---
_id: '3197'
abstract:
- lang: eng
text: |-
The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.
We show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.
author:
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Philip
full_name: Torr, Philip H
last_name: Torr
citation:
ama: Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation
of discrete MRFs. Journal of Machine Learning Research. 2009;10:71-106.
apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2009). An analysis of convex
relaxations for MAP estimation of discrete MRFs. Journal of Machine Learning
Research. Microtome Publishing.
chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex
Relaxations for MAP Estimation of Discrete MRFs.” Journal of Machine Learning
Research. Microtome Publishing, 2009.
ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations
for MAP estimation of discrete MRFs,” Journal of Machine Learning Research,
vol. 10. Microtome Publishing, pp. 71–106, 2009.
ista: Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for
MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.
mla: Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation
of Discrete MRFs.” Journal of Machine Learning Research, vol. 10, Microtome
Publishing, 2009, pp. 71–106.
short: M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research
10 (2009) 71–106.
date_created: 2018-12-11T12:01:57Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
extern: 1
intvolume: ' 10'
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-00773608
month: '01'
oa: 1
page: 71 - 106
publication: Journal of Machine Learning Research
publication_status: published
publisher: Microtome Publishing
publist_id: '3484'
quality_controlled: 0
status: public
title: An analysis of convex relaxations for MAP estimation of discrete MRFs
type: journal_article
volume: 10
year: '2009'
...
---
_id: '11103'
abstract:
- lang: eng
text: Over the last decade, the nuclear envelope (NE) has emerged as a key component
in the organization and function of the nuclear genome. As many as 100 different
proteins are thought to specifically localize to this double membrane that separates
the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through
the NE are formed at sites where the inner and outer nuclear membranes are fused,
and the coincident assembly of ∼30 proteins into nuclear pore complexes occurs.
These nuclear pore complexes are essential for the control of nucleocytoplasmic
exchange. Many of the NE and nuclear pore proteins are thought to play crucial
roles in gene regulation and thus are increasingly linked to human diseases.
article_processing_charge: No
article_type: review
author:
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Susan R.
full_name: Wente, Susan R.
last_name: Wente
citation:
ama: 'Hetzer M, Wente SR. Border control at the nucleus: Biogenesis and organization
of the nuclear membrane and pore complexes. Developmental Cell. 2009;17(5):606-616.
doi:10.1016/j.devcel.2009.10.007'
apa: 'Hetzer, M., & Wente, S. R. (2009). Border control at the nucleus: Biogenesis
and organization of the nuclear membrane and pore complexes. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2009.10.007'
chicago: 'Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis
and Organization of the Nuclear Membrane and Pore Complexes.” Developmental
Cell. Elsevier, 2009. https://doi.org/10.1016/j.devcel.2009.10.007.'
ieee: 'M. Hetzer and S. R. Wente, “Border control at the nucleus: Biogenesis and
organization of the nuclear membrane and pore complexes,” Developmental Cell,
vol. 17, no. 5. Elsevier, pp. 606–616, 2009.'
ista: 'Hetzer M, Wente SR. 2009. Border control at the nucleus: Biogenesis and organization
of the nuclear membrane and pore complexes. Developmental Cell. 17(5), 606–616.'
mla: 'Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis
and Organization of the Nuclear Membrane and Pore Complexes.” Developmental
Cell, vol. 17, no. 5, Elsevier, 2009, pp. 606–16, doi:10.1016/j.devcel.2009.10.007.'
short: M. Hetzer, S.R. Wente, Developmental Cell 17 (2009) 606–616.
date_created: 2022-04-07T07:53:45Z
date_published: 2009-11-17T00:00:00Z
date_updated: 2022-07-18T08:55:01Z
day: '17'
doi: 10.1016/j.devcel.2009.10.007
extern: '1'
external_id:
pmid:
- '19922866'
intvolume: ' 17'
issue: '5'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2009.10.007
month: '11'
oa: 1
oa_version: Published Version
page: 606-616
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Border control at the nucleus: Biogenesis and organization of the nuclear
membrane and pore complexes'
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 17
year: '2009'
...
---
_id: '11105'
abstract:
- lang: eng
text: Nuclear-pore complexes (NPCs) are large protein channels that span the nuclear
envelope (NE), which is a double membrane that encloses the nuclear genome of
eukaryotes. Each of the typically 2,000–4,000 pores in the NE of vertebrate cells
is composed of multiple copies of 30 different proteins known as nucleoporins.
The evolutionarily conserved NPC proteins have the well-characterized function
of mediating the transport of molecules between the nucleoplasm and the cytoplasm.
Mutations in nucleoporins are often linked to specific developmental defects and
disease, and the resulting phenotypes are usually interpreted as the consequences
of perturbed nuclear transport activity. However, recent evidence suggests that
NPCs have additional functions in chromatin organization and gene regulation,
some of which might be independent of nuclear transport. Here, we review the transport-dependent
and transport-independent roles of NPCs in the regulation of nuclear function
and gene expression.
article_processing_charge: No
article_type: original
author:
- first_name: Maya
full_name: Capelson, Maya
last_name: Capelson
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Capelson M, Hetzer M. The role of nuclear pores in gene regulation, development
and disease. EMBO reports. 2009;10(7):697-705. doi:10.1038/embor.2009.147
apa: Capelson, M., & Hetzer, M. (2009). The role of nuclear pores in gene regulation,
development and disease. EMBO Reports. EMBO. https://doi.org/10.1038/embor.2009.147
chicago: Capelson, Maya, and Martin Hetzer. “The Role of Nuclear Pores in Gene Regulation,
Development and Disease.” EMBO Reports. EMBO, 2009. https://doi.org/10.1038/embor.2009.147.
ieee: M. Capelson and M. Hetzer, “The role of nuclear pores in gene regulation,
development and disease,” EMBO reports, vol. 10, no. 7. EMBO, pp. 697–705,
2009.
ista: Capelson M, Hetzer M. 2009. The role of nuclear pores in gene regulation,
development and disease. EMBO reports. 10(7), 697–705.
mla: Capelson, Maya, and Martin Hetzer. “The Role of Nuclear Pores in Gene Regulation,
Development and Disease.” EMBO Reports, vol. 10, no. 7, EMBO, 2009, pp.
697–705, doi:10.1038/embor.2009.147.
short: M. Capelson, M. Hetzer, EMBO Reports 10 (2009) 697–705.
date_created: 2022-04-07T07:54:06Z
date_published: 2009-07-01T00:00:00Z
date_updated: 2022-07-18T08:42:44Z
day: '01'
doi: 10.1038/embor.2009.147
extern: '1'
external_id:
pmid:
- '19543230'
intvolume: ' 10'
issue: '7'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/embor.2009.147
month: '07'
oa: 1
oa_version: Published Version
page: 697-705
pmid: 1
publication: EMBO reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: EMBO
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/embor.2009.176
scopus_import: '1'
status: public
title: The role of nuclear pores in gene regulation, development and disease
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 10
year: '2009'
...
---
_id: '11106'
abstract:
- lang: eng
text: Formation of the nuclear envelope (NE) around segregated chromosomes occurs
by the reshaping of the endoplasmic reticulum (ER), a reservoir for disassembled
nuclear membrane components during mitosis. In this study, we show that inner
nuclear membrane proteins such as lamin B receptor (LBR), MAN1, Lap2β, and the
trans-membrane nucleoporins Ndc1 and POM121 drive the spreading of ER membranes
into the emerging NE via their capacity to bind chromatin in a collaborative manner.
Despite their redundant functions, decreasing the levels of any of these trans-membrane
proteins by RNAi-mediated knockdown delayed NE formation, whereas increasing the
levels of any of them had the opposite effect. Furthermore, acceleration of NE
formation interferes with chromosome separation during mitosis, indicating that
the time frame over which chromatin becomes membrane enclosed is physiologically
relevant and regulated. These data suggest that functionally distinct classes
of chromatin-interacting membrane proteins, which are present at nonsaturating
levels, collaborate to rapidly reestablish the nuclear compartment at the end
of mitosis.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel J.
full_name: Anderson, Daniel J.
last_name: Anderson
- first_name: Jesse D.
full_name: Vargas, Jesse D.
last_name: Vargas
- first_name: Joshua P.
full_name: Hsiao, Joshua P.
last_name: Hsiao
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Anderson DJ, Vargas JD, Hsiao JP, Hetzer M. Recruitment of functionally distinct
membrane proteins to chromatin mediates nuclear envelope formation in vivo. Journal
of Cell Biology. 2009;186(2):183-191. doi:10.1083/jcb.200901106
apa: Anderson, D. J., Vargas, J. D., Hsiao, J. P., & Hetzer, M. (2009). Recruitment
of functionally distinct membrane proteins to chromatin mediates nuclear envelope
formation in vivo. Journal of Cell Biology. Rockefeller University Press.
https://doi.org/10.1083/jcb.200901106
chicago: Anderson, Daniel J., Jesse D. Vargas, Joshua P. Hsiao, and Martin Hetzer.
“Recruitment of Functionally Distinct Membrane Proteins to Chromatin Mediates
Nuclear Envelope Formation in Vivo.” Journal of Cell Biology. Rockefeller
University Press, 2009. https://doi.org/10.1083/jcb.200901106.
ieee: D. J. Anderson, J. D. Vargas, J. P. Hsiao, and M. Hetzer, “Recruitment of
functionally distinct membrane proteins to chromatin mediates nuclear envelope
formation in vivo,” Journal of Cell Biology, vol. 186, no. 2. Rockefeller
University Press, pp. 183–191, 2009.
ista: Anderson DJ, Vargas JD, Hsiao JP, Hetzer M. 2009. Recruitment of functionally
distinct membrane proteins to chromatin mediates nuclear envelope formation in
vivo. Journal of Cell Biology. 186(2), 183–191.
mla: Anderson, Daniel J., et al. “Recruitment of Functionally Distinct Membrane
Proteins to Chromatin Mediates Nuclear Envelope Formation in Vivo.” Journal
of Cell Biology, vol. 186, no. 2, Rockefeller University Press, 2009, pp.
183–91, doi:10.1083/jcb.200901106.
short: D.J. Anderson, J.D. Vargas, J.P. Hsiao, M. Hetzer, Journal of Cell Biology
186 (2009) 183–191.
date_created: 2022-04-07T07:54:18Z
date_published: 2009-07-20T00:00:00Z
date_updated: 2022-07-18T08:58:35Z
day: '20'
doi: 10.1083/jcb.200901106
extern: '1'
external_id:
pmid:
- '19620630'
intvolume: ' 186'
issue: '2'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1083/jcb.200901106
month: '07'
oa: 1
oa_version: Published Version
page: 183-191
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1083/jcb.20090110620090903c
scopus_import: '1'
status: public
title: Recruitment of functionally distinct membrane proteins to chromatin mediates
nuclear envelope formation in vivo
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 186
year: '2009'
...
---
_id: '11107'
abstract:
- lang: eng
text: Nucleocytoplasmic transport occurs exclusively through nuclear pore complexes
(NPCs) embedded in pores formed by inner and outer nuclear membrane fusion. The
mechanism for de novo pore and NPC biogenesis remains unclear. Reticulons (RTNs)
and Yop1/DP1 are conserved membrane protein families required to form and maintain
the tubular endoplasmic reticulum (ER) and the postmitotic nuclear envelope. In
this study, we report that members of the RTN and Yop1/DP1 families are required
for nuclear pore formation. Analysis of Saccharomyces cerevisiae prp20-G282S and
nup133Δ NPC assembly mutants revealed perturbations in Rtn1–green fluorescent
protein (GFP) and Yop1-GFP ER distribution and colocalization to NPC clusters.
Combined deletion of RTN1 and YOP1 resulted in NPC clustering, nuclear import
defects, and synthetic lethality with the additional absence of Pom34, Pom152,
and Nup84 subcomplex members. We tested for a direct role in NPC biogenesis using
Xenopus laevis in vitro assays and found that anti-Rtn4a antibodies specifically
inhibited de novo nuclear pore formation. We hypothesize that these ER membrane–bending
proteins mediate early NPC assembly steps.
article_processing_charge: No
article_type: original
author:
- first_name: T. Renee
full_name: Dawson, T. Renee
last_name: Dawson
- first_name: Michelle D.
full_name: Lazarus, Michelle D.
last_name: Lazarus
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Susan R.
full_name: Wente, Susan R.
last_name: Wente
citation:
ama: Dawson TR, Lazarus MD, Hetzer M, Wente SR. ER membrane–bending proteins are
necessary for de novo nuclear pore formation. Journal of Cell Biology.
2009;184(5):659-675. doi:10.1083/jcb.200806174
apa: Dawson, T. R., Lazarus, M. D., Hetzer, M., & Wente, S. R. (2009). ER membrane–bending
proteins are necessary for de novo nuclear pore formation. Journal of Cell
Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200806174
chicago: Dawson, T. Renee, Michelle D. Lazarus, Martin Hetzer, and Susan R. Wente.
“ER Membrane–Bending Proteins Are Necessary for de Novo Nuclear Pore Formation.”
Journal of Cell Biology. Rockefeller University Press, 2009. https://doi.org/10.1083/jcb.200806174.
ieee: T. R. Dawson, M. D. Lazarus, M. Hetzer, and S. R. Wente, “ER membrane–bending
proteins are necessary for de novo nuclear pore formation,” Journal of Cell
Biology, vol. 184, no. 5. Rockefeller University Press, pp. 659–675, 2009.
ista: Dawson TR, Lazarus MD, Hetzer M, Wente SR. 2009. ER membrane–bending proteins
are necessary for de novo nuclear pore formation. Journal of Cell Biology. 184(5),
659–675.
mla: Dawson, T. Renee, et al. “ER Membrane–Bending Proteins Are Necessary for de
Novo Nuclear Pore Formation.” Journal of Cell Biology, vol. 184, no. 5,
Rockefeller University Press, 2009, pp. 659–75, doi:10.1083/jcb.200806174.
short: T.R. Dawson, M.D. Lazarus, M. Hetzer, S.R. Wente, Journal of Cell Biology
184 (2009) 659–675.
date_created: 2022-04-07T07:54:44Z
date_published: 2009-03-09T00:00:00Z
date_updated: 2022-07-18T08:55:05Z
day: '09'
doi: 10.1083/jcb.200806174
extern: '1'
external_id:
pmid:
- '19273614'
intvolume: ' 184'
issue: '5'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1083/jcb.200806174
month: '03'
oa: 1
oa_version: Published Version
page: 659-675
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: ER membrane–bending proteins are necessary for de novo nuclear pore formation
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 184
year: '2009'
...
---
_id: '11108'
abstract:
- lang: eng
text: In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis
and reassemble into the newly forming nuclei. However, the fate of nuclear pores
in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear
structures, do not turn over in differentiated cells. While a subset of NPC components,
like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like
the Nup107/160 complex, are extremely long-lived and remain incorporated in the
nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin
expression and NPC turnover, we discovered an age-related deterioration of NPCs,
leading to an increase in nuclear permeability and the leaking of cytoplasmic
proteins into the nucleus. Our finding that nuclear “leakiness” is dramatically
accelerated during aging and that a subset of nucleoporins is oxidatively damaged
in old cells suggests that the accumulation of damage at the NPC might be a crucial
aging event.
article_processing_charge: No
article_type: original
author:
- first_name: Maximiliano A.
full_name: D'Angelo, Maximiliano A.
last_name: D'Angelo
- first_name: Marcela
full_name: Raices, Marcela
last_name: Raices
- first_name: Siler H.
full_name: Panowski, Siler H.
last_name: Panowski
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: D’Angelo MA, Raices M, Panowski SH, Hetzer M. Age-dependent deterioration of
nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells.
Cell. 2009;136(2):284-295. doi:10.1016/j.cell.2008.11.037
apa: D’Angelo, M. A., Raices, M., Panowski, S. H., & Hetzer, M. (2009). Age-dependent
deterioration of nuclear pore complexes causes a loss of nuclear integrity in
postmitotic cells. Cell. Elsevier. https://doi.org/10.1016/j.cell.2008.11.037
chicago: D’Angelo, Maximiliano A., Marcela Raices, Siler H. Panowski, and Martin
Hetzer. “Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of
Nuclear Integrity in Postmitotic Cells.” Cell. Elsevier, 2009. https://doi.org/10.1016/j.cell.2008.11.037.
ieee: M. A. D’Angelo, M. Raices, S. H. Panowski, and M. Hetzer, “Age-dependent deterioration
of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells,”
Cell, vol. 136, no. 2. Elsevier, pp. 284–295, 2009.
ista: D’Angelo MA, Raices M, Panowski SH, Hetzer M. 2009. Age-dependent deterioration
of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells.
Cell. 136(2), 284–295.
mla: D’Angelo, Maximiliano A., et al. “Age-Dependent Deterioration of Nuclear Pore
Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells.” Cell,
vol. 136, no. 2, Elsevier, 2009, pp. 284–95, doi:10.1016/j.cell.2008.11.037.
short: M.A. D’Angelo, M. Raices, S.H. Panowski, M. Hetzer, Cell 136 (2009) 284–295.
date_created: 2022-04-07T07:54:52Z
date_published: 2009-01-23T00:00:00Z
date_updated: 2022-07-18T08:55:29Z
day: '23'
doi: 10.1016/j.cell.2008.11.037
extern: '1'
external_id:
pmid:
- '19167330'
intvolume: ' 136'
issue: '2'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2008.11.037
month: '01'
oa: 1
oa_version: Published Version
page: 284-295
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear
integrity in postmitotic cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 136
year: '2009'
...
---
_id: '11912'
abstract:
- lang: eng
text: As the World Wide Web is growing rapidly, it is getting increasingly challenging
to gather representative information about it. Instead of crawling the web exhaustively
one has to resort to other techniques like sampling to determine the properties
of the web. A uniform random sample of the web would be useful to determine the
percentage of web pages in a specific language, on a topic or in a top level domain.
Unfortunately, no approach has been shown to sample the web pages in an unbiased
way. Three promising web sampling algorithms are based on random walks. They each
have been evaluated individually, but making a comparison on different data sets
is not possible. We directly compare these algorithms in this paper. We performed
three random walks on the web under the same conditions and analyzed their outcomes
in detail. We discuss the strengths and the weaknesses of each algorithm and propose
improvements based on experimental results.
alternative_title:
- LIPIcs
article_processing_charge: No
arxiv: 1
author:
- first_name: ' Eda'
full_name: Baykan, Eda
last_name: Baykan
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan F.
full_name: Keller, Stefan F.
last_name: Keller
- first_name: Sebastian
full_name: de Castelberg, Sebastian
last_name: de Castelberg
- first_name: Markus
full_name: Kinzler, Markus
last_name: Kinzler
citation:
ama: 'Baykan Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. A comparison
of techniques for sampling web pages. In: 26th International Symposium on Theoretical
Aspects of Computer Science. Vol 3. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2009:13-30. doi:10.4230/LIPICS.STACS.2009.1809'
apa: 'Baykan, Eda, Henzinger, M. H., Keller, S. F., de Castelberg, S., & Kinzler,
M. (2009). A comparison of techniques for sampling web pages. In 26th International
Symposium on Theoretical Aspects of Computer Science (Vol. 3, pp. 13–30).
Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2009.1809'
chicago: Baykan, Eda, Monika H Henzinger, Stefan F. Keller, Sebastian de Castelberg,
and Markus Kinzler. “A Comparison of Techniques for Sampling Web Pages.” In 26th
International Symposium on Theoretical Aspects of Computer Science, 3:13–30.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009. https://doi.org/10.4230/LIPICS.STACS.2009.1809.
ieee: Eda Baykan, M. H. Henzinger, S. F. Keller, S. de Castelberg, and M. Kinzler,
“A comparison of techniques for sampling web pages,” in 26th International
Symposium on Theoretical Aspects of Computer Science, Freiburg, Germany, 2009,
vol. 3, pp. 13–30.
ista: 'Baykan Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. 2009. A
comparison of techniques for sampling web pages. 26th International Symposium
on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects
of Computer Science, LIPIcs, vol. 3, 13–30.'
mla: Baykan, Eda, et al. “A Comparison of Techniques for Sampling Web Pages.” 26th
International Symposium on Theoretical Aspects of Computer Science, vol. 3,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30, doi:10.4230/LIPICS.STACS.2009.1809.
short: Eda Baykan, M.H. Henzinger, S.F. Keller, S. de Castelberg, M. Kinzler, in:,
26th International Symposium on Theoretical Aspects of Computer Science, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30.
conference:
end_date: 2009-02-28
location: Freiburg, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2009-02-26
date_created: 2022-08-18T06:57:25Z
date_published: 2009-02-01T00:00:00Z
date_updated: 2023-02-17T08:57:16Z
day: '01'
doi: 10.4230/LIPICS.STACS.2009.1809
extern: '1'
external_id:
arxiv:
- '0902.1604'
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.STACS.2009.1809
month: '02'
oa: 1
oa_version: Published Version
page: 13-30
publication: 26th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- 978-3-939897-09-5
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of techniques for sampling web pages
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2009'
...
---
_id: '1763'
abstract:
- lang: eng
text: The field of cavity quantum electrodynamics (QED), traditionally studied in
atomic systems, has gained new momentum by recent reports of quantum optical experiments
with solid-state semiconducting and superconducting systems. In cavity QED, the
observation of the vacuum Rabi mode splitting is used to investigate the nature
of matter-light interaction at a quantum-mechanical level. However, this effect
can, at least in principle, be explained classically as the normal mode splitting
of two coupled linear oscillators. It has been suggested that an observation of
the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings
energy ladder with the square root of photon number n is sufficient to prove that
the system is quantum mechanical in nature. Here we report a direct spectroscopic
observation of this characteristic quantum nonlinearity. Measuring the photonic
degree of freedom of the coupled system, our measurements provide unambiguous
spectroscopic evidence for the quantum nature of the resonant atom-field interaction
in cavity QED. We explore atom-photon superposition states involving up to two
photons, using a spectroscopic pump and probe technique. The experiments have
been performed in a circuit QED set-up, in which very strong coupling is realized
by the large dipole coupling strength and the long coherence time of a superconducting
qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems
also provide a natural quantum interface between flying qubits (photons) and stationary
qubits for applications in quantum information processing and communication.
acknowledgement: This work was supported by SNF and ETHZ. P.J.L. was supported by
the EU with an MC-EIF. A.B. was supported by NSERC, CIFAR and FQRNT
author:
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Fink JM, Göppl M, Baur M, et al. Climbing the Jaynes-Cummings ladder and observing
its √n nonlinearity in a cavity QED system. Nature. 2008;454(7202):315-318.
doi:10.1038/nature07112
apa: Fink, J. M., Göppl, M., Baur, M., Bianchetti, R., Leek, P., Blais, A., &
Wallraff, A. (2008). Climbing the Jaynes-Cummings ladder and observing its √n
nonlinearity in a cavity QED system. Nature. Nature Publishing Group. https://doi.org/10.1038/nature07112
chicago: Fink, Johannes M, M Göppl, Matthias Baur, R Bianchetti, Peter Leek, Alexandre
Blais, and Andreas Wallraff. “Climbing the Jaynes-Cummings Ladder and Observing
Its √n Nonlinearity in a Cavity QED System.” Nature. Nature Publishing
Group, 2008. https://doi.org/10.1038/nature07112.
ieee: J. M. Fink et al., “Climbing the Jaynes-Cummings ladder and observing
its √n nonlinearity in a cavity QED system,” Nature, vol. 454, no. 7202.
Nature Publishing Group, pp. 315–318, 2008.
ista: Fink JM, Göppl M, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008.
Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity
QED system. Nature. 454(7202), 315–318.
mla: Fink, Johannes M., et al. “Climbing the Jaynes-Cummings Ladder and Observing
Its √n Nonlinearity in a Cavity QED System.” Nature, vol. 454, no. 7202,
Nature Publishing Group, 2008, pp. 315–18, doi:10.1038/nature07112.
short: J.M. Fink, M. Göppl, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff,
Nature 454 (2008) 315–318.
date_created: 2018-12-11T11:53:53Z
date_published: 2008-07-17T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '17'
doi: 10.1038/nature07112
extern: 1
intvolume: ' 454'
issue: '7202'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0902.1827
month: '07'
oa: 1
page: 315 - 318
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5358'
quality_controlled: 0
status: public
title: Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a
cavity QED system
type: journal_article
volume: 454
year: '2008'
...
---
_id: '1765'
abstract:
- lang: eng
text: High quality on-chip microwave resonators have recently found prominent new
applications in quantum optics and quantum information processing experiments
with superconducting electronic circuits, a field now known as circuit quantum
electrodynamics (QED). They are also used as single photon detectors and parametric
amplifiers. Here we analyze the physical properties of coplanar waveguide resonators
and their relation to the materials properties for use in circuit QED. We have
designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz
and quality factors ranging from a few hundreds to a several hundred thousands
controlled by appropriately designed input and output coupling capacitors. The
microwave transmission spectra measured at temperatures of 20 mK are shown to
be in good agreement with theoretical lumped element and distributed element transmission
matrix models. In particular, the experimentally determined resonance frequencies,
quality factors, and insertion losses are fully and consistently explained by
the two models for all measured devices. The high level of control and flexibility
in design renders these resonators ideal for storing and manipulating quantum
electromagnetic fields in integrated superconducting electronic circuits.
acknowledgement: This work was supported by Swiss National Fund (SNF) and ETH Zürich.
P.J.L. was supported by the EC with a MC-EIF
author:
- first_name: M
full_name: Göppl, M
last_name: Göppl
- first_name: A
full_name: Fragner, A
last_name: Fragner
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: G
full_name: Puebla, G
last_name: Puebla
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Göppl M, Fragner A, Baur M, et al. Coplanar waveguide resonators for circuit
quantum electrodynamics. Journal of Applied Physics. 2008;104(11). doi:10.1063/1.3010859
apa: Göppl, M., Fragner, A., Baur, M., Bianchetti, R., Filipp, S., Fink, J. M.,
… Wallraff, A. (2008). Coplanar waveguide resonators for circuit quantum electrodynamics.
Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3010859
chicago: Göppl, M, A Fragner, Matthias Baur, R Bianchetti, Stefan Filipp, Johannes
M Fink, Peter Leek, G Puebla, L. Steffen, and Andreas Wallraff. “Coplanar Waveguide
Resonators for Circuit Quantum Electrodynamics.” Journal of Applied Physics.
American Institute of Physics, 2008. https://doi.org/10.1063/1.3010859.
ieee: M. Göppl et al., “Coplanar waveguide resonators for circuit quantum
electrodynamics,” Journal of Applied Physics, vol. 104, no. 11. American
Institute of Physics, 2008.
ista: Göppl M, Fragner A, Baur M, Bianchetti R, Filipp S, Fink JM, Leek P, Puebla
G, Steffen L, Wallraff A. 2008. Coplanar waveguide resonators for circuit quantum
electrodynamics. Journal of Applied Physics. 104(11).
mla: Göppl, M., et al. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.”
Journal of Applied Physics, vol. 104, no. 11, American Institute of Physics,
2008, doi:10.1063/1.3010859.
short: M. Göppl, A. Fragner, M. Baur, R. Bianchetti, S. Filipp, J.M. Fink, P. Leek,
G. Puebla, L. Steffen, A. Wallraff, Journal of Applied Physics 104 (2008).
date_created: 2018-12-11T11:53:53Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:03Z
day: '01'
doi: 10.1063/1.3010859
extern: 1
intvolume: ' 104'
issue: '11'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0807.4094
month: '01'
oa: 1
publication: Journal of Applied Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5355'
quality_controlled: 0
status: public
title: Coplanar waveguide resonators for circuit quantum electrodynamics
type: journal_article
volume: 104
year: '2008'
...
---
_id: '1460'
abstract:
- lang: eng
text: 'We calculate the E-polynomials of certain twisted GL(n,ℂ)-character varieties
Mn of Riemann surfaces by counting points over finite fields using the character
table of the finite group of Lie-type GL(n, q) and a theorem proved in the appendix
by N. Katz. We deduce from this calculation several geometric results, for example,
the value of the topological Euler characteristic of the associated PGL(n,ℂ)-character
variety. The calculation also leads to several conjectures about the cohomology
of Mn: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious
hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable
representations of a certain quiver. We prove these conjectures for n=2.'
acknowledgement: The first author was supported by NSF grants DMS-0305505 and DMS-
0604775 an Alfred Sloan Fellowship and a Royal Society University Research Fellowship.
The second author was supported by an NSF grant DMS-0200605.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: 'Hausel T, Rodríguez Villegas F. Mixed Hodge polynomials of character varieties:
With an appendix by Nicholas M. Katz. Inventiones Mathematicae. 2008;174(3):555-624.
doi:10.1007/s00222-008-0142-x'
apa: 'Hausel, T., & Rodríguez Villegas, F. (2008). Mixed Hodge polynomials of
character varieties: With an appendix by Nicholas M. Katz. Inventiones Mathematicae.
Springer. https://doi.org/10.1007/s00222-008-0142-x'
chicago: 'Hausel, Tamás, and Fernando Rodríguez Villegas. “Mixed Hodge Polynomials
of Character Varieties: With an Appendix by Nicholas M. Katz.” Inventiones
Mathematicae. Springer, 2008. https://doi.org/10.1007/s00222-008-0142-x.'
ieee: 'T. Hausel and F. Rodríguez Villegas, “Mixed Hodge polynomials of character
varieties: With an appendix by Nicholas M. Katz,” Inventiones Mathematicae,
vol. 174, no. 3. Springer, pp. 555–624, 2008.'
ista: 'Hausel T, Rodríguez Villegas F. 2008. Mixed Hodge polynomials of character
varieties: With an appendix by Nicholas M. Katz. Inventiones Mathematicae. 174(3),
555–624.'
mla: 'Hausel, Tamás, and Fernando Rodríguez Villegas. “Mixed Hodge Polynomials of
Character Varieties: With an Appendix by Nicholas M. Katz.” Inventiones Mathematicae,
vol. 174, no. 3, Springer, 2008, pp. 555–624, doi:10.1007/s00222-008-0142-x.'
short: T. Hausel, F. Rodríguez Villegas, Inventiones Mathematicae 174 (2008) 555–624.
date_created: 2018-12-11T11:52:09Z
date_published: 2008-12-01T00:00:00Z
date_updated: 2021-01-12T06:50:54Z
day: '01'
doi: 10.1007/s00222-008-0142-x
extern: 1
intvolume: ' 174'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0612668
month: '12'
oa: 1
page: 555 - 624
publication: Inventiones Mathematicae
publication_status: published
publisher: Springer
publist_id: '5732'
quality_controlled: 0
status: public
title: 'Mixed Hodge polynomials of character varieties: With an appendix by Nicholas
M. Katz'
type: journal_article
volume: 174
year: '2008'
...
---
_id: '6146'
abstract:
- lang: eng
text: Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental
to all animals. Here we examine the CO2 response of the nematode Caenorhabditis
elegans. This species inhabits rotting material, which typically has a broad CO2
concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%.
Animals can respond to both absolute CO2 concentrations and changes in CO2 levels
within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear
to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated
ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust
CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription
factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16,
strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses
CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1.
The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1,
besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes
avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs
so that one response dominates. Food and allelic variation at NPR-1 regulate which
response prevails. Our results suggest that multiple sensory inputs are coordinated
by C. elegans to generate different coherent foraging strategies.
author:
- first_name: A. J.
full_name: Bretscher, A. J.
last_name: Bretscher
- first_name: K. E.
full_name: Busch, K. E.
last_name: Busch
- 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, Busch KE, de Bono M. A carbon dioxide avoidance behavior is integrated
with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings
of the National Academy of Sciences. 2008;105(23):8044-8049. doi:10.1073/pnas.0707607105
apa: Bretscher, A. J., Busch, K. E., & de Bono, M. (2008). A carbon dioxide
avoidance behavior is integrated with responses to ambient oxygen and food in
Caenorhabditis elegans. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0707607105
chicago: Bretscher, A. J., K. E. Busch, and Mario de Bono. “A Carbon Dioxide Avoidance
Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis
Elegans.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0707607105.
ieee: A. J. Bretscher, K. E. Busch, and M. de Bono, “A carbon dioxide avoidance
behavior is integrated with responses to ambient oxygen and food in Caenorhabditis
elegans,” Proceedings of the National Academy of Sciences, vol. 105, no.
23. Proceedings of the National Academy of Sciences, pp. 8044–8049, 2008.
ista: Bretscher AJ, Busch KE, de Bono M. 2008. A carbon dioxide avoidance behavior
is integrated with responses to ambient oxygen and food in Caenorhabditis elegans.
Proceedings of the National Academy of Sciences. 105(23), 8044–8049.
mla: Bretscher, A. J., et al. “A Carbon Dioxide Avoidance Behavior Is Integrated
with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings
of the National Academy of Sciences, vol. 105, no. 23, Proceedings of the
National Academy of Sciences, 2008, pp. 8044–49, doi:10.1073/pnas.0707607105.
short: A.J. Bretscher, K.E. Busch, M. de Bono, Proceedings of the National Academy
of Sciences 105 (2008) 8044–8049.
date_created: 2019-03-21T08:10:15Z
date_published: 2008-06-10T00:00:00Z
date_updated: 2021-01-12T08:06:21Z
day: '10'
ddc:
- '570'
doi: 10.1073/pnas.0707607105
extern: '1'
external_id:
pmid:
- '18524954'
file:
- access_level: open_access
checksum: eac0413064b022c1489f7b6719e7228c
content_type: application/pdf
creator: kschuh
date_created: 2019-03-21T08:14:54Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6147'
file_name: 2008_PNAS_Bretscher.pdf
file_size: 501506
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 105'
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 8044-8049
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: A carbon dioxide avoidance behavior is integrated with responses to ambient
oxygen and food in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2008'
...
---
_id: '1036'
abstract:
- lang: eng
text: We report on the control of interaction-induced dephasing of Bloch oscillations
for an atomic Bose-Einstein condensate in an optical lattice. We quantify the
dephasing in terms of the width of the quasimomentum distribution and measure
its dependence on time for different interaction strengths which we control by
means of a Feshbach resonance. For minimal interaction, the dephasing time is
increased from a few to more than 20 thousand Bloch oscillation periods, allowing
us to realize a BEC-based atom interferometer in the noninteracting limit.
acknowledgement: "We thank A. Daley for theoretical support and for help with\r\nsetting
\ up the numerical calculations and A. Buchleitner\r\nand his group for useful
\ discussions. We are grateful to\r\nA. Liem and H. Zellmer for valuable assistance
in setting\r\nup the 1064 nm fiber amplifier system. We acknowledge\r\ncontributions
\ by P. Unterwaditzer and T. Flir during the\r\nearly stages of the
\ experiment. We are indebted to\r\nR. Grimm for generous support and
\ gratefully acknowledge funding by the Austrian Ministry of Science and\r\nResearch
(BMWF) and the Austrian Science Fund (FWF)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gabriel
full_name: Rojas Kopeinig, Gabriel
last_name: Rojas Kopeinig
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Gustavsson M, Haller E, Mark M, Danzl JG, Rojas Kopeinig G, Nägerl H. Control
of interaction-induced dephasing of bloch oscillations. Physical Review Letters.
2008;100(8). doi:10.1103/PhysRevLett.100.080404
apa: Gustavsson, M., Haller, E., Mark, M., Danzl, J. G., Rojas Kopeinig, G., &
Nägerl, H. (2008). Control of interaction-induced dephasing of bloch oscillations.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.100.080404
chicago: Gustavsson, Mattias, Elmar Haller, Manfred Mark, Johann G Danzl, Gabriel
Rojas Kopeinig, and Hanns Nägerl. “Control of Interaction-Induced Dephasing of
Bloch Oscillations.” Physical Review Letters. American Physical Society,
2008. https://doi.org/10.1103/PhysRevLett.100.080404.
ieee: M. Gustavsson, E. Haller, M. Mark, J. G. Danzl, G. Rojas Kopeinig, and H.
Nägerl, “Control of interaction-induced dephasing of bloch oscillations,” Physical
Review Letters, vol. 100, no. 8. American Physical Society, 2008.
ista: Gustavsson M, Haller E, Mark M, Danzl JG, Rojas Kopeinig G, Nägerl H. 2008.
Control of interaction-induced dephasing of bloch oscillations. Physical Review
Letters. 100(8).
mla: Gustavsson, Mattias, et al. “Control of Interaction-Induced Dephasing of Bloch
Oscillations.” Physical Review Letters, vol. 100, no. 8, American Physical
Society, 2008, doi:10.1103/PhysRevLett.100.080404.
short: M. Gustavsson, E. Haller, M. Mark, J.G. Danzl, G. Rojas Kopeinig, H. Nägerl,
Physical Review Letters 100 (2008).
date_created: 2018-12-11T11:49:48Z
date_published: 2008-02-28T00:00:00Z
date_updated: 2021-01-12T06:47:49Z
day: '28'
doi: 10.1103/PhysRevLett.100.080404
extern: '1'
external_id:
arxiv:
- '0710.5083'
intvolume: ' 100'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0710.5083
month: '02'
oa: 1
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6353'
status: public
title: Control of interaction-induced dephasing of bloch oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2008'
...
---
_id: '1037'
abstract:
- lang: eng
text: We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation
threshold, which are stable against spontaneous decay on the time scale of 1s.
An optically trapped sample of ultracold dimers is prepared in a high rotational
state and magnetically tuned into a region with a negative binding energy. The
metastable character of these molecules arises from the large centrifugal barrier
in combination with negligible coupling to states with low rotational angular
momentum. A sharp onset of dissociation with increasing magnetic field is mediated
by a crossing with a lower rotational dimer state and facilitates dissociation
on demand with a well-defined energy.
acknowledgement: We thank S. Du ̈rr and T. Volz for fruitful discussions. We acknowledge
support by the Austrian Science Fund (FWF) within No. SFB 15 (project part 16).
S.K. is supported within the Marie Curie Intra-European Program of the European
Commission. F.F. is supported within the Lise Meitner program of the FWF.
article_processing_charge: No
arxiv: 1
author:
- first_name: Steven
full_name: Knoop, Steven
last_name: Knoop
- first_name: Michael
full_name: Mark, Michael
last_name: Mark
- first_name: Francesca
full_name: Ferlaino, Francesca
last_name: Ferlaino
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Tobias
full_name: Kraemer, Tobias
last_name: Kraemer
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
- first_name: Rudolf
full_name: Grimm, Rudolf
last_name: Grimm
citation:
ama: Knoop S, Mark M, Ferlaino F, et al. Metastable feshbach molecules in high rotational
states. Physical Review Letters. 2008;100(8). doi:10.1103/PhysRevLett.100.083002
apa: Knoop, S., Mark, M., Ferlaino, F., Danzl, J. G., Kraemer, T., Nägerl, H., &
Grimm, R. (2008). Metastable feshbach molecules in high rotational states. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.100.083002
chicago: Knoop, Steven, Michael Mark, Francesca Ferlaino, Johann G Danzl, Tobias
Kraemer, Hanns Nägerl, and Rudolf Grimm. “Metastable Feshbach Molecules in High
Rotational States.” Physical Review Letters. American Physical Society,
2008. https://doi.org/10.1103/PhysRevLett.100.083002.
ieee: S. Knoop et al., “Metastable feshbach molecules in high rotational
states,” Physical Review Letters, vol. 100, no. 8. American Physical Society,
2008.
ista: Knoop S, Mark M, Ferlaino F, Danzl JG, Kraemer T, Nägerl H, Grimm R. 2008.
Metastable feshbach molecules in high rotational states. Physical Review Letters.
100(8).
mla: Knoop, Steven, et al. “Metastable Feshbach Molecules in High Rotational States.”
Physical Review Letters, vol. 100, no. 8, American Physical Society, 2008,
doi:10.1103/PhysRevLett.100.083002.
short: S. Knoop, M. Mark, F. Ferlaino, J.G. Danzl, T. Kraemer, H. Nägerl, R. Grimm,
Physical Review Letters 100 (2008).
date_created: 2018-12-11T11:49:49Z
date_published: 2008-02-29T00:00:00Z
date_updated: 2021-01-12T06:47:50Z
day: '29'
doi: 10.1103/PhysRevLett.100.083002
extern: '1'
external_id:
arxiv:
- '0710.4052'
intvolume: ' 100'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0710.4052
month: '02'
oa: 1
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6352'
status: public
title: Metastable feshbach molecules in high rotational states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2008'
...
---
_id: '1039'
abstract:
- lang: eng
text: Molecular cooling techniques face the hurdle of dissipating translational
as well as internal energy in the presence of a rich electronic, vibrational,
and rotational energy spectrum. In our experiment, we create a translationally
ultracold, dense quantum gas of molecules bound by more than 1000 wave numbers
in the electronic ground state. Specifically, we stimulate with 80% efficiency,
a two-photon transfer of molecules associated on a Feshbach resonance from a Bose-Einstein
condensate of cesium atoms. In the process, the initial loose, long-range electrostatic
bond of the Feshbach molecule is coherently transformed into a tight chemical
bond. We demonstrate coherence of the transfer in a Ramsey-type experiment and
show that the molecular sample is not heated during the transfer. Our results
show that the preparation of a quantum gas of molecules in specific rovibrational
states is possible and that the creation of a Bose-Einstein condensate of molecules
in their rovibronic ground state is within reach.
acknowledgement: " We thank the team of J. Hecker Denschlag, the LevT team in our
group, and T. Bergeman for very helpful discussions and M. Prevedelli for technical
assistance. We are indebted to R. Grimm for generous support and gratefully acknowledge
funding by the Austrian Ministry of Science and Research (Bundesministerium für
Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der
wissenschaftlichen Forschung) in the form of a START prize grant and by the European
Science Foundation in the framework of the EuroQUAM collective research project
QuDipMol.\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Nadia
full_name: Bouloufa, Nadia
last_name: Bouloufa
- first_name: Olivier
full_name: Dulieu, Olivier
last_name: Dulieu
- first_name: Helmut
full_name: Ritsch, Helmut
last_name: Ritsch
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: Danzl JG, Haller E, Gustavsson M, et al. Quantum gas of deeply bound ground
state molecules. Science. 2008;321(5892):1062-1066. doi:10.1126/science.1159909
apa: Danzl, J. G., Haller, E., Gustavsson, M., Mark, M., Hart, R., Bouloufa, N.,
… Nägerl, H. (2008). Quantum gas of deeply bound ground state molecules. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1159909
chicago: Danzl, Johann G, Elmar Haller, Mattias Gustavsson, Manfred Mark, Russell
Hart, Nadia Bouloufa, Olivier Dulieu, Helmut Ritsch, and Hanns Nägerl. “Quantum
Gas of Deeply Bound Ground State Molecules.” Science. American Association
for the Advancement of Science, 2008. https://doi.org/10.1126/science.1159909.
ieee: J. G. Danzl et al., “Quantum gas of deeply bound ground state molecules,”
Science, vol. 321, no. 5892. American Association for the Advancement of
Science, pp. 1062–1066, 2008.
ista: Danzl JG, Haller E, Gustavsson M, Mark M, Hart R, Bouloufa N, Dulieu O, Ritsch
H, Nägerl H. 2008. Quantum gas of deeply bound ground state molecules. Science.
321(5892), 1062–1066.
mla: Danzl, Johann G., et al. “Quantum Gas of Deeply Bound Ground State Molecules.”
Science, vol. 321, no. 5892, American Association for the Advancement of
Science, 2008, pp. 1062–66, doi:10.1126/science.1159909.
short: J.G. Danzl, E. Haller, M. Gustavsson, M. Mark, R. Hart, N. Bouloufa, O. Dulieu,
H. Ritsch, H. Nägerl, Science 321 (2008) 1062–1066.
date_created: 2018-12-11T11:49:49Z
date_published: 2008-08-22T00:00:00Z
date_updated: 2021-01-12T06:47:50Z
day: '22'
doi: 10.1126/science.1159909
extern: '1'
external_id:
arxiv:
- '0806.2284'
intvolume: ' 321'
issue: '5892'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0806.2284
month: '08'
oa: 1
oa_version: None
page: 1062 - 1066
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6351'
status: public
title: Quantum gas of deeply bound ground state molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 321
year: '2008'
...
---
_id: '9457'
abstract:
- lang: eng
text: Eukaryotic chromatin is separated into functional domains differentiated by
posttranslational histone modifications, histone variants, and DNA methylation1–6.
Methylation is associated with repression of transcriptional initiation in plants
and animals, and is frequently found in transposable elements. Proper methylation
patterns are critical for eukaryotic development4,5, and aberrant methylation-induced
silencing of tumor suppressor genes is a common feature of human cancer7. In contrast
to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1
ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20.
How DNA methylation and H2A.Z influence transcription remains largely unknown.
Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation
are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of
DNA methylation in the bodies of actively transcribed genes and in methylated
transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses
and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition,
while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads
to genome-wide hypermethylation. Our findings indicate that DNA methylation can
influence chromatin structure and effect gene silencing by excluding H2A.Z, and
that H2A.Z protects genes from DNA methylation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA
methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129.
doi:10.1038/nature07324
apa: Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008).
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature.
Springer Nature. https://doi.org/10.1038/nature07324
chicago: Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff.
“Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”
Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324.
ieee: D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks,” Nature,
vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.
ista: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218),
125–129.
mla: Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic
Chromatin Marks.” Nature, vol. 456, no. 7218, Springer Nature, 2008, pp.
125–29, doi:10.1038/nature07324.
short: D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008)
125–129.
date_created: 2021-06-04T11:49:32Z
date_published: 2008-11-06T00:00:00Z
date_updated: 2021-12-14T08:54:36Z
day: '06'
department:
- _id: DaZi
doi: 10.1038/nature07324
extern: '1'
external_id:
pmid:
- '18815594'
intvolume: ' 456'
issue: '7218'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/
month: '11'
oa: 1
oa_version: Submitted Version
page: 125-129
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 456
year: '2008'
...
---
_id: '965'
abstract:
- lang: eng
text: We give many examples of applying Bogoliubov's forest formula to iterative
solutions of various nonlinear equations. The same formula describes an extremely
wide class of objects, from an ordinary quadratic equation to renormalization
in quantum field theory.
acknowledgement: |-
This work is supported in part by the Dynasty Foundation (M. N. S.), the
Russian Foundation for Basic Research (Grant No
s. 07-02-00878 and 07-02-00645), a joint grant (Grant
No. 06-01-92059-CE), the NWO (Project No. 047.011.2004.026), INTAS (Grant No. 05-1000008-7865), the
Program for Supporting Leading Scientific School
s (Grant No. NSh-8004.2006.2), and also by a project
(Project No. ANR-05-BLAN-0029-01, A. Yu. M.).
author:
- first_name: Alexei
full_name: Morozov, Alexei Y
last_name: Morozov
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Morozov A, Serbyn M. Nonlinear algebra and Bogoliubov’s recursion. Theoretical
and Mathematical Physics. 2008;154(2):270-293. doi:10.1007/s11232-008-0026-7
apa: Morozov, A., & Serbyn, M. (2008). Nonlinear algebra and Bogoliubov’s recursion.
Theoretical and Mathematical Physics. Elsevier. https://doi.org/10.1007/s11232-008-0026-7
chicago: Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s
Recursion.” Theoretical and Mathematical Physics. Elsevier, 2008. https://doi.org/10.1007/s11232-008-0026-7.
ieee: A. Morozov and M. Serbyn, “Nonlinear algebra and Bogoliubov’s recursion,”
Theoretical and Mathematical Physics, vol. 154, no. 2. Elsevier, pp. 270–293,
2008.
ista: Morozov A, Serbyn M. 2008. Nonlinear algebra and Bogoliubov’s recursion. Theoretical
and Mathematical Physics. 154(2), 270–293.
mla: Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.”
Theoretical and Mathematical Physics, vol. 154, no. 2, Elsevier, 2008,
pp. 270–93, doi:10.1007/s11232-008-0026-7.
short: A. Morozov, M. Serbyn, Theoretical and Mathematical Physics 154 (2008) 270–293.
date_created: 2018-12-11T11:49:26Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:17Z
day: '01'
doi: 10.1007/s11232-008-0026-7
extern: 1
intvolume: ' 154'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/hep-th/0703258
month: '01'
oa: 1
page: 270 - 293
publication: Theoretical and Mathematical Physics
publication_status: published
publisher: Elsevier
publist_id: '6437'
quality_controlled: 0
status: public
title: Nonlinear algebra and Bogoliubov's recursion
type: journal_article
volume: 154
year: '2008'
...
---
_id: '3435'
abstract:
- lang: eng
text: We develop a new method for estimating effective population sizes, Ne, and
selection coefficients, s, from time-series data of allele frequencies sampled
from a single diallelic locus. The method is based on calculating transition probabilities,
using a numerical solution of the diffusion process, and assuming independent
binomial sampling from this diffusion process at each time point. We apply the
method in two example applications. First, we estimate selection coefficients
acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary
and ancient human DNA. We show that the data are compatible with the assumption
of s = 0, although moderate amounts of selection acting on this mutation cannot
be excluded. In our second example, we estimate the selection coefficient acting
on a mutation segregating in an experimental phage population. We show that the
selection coefficient acting on this mutation is ~0.43.
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Thomas
full_name: York, Thomas L
last_name: York
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency
Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019
apa: Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From
Temporal Allele Frequency Data. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.107.085019
chicago: Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes
From Temporal Allele Frequency Data.” Genetics. Genetics Society of America,
2008. https://doi.org/10.1534/genetics.107.085019.
ieee: J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal
Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of
America, pp. 497–502, 2008.
ista: Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele
Frequency Data. Genetics. 179(1), 497–502.
mla: Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency
Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp.
497–502, doi:10.1534/genetics.107.085019.
short: J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.
date_created: 2018-12-11T12:03:19Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1534/genetics.107.085019
extern: 1
intvolume: ' 179'
issue: '1'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626
month: '05'
oa: 1
page: 497 - 502
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2965'
quality_controlled: 0
status: public
title: Estimation of 2Nes From Temporal Allele Frequency Data
type: journal_article
volume: 179
year: '2008'
...
---
_id: '3504'
abstract:
- lang: eng
text: "Simulation and bisimulation metrics for stochastic systems provide a quantitative
gen- eralization of the classical simulation and bisimulation relations. These
metrics capture the similarity of states with respect to quantitative specifications
written in the quantitative μ-calculus and related probabilistic logics.\r\nWe
present algorithms for computing the metrics on Markov decision processes (MDPs),
turn- based stochastic games, and concurrent games. For turn-based games and MDPs,
we provide a polynomial-time algorithm based on linear programming for the computation
of the one-step metric distance between states. The algorithm improves on the
previously known exponential-time algo- rithm based on a reduction to the theory
of reals. We then present PSPACE algorithms for both the decision problem and
the problem of approximating the metric distance between two states, matching
the best known bound for Markov chains. For the bisimulation kernel of the metric,
which corresponds to probabilistic bisimulation, our algorithm works in time O(n4)
for both turn-based games and MDPs; improving the previously best known O(n9 ·
log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing
the exact distance between states is at least as hard as computing the value of
concurrent reachability games and the square-root-sum problem in computational
geometry. We show that checking whether the metric distance is bounded by a rational
r, can be accomplished via a reduction to the theory of real closed fields, involving
a\r\nformula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity,
improving the previously known reduction with O(|G|O(|G|7)) time complexity. These
algorithms can be iterated\r\nto approximate the metrics using binary search."
acknowledgement: This research was supported in part by the NSF grants CCR-0132780
and CNS-0720884.
alternative_title:
- LIPIcs
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics.
In: Vol 2. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:107-118. doi:10.4230/LIPIcs.FSTTCS.2008.1745'
apa: 'Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2008). Algorithms
for game metrics (Vol. 2, pp. 107–118). Presented at the FSTTCS: Foundations of
Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath
Raman. “Algorithms for Game Metrics,” 2:107–18. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2008. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745.
ieee: 'K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game
metrics,” presented at the FSTTCS: Foundations of Software Technology and Theoretical
Computer Science, 2008, vol. 2, pp. 107–118.'
ista: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2008. Algorithms for game
metrics. FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
LIPIcs, vol. 2, 107–118.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Game Metrics. Vol. 2,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–18, doi:10.4230/LIPIcs.FSTTCS.2008.1745.
short: K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2008, pp. 107–118.
conference:
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
date_created: 2018-12-11T12:03:40Z
date_published: 2008-12-05T00:00:00Z
date_updated: 2023-02-23T11:46:14Z
day: '05'
ddc:
- '000'
doi: 10.4230/LIPIcs.FSTTCS.2008.1745
extern: '1'
file:
- access_level: open_access
checksum: 0a447454a24e273f7ddf51dbfe47f877
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:01:21Z
date_updated: 2020-07-14T12:46:12Z
file_id: '6398'
file_name: 2008_LIPIcs_Chatterjee.pdf
file_size: 442139
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 107 - 118
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2883'
quality_controlled: '1'
related_material:
record:
- id: '3868'
relation: later_version
status: public
status: public
title: Algorithms for game metrics
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2008'
...
---
_id: '3734'
abstract:
- lang: eng
text: Gene expression levels fluctuate even under constant external conditions.
Much emphasis has usually been placed on the components of this noise that are
due to randomness in transcription and translation. Here we focus on the role
of noise associated with the inputs to transcriptional regulation; in particular,
we analyze the effects of random arrival times and binding of transcription factors
to their target sites along the genome. This contribution to the total noise sets
a fundamental physical limit to the reliability of genetic control, and has clear
signatures, but we show that these are easily obscured by experimental limitations
and even by conventional methods for plotting the variance vs. mean expression
level. We argue that simple, universal models of noise dominated by transcription
and translation are inconsistent with the embedding of gene expression in a network
of regulatory interactions. Analysis of recent experiments on transcriptional
control in the early Drosophila embryo shows that these results are quantitatively
consistent with the predicted signatures of input noise, and we discuss the experiments
needed to test the importance of input noise more generally.
acknowledgement: NSF Grant PHY-0650617; NIH grants P50 GM071508, R01 GM077599; Burroughs
Wellcome Program in Biological Dynamics
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation.
PLoS One. 2008;3(7). doi:10.1371/journal.pone.0002774
apa: Tkačik, G., Gregor, T., & Bialek, W. (2008). The role of input noise in
transcriptional regulation. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002774
chicago: Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise
in Transcriptional Regulation.” PLoS One. Public Library of Science, 2008.
https://doi.org/10.1371/journal.pone.0002774.
ieee: G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional
regulation,” PLoS One, vol. 3, no. 7. Public Library of Science, 2008.
ista: Tkačik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional
regulation. PLoS One. 3(7).
mla: Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.”
PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
short: G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).
date_created: 2018-12-11T12:04:52Z
date_published: 2008-07-23T00:00:00Z
date_updated: 2021-01-12T07:51:49Z
day: '23'
doi: 10.1371/journal.pone.0002774
extern: 1
intvolume: ' 3'
issue: '7'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475664
month: '07'
oa: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2498'
quality_controlled: 0
status: public
title: The role of input noise in transcriptional regulation
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
volume: 3
year: '2008'
...
---
_id: '3740'
abstract:
- lang: eng
text: In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it should
be possible to transmit much more than just one regulatory bit. Realizing this
optimal information capacity would require that the dynamic range of TF concentrations
used by the cell, the input/output relation of the regulatory module, and the
noise in gene expression satisfy certain matching relations, which we derive.
These results provide parameter-free, quantitative predictions connecting independently
measurable quantities. Although we have considered only the simplified problem
of a single gene responding to a single TF, we find that these predictions are
in surprisingly good agreement with recent experiments on the Bicoid/Hunchback
system in the early Drosophila embryo and that this system achieves approximately
90% of its theoretical maximum information transmission.
acknowledgement: P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS
NIH HHS/United States
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional
regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization
in transcriptional regulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0806077105
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and
Optimization in Transcriptional Regulation.” PNAS. National Academy of
Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in
transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of
Sciences, pp. 12265–12270, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional
regulation. PNAS. 105(34), 12265–12270.
mla: Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional
Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008,
pp. 12265–70, doi:10.1073/pnas.0806077105.
short: G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.
date_created: 2018-12-11T12:04:54Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '01'
doi: 10.1073/pnas.0806077105
extern: 1
intvolume: ' 105'
issue: '34'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900
month: '01'
oa: 1
page: 12265 - 12270
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2489'
quality_controlled: 0
status: public
title: Information flow and optimization in transcriptional regulation
type: journal_article
volume: 105
year: '2008'
...