini, E.B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, D. Weitz,
Proceedings of the National Academy of Sciences of the United States of America
108 (2011) 4714–4719.
date_created: 2018-12-11T11:49:12Z
date_published: 2011-03-22T00:00:00Z
date_updated: 2021-01-12T08:21:54Z
day: '22'
doi: 10.1073/pnas.1010059108
extern: '1'
intvolume: ' 108'
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
page: 4714 - 4719
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_status: published
publisher: PNAS
publist_id: '6522'
quality_controlled: '1'
status: public
title: Glass-like dynamics of collective cell migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '923'
abstract:
- lang: eng
text: The conserved role of Notch signaling in controlling intestinal cell fate
specification and homeostasis has been extensively studied. Nevertheless, the
precise identity of the cells in which Notch signaling is active and the role
of different Notch receptor paralogues in the intestine remain ambiguous, due
to the lack of reliable tools to investigate Notch expression and function in
vivo. We generated a new series of transgenic mice that allowed us, by lineage
analysis, to formally prove that Notch1 and Notch2 are specifically expressed
in crypt stem cells. In addition, a novel Notch reporter mouse, Hes1-EmGFP SAT,
demonstrated exclusive Notch activity in crypt stem cells and absorptive progenitors.
This roster of knock-in and reporter mice represents a valuable resource to functionally
explore the Notch pathway in vivo in virtually all tissues.
article_number: e25785
author:
- first_name: Silvia
full_name: Fré, Silvia
last_name: Fré
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Sanja
full_name: Šale, Sanja
last_name: Šale
- first_name: Mathilde
full_name: Huyghe, Mathilde
last_name: Huyghe
- first_name: Daniel
full_name: Lafkas, Daniel
last_name: Lafkas
- first_name: Holger
full_name: Kissel, Holger
last_name: Kissel
- first_name: Angeliki
full_name: Louvi, Angeliki
last_name: Louvi
- first_name: Jeffrey
full_name: Greve, Jeffrey
last_name: Greve
- first_name: Daniel
full_name: Louvard, Daniel
last_name: Louvard
- first_name: Spyros
full_name: Artavanis Tsakonas, Spyros
last_name: Artavanis Tsakonas
citation:
ama: Fré S, Hannezo EB, Šale S, et al. Notch lineages and activity in intestinal
stem cells determined by a new set of knock in mice. PLoS One. 2011;6(10).
doi:10.1371/journal.pone.0025785
apa: Fré, S., Hannezo, E. B., Šale, S., Huyghe, M., Lafkas, D., Kissel, H., … Artavanis
Tsakonas, S. (2011). Notch lineages and activity in intestinal stem cells determined
by a new set of knock in mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0025785
chicago: Fré, Silvia, Edouard B Hannezo, Sanja Šale, Mathilde Huyghe, Daniel Lafkas,
Holger Kissel, Angeliki Louvi, Jeffrey Greve, Daniel Louvard, and Spyros Artavanis
Tsakonas. “Notch Lineages and Activity in Intestinal Stem Cells Determined by
a New Set of Knock in Mice.” PLoS One. Public Library of Science, 2011.
https://doi.org/10.1371/journal.pone.0025785.
ieee: S. Fré et al., “Notch lineages and activity in intestinal stem cells
determined by a new set of knock in mice,” PLoS One, vol. 6, no. 10. Public
Library of Science, 2011.
ista: Fré S, Hannezo EB, Šale S, Huyghe M, Lafkas D, Kissel H, Louvi A, Greve J,
Louvard D, Artavanis Tsakonas S. 2011. Notch lineages and activity in intestinal
stem cells determined by a new set of knock in mice. PLoS One. 6(10), e25785.
mla: Fré, Silvia, et al. “Notch Lineages and Activity in Intestinal Stem Cells Determined
by a New Set of Knock in Mice.” PLoS One, vol. 6, no. 10, e25785, Public
Library of Science, 2011, doi:10.1371/journal.pone.0025785.
short: S. Fré, E.B. Hannezo, S. Šale, M. Huyghe, D. Lafkas, H. Kissel, A. Louvi,
J. Greve, D. Louvard, S. Artavanis Tsakonas, PLoS One 6 (2011).
date_created: 2018-12-11T11:49:13Z
date_published: 2011-10-03T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '03'
ddc:
- '570'
doi: 10.1371/journal.pone.0025785
extern: '1'
file:
- access_level: open_access
checksum: b4e864125dfcb9fa57a9e01688838081
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T11:20:26Z
date_updated: 2020-07-14T12:48:15Z
file_id: '6401'
file_name: 2011_PLOS1_Fre.PDF
file_size: 2860615
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 6'
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: '6520'
quality_controlled: '1'
status: public
title: Notch lineages and activity in intestinal stem cells determined by a new set
of knock in mice
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: 6
year: '2011'
...
---
_id: '9483'
abstract:
- lang: eng
text: Imprinted genes are expressed primarily or exclusively from either the maternal
or paternal allele, a phenomenon that occurs in flowering plants and mammals.
Flowering plant imprinted gene expression has been described primarily in endosperm,
a terminal nutritive tissue consumed by the embryo during seed development or
after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated
by differences in cytosine DNA methylation between the paternal and maternal genomes
as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana
genes are known. Here, we use extensive sequencing of cDNA libraries to identify
9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana
endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the
DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These
genes encode transcription factors, proteins involved in hormone signaling, components
of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation,
and small RNA pathway proteins. We also identify maternally expressed genes that
may be regulated by unknown mechanisms or deposited from maternal tissues. We
did not detect any imprinted genes in the embryo. Our results show that imprinted
gene expression is an extensive mechanistically complex phenomenon that likely
affects multiple aspects of seed development.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Juhyun
full_name: Shin, Juhyun
last_name: Shin
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Stephanie
full_name: Cohen, Stephanie
last_name: Cohen
- first_name: Matthew J.
full_name: Bauer, Matthew J.
last_name: Bauer
- first_name: Meryl
full_name: Hashimoto, Meryl
last_name: Hashimoto
- first_name: Ryan C.
full_name: Kirkbride, Ryan C.
last_name: Kirkbride
- first_name: John J.
full_name: Harada, John J.
last_name: Harada
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences.
2011;108(5):1755-1762. doi:10.1073/pnas.1019273108
apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer,
R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1019273108
chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen,
Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression
in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.
ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis
endosperm,” Proceedings of the National Academy of Sciences, vol. 108,
no. 5. National Academy of Sciences, pp. 1755–1762, 2011.
ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride
RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5),
1755–1762.
mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis
Endosperm.” Proceedings of the National Academy of Sciences, vol. 108,
no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108.
short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto,
R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National
Academy of Sciences 108 (2011) 1755–1762.
date_created: 2021-06-07T07:40:38Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-12-14T08:33:49Z
day: '01'
department:
- _id: DaZi
doi: 10.1073/pnas.1019273108
extern: '1'
external_id:
pmid:
- '21257907'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1019273108
month: '02'
oa: 1
oa_version: Published Version
page: 1755-1762
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of imprinted gene expression in Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 108
year: '2011'
...