---
_id: '1462'
abstract:
- lang: eng
  text: A Fourier transform technique is introduced for counting the number of solutions
    of holomorphic moment map equations over a finite field. This technique in turn
    gives information on Betti numbers of holomorphic symplectic quotients. As a consequence,
    simple unified proofs are obtained for formulas of Poincaré polynomials of toric
    hyperkähler varieties (recovering results of Bielawski-Dancer and Hausel-Sturmfels),
    Poincaré polynomials of Hubert schemes of points and twisted Atiyah-Drinfeld-Hitchin-Manin
    (ADHM) spaces of instantons on ℂ2 (recovering results of Nakajima-Yoshioka), and
    Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof
    of a conjecture of Kac on the number of absolutely indecomposable representations
    of a quiver is announced.
acknowledgement: This work was supported by a Royal Society University Research Fellowship,
  National Science Foundation Grant DMS-0305505, an Alfred P. Sloan Research Fellowship,
  and a Summer Research Assignment of the University of Texas at Austin.
author:
- first_name: Tamas
  full_name: Tamas Hausel
  id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
  last_name: Hausel
citation:
  ama: Hausel T. Betti numbers of holomorphic symplectic quotients via arithmetic
    Fourier transform. <i>PNAS</i>. 2006;103(16):6120-6124. doi:<a href="https://doi.org/10.1073/pnas.0601337103">10.1073/pnas.0601337103</a>
  apa: Hausel, T. (2006). Betti numbers of holomorphic symplectic quotients via arithmetic
    Fourier transform. <i>PNAS</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.0601337103">https://doi.org/10.1073/pnas.0601337103</a>
  chicago: Hausel, Tamás. “Betti Numbers of Holomorphic Symplectic Quotients via Arithmetic
    Fourier Transform.” <i>PNAS</i>. National Academy of Sciences, 2006. <a href="https://doi.org/10.1073/pnas.0601337103">https://doi.org/10.1073/pnas.0601337103</a>.
  ieee: T. Hausel, “Betti numbers of holomorphic symplectic quotients via arithmetic
    Fourier transform,” <i>PNAS</i>, vol. 103, no. 16. National Academy of Sciences,
    pp. 6120–6124, 2006.
  ista: Hausel T. 2006. Betti numbers of holomorphic symplectic quotients via arithmetic
    Fourier transform. PNAS. 103(16), 6120–6124.
  mla: Hausel, Tamás. “Betti Numbers of Holomorphic Symplectic Quotients via Arithmetic
    Fourier Transform.” <i>PNAS</i>, vol. 103, no. 16, National Academy of Sciences,
    2006, pp. 6120–24, doi:<a href="https://doi.org/10.1073/pnas.0601337103">10.1073/pnas.0601337103</a>.
  short: T. Hausel, PNAS 103 (2006) 6120–6124.
date_created: 2018-12-11T11:52:10Z
date_published: 2006-04-18T00:00:00Z
date_updated: 2021-01-12T06:50:55Z
day: '18'
doi: 10.1073/pnas.0601337103
extern: 1
intvolume: '       103'
issue: '16'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/math/0511163
month: '04'
oa: 1
page: 6120 - 6124
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5734'
quality_controlled: 0
status: public
title: Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform
type: journal_article
volume: 103
year: '2006'
...
---
_id: '13428'
abstract:
- lang: eng
  text: Mixtures of oppositely charged nanoparticles of various sizes and charge ratios
    precipitate only at the point of electroneutrality. This phenomenonspecific to
    the nanoscale and reminiscent of threshold precipitation of ionsis a consequence
    of the formation of core-and-shell nanoparticle aggregates, in which the shells
    are composed of like-charged particles and are stabilized by efficient electrostatic
    screening.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander M.
  full_name: Kalsin, Alexander M.
  last_name: Kalsin
- first_name: Bartlomiej
  full_name: Kowalczyk, Bartlomiej
  last_name: Kowalczyk
- first_name: Stoyan K.
  full_name: Smoukov, Stoyan K.
  last_name: Smoukov
- first_name: Rafal
  full_name: Klajn, Rafal
  id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
  last_name: Klajn
- first_name: Bartosz A.
  full_name: Grzybowski, Bartosz A.
  last_name: Grzybowski
citation:
  ama: Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. Ionic-like behavior
    of oppositely charged nanoparticles. <i>Journal of the American Chemical Society</i>.
    2006;128(47):15046-15047. doi:<a href="https://doi.org/10.1021/ja0642966">10.1021/ja0642966</a>
  apa: Kalsin, A. M., Kowalczyk, B., Smoukov, S. K., Klajn, R., &#38; Grzybowski,
    B. A. (2006). Ionic-like behavior of oppositely charged nanoparticles. <i>Journal
    of the American Chemical Society</i>. American Chemical Society. <a href="https://doi.org/10.1021/ja0642966">https://doi.org/10.1021/ja0642966</a>
  chicago: Kalsin, Alexander M., Bartlomiej Kowalczyk, Stoyan K. Smoukov, Rafal Klajn,
    and Bartosz A. Grzybowski. “Ionic-like Behavior of Oppositely Charged Nanoparticles.”
    <i>Journal of the American Chemical Society</i>. American Chemical Society, 2006.
    <a href="https://doi.org/10.1021/ja0642966">https://doi.org/10.1021/ja0642966</a>.
  ieee: A. M. Kalsin, B. Kowalczyk, S. K. Smoukov, R. Klajn, and B. A. Grzybowski,
    “Ionic-like behavior of oppositely charged nanoparticles,” <i>Journal of the American
    Chemical Society</i>, vol. 128, no. 47. American Chemical Society, pp. 15046–15047,
    2006.
  ista: Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. 2006. Ionic-like
    behavior of oppositely charged nanoparticles. Journal of the American Chemical
    Society. 128(47), 15046–15047.
  mla: Kalsin, Alexander M., et al. “Ionic-like Behavior of Oppositely Charged Nanoparticles.”
    <i>Journal of the American Chemical Society</i>, vol. 128, no. 47, American Chemical
    Society, 2006, pp. 15046–47, doi:<a href="https://doi.org/10.1021/ja0642966">10.1021/ja0642966</a>.
  short: A.M. Kalsin, B. Kowalczyk, S.K. Smoukov, R. Klajn, B.A. Grzybowski, Journal
    of the American Chemical Society 128 (2006) 15046–15047.
date_created: 2023-08-01T10:36:27Z
date_published: 2006-11-29T00:00:00Z
date_updated: 2023-08-08T11:30:06Z
day: '29'
doi: 10.1021/ja0642966
extern: '1'
external_id:
  pmid:
  - '17117829'
intvolume: '       128'
issue: '47'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '11'
oa_version: None
page: 15046-15047
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
  eissn:
  - 1520-5126
  issn:
  - 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ionic-like behavior of oppositely charged nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2006'
...
---
_id: '13429'
abstract:
- lang: eng
  text: 'The fruitful core: Organic syntheses reported in the literature from 1850
    to 2004 are analyzed with mathematical tools from network theory and statistical
    physics. There is a set of substances (the core) from which the majority of other
    organic compounds can be made (see picture; red: core, blue: periphery, green:
    islands). Search algorithms are used to identify small optimal sets of maximally
    useful chemicals.'
article_processing_charge: No
article_type: original
author:
- first_name: Kyle J. M.
  full_name: Bishop, Kyle J. M.
  last_name: Bishop
- first_name: Rafal
  full_name: Klajn, Rafal
  id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
  last_name: Klajn
- first_name: Bartosz A.
  full_name: Grzybowski, Bartosz A.
  last_name: Grzybowski
citation:
  ama: Bishop KJM, Klajn R, Grzybowski BA. The core and most useful molecules in organic
    chemistry. <i>Angewandte Chemie International Edition</i>. 2006;45(32):5348-5354.
    doi:<a href="https://doi.org/10.1002/anie.200600881">10.1002/anie.200600881</a>
  apa: Bishop, K. J. M., Klajn, R., &#38; Grzybowski, B. A. (2006). The core and most
    useful molecules in organic chemistry. <i>Angewandte Chemie International Edition</i>.
    Wiley. <a href="https://doi.org/10.1002/anie.200600881">https://doi.org/10.1002/anie.200600881</a>
  chicago: Bishop, Kyle J. M., Rafal Klajn, and Bartosz A. Grzybowski. “The Core and
    Most Useful Molecules in Organic Chemistry.” <i>Angewandte Chemie International
    Edition</i>. Wiley, 2006. <a href="https://doi.org/10.1002/anie.200600881">https://doi.org/10.1002/anie.200600881</a>.
  ieee: K. J. M. Bishop, R. Klajn, and B. A. Grzybowski, “The core and most useful
    molecules in organic chemistry,” <i>Angewandte Chemie International Edition</i>,
    vol. 45, no. 32. Wiley, pp. 5348–5354, 2006.
  ista: Bishop KJM, Klajn R, Grzybowski BA. 2006. The core and most useful molecules
    in organic chemistry. Angewandte Chemie International Edition. 45(32), 5348–5354.
  mla: Bishop, Kyle J. M., et al. “The Core and Most Useful Molecules in Organic Chemistry.”
    <i>Angewandte Chemie International Edition</i>, vol. 45, no. 32, Wiley, 2006,
    pp. 5348–54, doi:<a href="https://doi.org/10.1002/anie.200600881">10.1002/anie.200600881</a>.
  short: K.J.M. Bishop, R. Klajn, B.A. Grzybowski, Angewandte Chemie International
    Edition 45 (2006) 5348–5354.
date_created: 2023-08-01T10:37:16Z
date_published: 2006-08-11T00:00:00Z
date_updated: 2023-08-08T11:31:27Z
day: '11'
doi: 10.1002/anie.200600881
extern: '1'
external_id:
  pmid:
  - '16835857'
intvolume: '        45'
issue: '32'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '08'
oa_version: None
page: 5348-5354
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
  eissn:
  - 1521-3773
  issn:
  - 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The core and most useful molecules in organic chemistry
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2006'
...
---
_id: '13430'
abstract:
- lang: eng
  text: Dynamic self-assembly (DySA) processes occurring outside of thermodynamic
    equilibrium underlie many forms of adaptive and intellligent behaviors in natural
    systems. Relatively little, however, is known about the principles that govern
    DySA and the ways in which it can be extended to artificial ensembles. This article
    discusses recent advances in both the theory and the practice of nonequilibrium
    self-assembly. It is argued that a union of ideas from thermodynamics and dynamic
    systems' theory can provide a general description of DySA. In parallel, heuristic
    design rules can be used to construct DySA systems of increasing complexities
    based on a variety of suitable interactions/potentials on length scales from nanoscopic
    to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also
    discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Marcin
  full_name: Fialkowski, Marcin
  last_name: Fialkowski
- first_name: Kyle J. M.
  full_name: Bishop, Kyle J. M.
  last_name: Bishop
- first_name: Rafal
  full_name: Klajn, Rafal
  id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
  last_name: Klajn
- first_name: Stoyan K.
  full_name: Smoukov, Stoyan K.
  last_name: Smoukov
- first_name: Christopher J.
  full_name: Campbell, Christopher J.
  last_name: Campbell
- first_name: Bartosz A.
  full_name: Grzybowski, Bartosz A.
  last_name: Grzybowski
citation:
  ama: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA.
    Principles and implementations of dissipative (dynamic) self-assembly. <i>The
    Journal of Physical Chemistry B</i>. 2006;110(6):2482-2496. doi:<a href="https://doi.org/10.1021/jp054153q">10.1021/jp054153q</a>
  apa: Fialkowski, M., Bishop, K. J. M., Klajn, R., Smoukov, S. K., Campbell, C. J.,
    &#38; Grzybowski, B. A. (2006). Principles and implementations of dissipative
    (dynamic) self-assembly. <i>The Journal of Physical Chemistry B</i>. American
    Chemical Society. <a href="https://doi.org/10.1021/jp054153q">https://doi.org/10.1021/jp054153q</a>
  chicago: Fialkowski, Marcin, Kyle J. M. Bishop, Rafal Klajn, Stoyan K. Smoukov,
    Christopher J. Campbell, and Bartosz A. Grzybowski. “Principles and Implementations
    of Dissipative (Dynamic) Self-Assembly.” <i>The Journal of Physical Chemistry
    B</i>. American Chemical Society, 2006. <a href="https://doi.org/10.1021/jp054153q">https://doi.org/10.1021/jp054153q</a>.
  ieee: M. Fialkowski, K. J. M. Bishop, R. Klajn, S. K. Smoukov, C. J. Campbell, and
    B. A. Grzybowski, “Principles and implementations of dissipative (dynamic) self-assembly,”
    <i>The Journal of Physical Chemistry B</i>, vol. 110, no. 6. American Chemical
    Society, pp. 2482–2496, 2006.
  ista: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA.
    2006. Principles and implementations of dissipative (dynamic) self-assembly. The
    Journal of Physical Chemistry B. 110(6), 2482–2496.
  mla: Fialkowski, Marcin, et al. “Principles and Implementations of Dissipative (Dynamic)
    Self-Assembly.” <i>The Journal of Physical Chemistry B</i>, vol. 110, no. 6, American
    Chemical Society, 2006, pp. 2482–96, doi:<a href="https://doi.org/10.1021/jp054153q">10.1021/jp054153q</a>.
  short: M. Fialkowski, K.J.M. Bishop, R. Klajn, S.K. Smoukov, C.J. Campbell, B.A.
    Grzybowski, The Journal of Physical Chemistry B 110 (2006) 2482–2496.
date_created: 2023-08-01T10:37:35Z
date_published: 2006-01-25T00:00:00Z
date_updated: 2023-08-08T11:33:08Z
day: '25'
doi: 10.1021/jp054153q
extern: '1'
external_id:
  pmid:
  - '16471845'
intvolume: '       110'
issue: '6'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '01'
oa_version: None
page: 2482-2496
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
  issn:
  - 1520-6106
  - 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Principles and implementations of dissipative (dynamic) self-assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2006'
...
---
_id: '903'
abstract:
- lang: eng
  text: 'Background: Carcinogenesis typically involves multiple somatic mutations
    in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes.
    Analysis of mutation spectra of the tumor suppressor that is most commonly mutated
    in human cancers, p53, unexpectedly suggested that somatic evolution of the p53
    gene during tumorigenesis is dominated by positive selection for gain of function.
    This conclusion is supported by accumulating experimental evidence of evolution
    of new functions of p53 in tumors. These findings prompted a genome-wide analysis
    of possible positive selection during tumor evolution. Methods: A comprehensive
    analysis of probable somatic mutations in the sequences of Expressed Sequence
    Tags (ESTs) from malignant tumors and normal tissues was performed in order to
    access the prevalence of positive selection in cancer evolution. For each EST,
    the numbers of synonymous and non-synonymous substitutions were calculated. In
    order to identify genes with a signature of positive selection in cancers, these
    numbers were compared to: i) expected numbers and ii) the numbers for the respective
    genes in the ESTs from normal tissues. Results: We identified 112 genes with a
    signature of positive selection in cancers, i.e., a significantly elevated ratio
    of non-synonymous to synonymous substitutions, in tumors as compared to 37 such
    genes in an approximately equal-sized EST collection from normal tissues. A substantial
    fraction of the tumor-specific positive-selection candidates have experimentally
    demonstrated or strongly predicted links to cancer. Conclusion: The results of
    EST analysis should be interpreted with extreme caution given the noise introduced
    by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation
    of EST analysis is that multiple mutations amenable to statistical analysis can
    be detected only in relatively highly expressed genes. Nevertheless, the present
    results suggest that positive selection might affect a substantial number of genes
    during tumorigenic somatic evolution.'
acknowledgement: This work was supported by the Intramural Research Program of the
  National Library of Medicine at the National Institutes of Health/DHHS. FAK is an
  NSF Graduate Fellow. We thank Yuri Pavlov for helpful discussions.
author:
- first_name: Vladimir
  full_name: Babenko, Vladimir N
  last_name: Babenko
- first_name: Malay
  full_name: Basu, Malay K
  last_name: Basu
- first_name: Fyodor
  full_name: Fyodor Kondrashov
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Igor
  full_name: Rogozin, Igor B
  last_name: Rogozin
- first_name: Eugene
  full_name: Koonin, Eugene V
  last_name: Koonin
citation:
  ama: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. Signs of positive selection
    of somatic mutations in human cancers detected by EST sequence analysis. <i>BMC
    Cancer</i>. 2006;6. doi:<a href="https://doi.org/10.1186/1471-2407-6-36">10.1186/1471-2407-6-36</a>
  apa: Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., &#38; Koonin, E. (2006).
    Signs of positive selection of somatic mutations in human cancers detected by
    EST sequence analysis. <i>BMC Cancer</i>. BioMed Central. <a href="https://doi.org/10.1186/1471-2407-6-36">https://doi.org/10.1186/1471-2407-6-36</a>
  chicago: Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene
    Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected
    by EST Sequence Analysis.” <i>BMC Cancer</i>. BioMed Central, 2006. <a href="https://doi.org/10.1186/1471-2407-6-36">https://doi.org/10.1186/1471-2407-6-36</a>.
  ieee: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive
    selection of somatic mutations in human cancers detected by EST sequence analysis,”
    <i>BMC Cancer</i>, vol. 6. BioMed Central, 2006.
  ista: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive
    selection of somatic mutations in human cancers detected by EST sequence analysis.
    BMC Cancer. 6.
  mla: Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations
    in Human Cancers Detected by EST Sequence Analysis.” <i>BMC Cancer</i>, vol. 6,
    BioMed Central, 2006, doi:<a href="https://doi.org/10.1186/1471-2407-6-36">10.1186/1471-2407-6-36</a>.
  short: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006).
date_created: 2018-12-11T11:49:07Z
date_published: 2006-02-09T00:00:00Z
date_updated: 2021-01-12T08:21:47Z
day: '09'
doi: 10.1186/1471-2407-6-36
extern: 1
intvolume: '         6'
month: '02'
publication: BMC Cancer
publication_status: published
publisher: BioMed Central
publist_id: '6744'
quality_controlled: 0
status: public
title: Signs of positive selection of somatic mutations in human cancers detected
  by EST sequence analysis
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: 6
year: '2006'
...
---
_id: '9505'
abstract:
- lang: eng
  text: 'Cytosine methylation, a common form of DNA modification that antagonizes
    transcription, is found at transposons and repeats in vertebrates, plants and
    fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana
    genome at high resolution. DNA methylation covers transposons and is present within
    a large fraction of A. thaliana genes. Methylation within genes is conspicuously
    biased away from gene ends, suggesting a dependence on RNA polymerase transit.
    Genic methylation is strongly influenced by transcription: moderately transcribed
    genes are most likely to be methylated, whereas genes at either extreme are least
    likely. In turn, transcription is influenced by methylation: short methylated
    genes are poorly expressed, and loss of methylation in the body of a gene leads
    to enhanced transcription. Our results indicate that genic transcription and DNA
    methylation are closely interwoven processes.'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Mary
  full_name: Gehring, Mary
  last_name: Gehring
- first_name: Robert K.
  full_name: Tran, Robert K.
  last_name: Tran
- first_name: Tracy
  full_name: Ballinger, Tracy
  last_name: Ballinger
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis
    of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation
    and transcription. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href="https://doi.org/10.1038/ng1929">10.1038/ng1929</a>
  apa: Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S.
    (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers
    an interdependence between methylation and transcription. <i>Nature Genetics</i>.
    Nature Publishing Group. <a href="https://doi.org/10.1038/ng1929">https://doi.org/10.1038/ng1929</a>
  chicago: Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven
    Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers
    an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>.
    Nature Publishing Group, 2006. <a href="https://doi.org/10.1038/ng1929">https://doi.org/10.1038/ng1929</a>.
  ieee: D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide
    analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
    methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature
    Publishing Group, pp. 61–69, 2006.
  ista: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide
    analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
    methylation and transcription. Nature Genetics. 39(1), 61–69.
  mla: Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA
    Methylation Uncovers an Interdependence between Methylation and Transcription.”
    <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69,
    doi:<a href="https://doi.org/10.1038/ng1929">10.1038/ng1929</a>.
  short: D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics
    39 (2006) 61–69.
date_created: 2021-06-07T12:19:31Z
date_published: 2006-11-26T00:00:00Z
date_updated: 2021-12-14T09:02:51Z
day: '26'
department:
- _id: DaZi
doi: 10.1038/ng1929
extern: '1'
external_id:
  pmid:
  - '17128275'
intvolume: '        39'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 61-69
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence
  between methylation and transcription
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2006'
...
---
_id: '1033'
abstract:
- lang: eng
  text: Systems of three interacting particles are notorious for their complex physical
    behaviour. A landmark theoretical result in few-body quantum physics is Efimov\'s
    prediction1,2 of a universal set of bound trimer states appearing for three identical
    bosons with a resonant two-body interaction. Counterintuitively, these states
    even exist in the absence of a corresponding two-body bound state. Since the formulation
    of Efimov\'s problem in the context of nuclear physics 35 years ago, it has attracted
    great interest in many areas of physics3-8. However, the observation of Efimov
    quantum states has remained an elusive goal3,5. Here we report the observation
    of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs
    in the range of large negative two-body scattering lengths, arising from the coupling
    of three free atoms to an Efimov trimer. Experimentally, we observe its signature
    as a giant three-body recombination loss9,10 when the strength of the two-body
    interaction is varied. We also detect a minimum 9,11,12 in the recombination loss
    for positive scattering lengths, indicating destructive interference of decay
    pathways. Our results confirm central theoretical predictions of Efimov physics
    and represent a starting point with which to explore the universal properties
    of resonantly interacting few-body systems7. While Feshbach resonances13,14 have
    provided the key to control quantum-mechanical interactions on the two-body level,
    Efimov resonances connect ultracold matter15 to the world of few-body quantum
    phenomena.
acknowledgement: "We thank E. Braaten, C. Greene, B. Esry, H. Hammer and T. Ko ̈hler
  for many discussions and E. Kneringer for support regarding the data analysis. We
  acknowledge support by the Austrian Science Fund (FWF) within Spezialforschungsbereich
  15 and within the Lise Meitner programme, and by the\r\nEuropean Union in the frame
  of the TMR networks ‘Cold Molecules’ and ‘FASTNet’. M.M. is supported within the
  Doktorandenprogramm of the Austrian\r\nAcademy of Sciences."
article_processing_charge: No
author:
- first_name: Tobias
  full_name: Kraemer, Tobias
  last_name: Kraemer
- first_name: Michael
  full_name: Mark, Michael
  last_name: Mark
- first_name: Philipp
  full_name: Waldburger, Philipp
  last_name: Waldburger
- 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: Cheng
  full_name: Chin, Cheng
  last_name: Chin
- first_name: Bastian
  full_name: Engeser, Bastian
  last_name: Engeser
- first_name: Adam
  full_name: Lange, Adam
  last_name: Lange
- first_name: Karl
  full_name: Pilch, Karl
  last_name: Pilch
- first_name: Antti
  full_name: Jaakkola, Antti
  last_name: Jaakkola
- first_name: Hanns
  full_name: Nägerl, Hanns
  last_name: Nägerl
- first_name: Rudolf
  full_name: Grimm, Rudolf
  last_name: Grimm
citation:
  ama: Kraemer T, Mark M, Waldburger P, et al. Evidence for Efimov quantum states
    in an ultracold gas of caesium atoms. <i>Nature</i>. 2006;440(7082):315-318. doi:<a
    href="https://doi.org/10.1038/nature04626">10.1038/nature04626</a>
  apa: Kraemer, T., Mark, M., Waldburger, P., Danzl, J. G., Chin, C., Engeser, B.,
    … Grimm, R. (2006). Evidence for Efimov quantum states in an ultracold gas of
    caesium atoms. <i>Nature</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/nature04626">https://doi.org/10.1038/nature04626</a>
  chicago: Kraemer, Tobias, Michael Mark, Philipp Waldburger, Johann G Danzl, Cheng
    Chin, Bastian Engeser, Adam Lange, et al. “Evidence for Efimov Quantum States
    in an Ultracold Gas of Caesium Atoms.” <i>Nature</i>. Nature Publishing Group,
    2006. <a href="https://doi.org/10.1038/nature04626">https://doi.org/10.1038/nature04626</a>.
  ieee: T. Kraemer <i>et al.</i>, “Evidence for Efimov quantum states in an ultracold
    gas of caesium atoms,” <i>Nature</i>, vol. 440, no. 7082. Nature Publishing Group,
    pp. 315–318, 2006.
  ista: Kraemer T, Mark M, Waldburger P, Danzl JG, Chin C, Engeser B, Lange A, Pilch
    K, Jaakkola A, Nägerl H, Grimm R. 2006. Evidence for Efimov quantum states in
    an ultracold gas of caesium atoms. Nature. 440(7082), 315–318.
  mla: Kraemer, Tobias, et al. “Evidence for Efimov Quantum States in an Ultracold
    Gas of Caesium Atoms.” <i>Nature</i>, vol. 440, no. 7082, Nature Publishing Group,
    2006, pp. 315–18, doi:<a href="https://doi.org/10.1038/nature04626">10.1038/nature04626</a>.
  short: T. Kraemer, M. Mark, P. Waldburger, J.G. Danzl, C. Chin, B. Engeser, A. Lange,
    K. Pilch, A. Jaakkola, H. Nägerl, R. Grimm, Nature 440 (2006) 315–318.
date_created: 2018-12-11T11:49:47Z
date_published: 2006-03-16T00:00:00Z
date_updated: 2021-01-12T06:47:48Z
day: '16'
doi: 10.1038/nature04626
extern: '1'
intvolume: '       440'
issue: '7082'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/cond-mat/0512394
month: '03'
oa: 1
oa_version: None
page: 315 - 318
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6356'
status: public
title: Evidence for Efimov quantum states in an ultracold gas of caesium atoms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 440
year: '2006'
...
---
_id: '1034'
abstract:
- lang: eng
  text: Three interacting particles form a system which is well known for its complex
    physical behavior. A landmark theoretical result in few-body quantum physics is
    Efimov\'s prediction of a universal set of weakly bound trimer states appearing
    for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly,
    these states even exist in the absence of a corresponding two-body bound state
    and their precise nature is largely independent of the particular type of the
    two-body interaction potential. Efimov\'s scenario has attracted great interest
    in many areas of physics; an experimental test however has not been achieved.
    We report the observation of an Efimov resonance in an ultracold thermal gas of
    cesium atoms [3]. The resonance occurs in the range of large negative two-body
    scattering lengths and arises from the coupling of three free atoms to an Efimov
    trimer. We observe its signature as a giant three-body recombination loss when
    the strength of the two-body interaction is varied near a Feshbach resonance.
    This resonance develops into a continuum resonance at non-zero collision energies,
    and we observe a shift of the resonance position as a function of temperature.
    We also report on a minimum in the recombination loss for positive scattering
    lengths, indicating destructive interference of decay pathways. Our results confirm
    central theoretical predictions of Efimov physics and represent a starting point
    from which to explore the universal properties of resonantly interacting few-body
    systems.
acknowledgement: "We thank E. Braaten, C. Greene, B. Esry, H. Hammer, and T. Köhl\r\ner
  for many stimulat-\r\ning and fruitful discussions and E. Kneringer for support
  re\r\ngarding the data analysis. We\r\nacknowledge support by the Austrian Science
  Fund (FWF) with\r\nin Spezialforschungs-\r\nbereich 15 and within the Lise Meitner
  program, and by the Eur\r\nopean Union in the frame\r\nof the TMR networks “Cold
  Molecules” and “FASTNet”. M.M. is s\r\nupported within the\r\nDoktorandenprogramm
  of the Austrian Academy of Sciences."
article_processing_charge: No
author:
- first_name: Hanns
  full_name: Nägerl, Hanns
  last_name: Nägerl
- first_name: Tobias
  full_name: Kraemer, Tobias
  last_name: Kraemer
- first_name: Michael
  full_name: Mark, Michael
  last_name: Mark
- first_name: Philipp
  full_name: Waldburger, Philipp
  last_name: Waldburger
- 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: Bastian
  full_name: Engeser, Bastian
  last_name: Engeser
- first_name: Adam
  full_name: Lange, Adam
  last_name: Lange
- first_name: Karl
  full_name: Pilch, Karl
  last_name: Pilch
- first_name: Antti
  full_name: Jaakkola, Antti
  last_name: Jaakkola
- first_name: Cheng
  full_name: Chin, Cheng
  last_name: Chin
- first_name: Rudolf
  full_name: Grimm, Rudolf
  last_name: Grimm
citation:
  ama: 'Nägerl H, Kraemer T, Mark M, et al. Experimental evidence for Efimov quantum
    states. In: Vol 869. AIP; 2006:269-277. doi:<a href="https://doi.org/10.1063/1.2400657">10.1063/1.2400657</a>'
  apa: 'Nägerl, H., Kraemer, T., Mark, M., Waldburger, P., Danzl, J. G., Engeser,
    B., … Grimm, R. (2006). Experimental evidence for Efimov quantum states (Vol.
    869, pp. 269–277). Presented at the ICAP: International Conference on Atomic Physics,
    AIP. <a href="https://doi.org/10.1063/1.2400657">https://doi.org/10.1063/1.2400657</a>'
  chicago: Nägerl, Hanns, Tobias Kraemer, Michael Mark, Philipp Waldburger, Johann
    G Danzl, Bastian Engeser, Adam Lange, et al. “Experimental Evidence for Efimov
    Quantum States,” 869:269–77. AIP, 2006. <a href="https://doi.org/10.1063/1.2400657">https://doi.org/10.1063/1.2400657</a>.
  ieee: 'H. Nägerl <i>et al.</i>, “Experimental evidence for Efimov quantum states,”
    presented at the ICAP: International Conference on Atomic Physics, 2006, vol.
    869, pp. 269–277.'
  ista: 'Nägerl H, Kraemer T, Mark M, Waldburger P, Danzl JG, Engeser B, Lange A,
    Pilch K, Jaakkola A, Chin C, Grimm R. 2006. Experimental evidence for Efimov quantum
    states. ICAP: International Conference on Atomic Physics vol. 869, 269–277.'
  mla: Nägerl, Hanns, et al. <i>Experimental Evidence for Efimov Quantum States</i>.
    Vol. 869, AIP, 2006, pp. 269–77, doi:<a href="https://doi.org/10.1063/1.2400657">10.1063/1.2400657</a>.
  short: H. Nägerl, T. Kraemer, M. Mark, P. Waldburger, J.G. Danzl, B. Engeser, A.
    Lange, K. Pilch, A. Jaakkola, C. Chin, R. Grimm, in:, AIP, 2006, pp. 269–277.
conference:
  name: 'ICAP: International Conference on Atomic Physics'
date_created: 2018-12-11T11:49:48Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T06:47:49Z
day: '01'
doi: 10.1063/1.2400657
extern: '1'
intvolume: '       869'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/cond-mat/0611629
month: '01'
oa: 1
oa_version: None
page: 269 - 277
publication_status: published
publisher: AIP
publist_id: '6355'
status: public
title: Experimental evidence for Efimov quantum states
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 869
year: '2006'
...
---
_id: '11929'
abstract:
- lang: eng
  text: Broder et al.'s [3] shingling algorithm and Charikar's [4] random projection
    based approach are considered "state-of-the-art" algorithms for finding near-duplicate
    web pages. Both algorithms were either developed at or used by popular web search
    engines. We compare the two algorithms on a very large scale, namely on a set
    of 1.6B distinct web pages. The results show that neither of the algorithms works
    well for finding near-duplicate pairs on the same site, while both achieve high
    precision for near-duplicate pairs on different sites. Since Charikar's algorithm
    finds more near-duplicate pairs on different sites, it achieves a better precision
    overall, namely 0.50 versus 0.38 for Broder et al.'s algorithm. We present a combined
    algorithm which achieves precision 0.79 with 79% of the recall of the other algorithms.
article_processing_charge: No
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  ama: 'Henzinger MH. Finding near-duplicate web pages: A large-scale evaluation of
    algorithms. In: <i>29th Annual International ACM SIGIR Conference on Research
    and Development in Information Retrieval</i>. Association for Computing Machinery;
    2006:284-291. doi:<a href="https://doi.org/10.1145/1148170.1148222">10.1145/1148170.1148222</a>'
  apa: 'Henzinger, M. H. (2006). Finding near-duplicate web pages: A large-scale evaluation
    of algorithms. In <i>29th Annual International ACM SIGIR Conference on Research
    and Development in Information Retrieval</i> (pp. 284–291). Seattle, WA, United
    States: Association for Computing Machinery. <a href="https://doi.org/10.1145/1148170.1148222">https://doi.org/10.1145/1148170.1148222</a>'
  chicago: 'Henzinger, Monika H. “Finding Near-Duplicate Web Pages: A Large-Scale
    Evaluation of Algorithms.” In <i>29th Annual International ACM SIGIR Conference
    on Research and Development in Information Retrieval</i>, 284–91. Association
    for Computing Machinery, 2006. <a href="https://doi.org/10.1145/1148170.1148222">https://doi.org/10.1145/1148170.1148222</a>.'
  ieee: 'M. H. Henzinger, “Finding near-duplicate web pages: A large-scale evaluation
    of algorithms,” in <i>29th Annual International ACM SIGIR Conference on Research
    and Development in Information Retrieval</i>, Seattle, WA, United States, 2006,
    pp. 284–291.'
  ista: 'Henzinger MH. 2006. Finding near-duplicate web pages: A large-scale evaluation
    of algorithms. 29th Annual International ACM SIGIR Conference on Research and
    Development in Information Retrieval. SIGIR: International Conference on Research
    and Development in Information Retrieval, 284–291.'
  mla: 'Henzinger, Monika H. “Finding Near-Duplicate Web Pages: A Large-Scale Evaluation
    of Algorithms.” <i>29th Annual International ACM SIGIR Conference on Research
    and Development in Information Retrieval</i>, Association for Computing Machinery,
    2006, pp. 284–91, doi:<a href="https://doi.org/10.1145/1148170.1148222">10.1145/1148170.1148222</a>.'
  short: M.H. Henzinger, in:, 29th Annual International ACM SIGIR Conference on Research
    and Development in Information Retrieval, Association for Computing Machinery,
    2006, pp. 284–291.
conference:
  end_date: 2006-08-11
  location: Seattle, WA, United States
  name: 'SIGIR: International Conference on Research and Development in Information
    Retrieval'
  start_date: 2006-08-06
date_created: 2022-08-19T07:20:31Z
date_published: 2006-08-01T00:00:00Z
date_updated: 2023-02-17T13:49:03Z
day: '01'
doi: 10.1145/1148170.1148222
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 284-291
publication: 29th Annual International ACM SIGIR Conference on Research and Development
  in Information Retrieval
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Finding near-duplicate web pages: A large-scale evaluation of algorithms'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2006'
...
---
_id: '3404'
alternative_title:
- Manuals in Biomedical Research
author:
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Ravi
  full_name: Sawhney, Ravi K
  last_name: Sawhney
- first_name: Martin
  full_name: Stark, Martin
  last_name: Stark
- first_name: Daniel
  full_name: Mueller, Daniel J
  last_name: Mueller
citation:
  ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: <i>Techniques
    in Microscopy for Biomedical Applications</i>. Vol 2. World Scientific Publishing;
    2006:213-284.'
  apa: Janovjak, H. L., Sawhney, R., Stark, M., &#38; Mueller, D. (2006). Atomic force
    microscopy. In <i>Techniques in Microscopy for Biomedical Applications</i> (Vol.
    2, pp. 213–284). World Scientific Publishing.
  chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic
    Force Microscopy.” In <i>Techniques in Microscopy for Biomedical Applications</i>,
    2:213–84. World Scientific Publishing, 2006.
  ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,”
    in <i>Techniques in Microscopy for Biomedical Applications</i>, vol. 2, World
    Scientific Publishing, 2006, pp. 213–284.
  ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy.
    In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical
    Research, vol. 2, 213–284.'
  mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” <i>Techniques in Microscopy
    for Biomedical Applications</i>, vol. 2, World Scientific Publishing, 2006, pp.
    213–84.
  short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy
    for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.
date_created: 2018-12-11T12:03:09Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '28'
extern: 1
intvolume: '         2'
month: '09'
page: 213 - 284
publication: Techniques in Microscopy for Biomedical Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '2998'
quality_controlled: 0
status: public
title: Atomic force microscopy
type: book_chapter
volume: 2
year: '2006'
...
---
_id: '3413'
abstract:
- lang: eng
  text: |-
    Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.

    Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.

    We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
author:
- first_name: Max
  full_name: Kessler, Max
  last_name: Kessler
- first_name: Kay
  full_name: Gottschalk, Kay E
  last_name: Gottschalk
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Daniel
  full_name: Mueller, Daniel J
  last_name: Mueller
- first_name: Hermann
  full_name: Gaub, Hermann
  last_name: Gaub
citation:
  ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin
    folds into the membrane against an external force. <i>Journal of Molecular Biology</i>.
    2006;357(2):644-654. doi:<a href="https://doi.org/10.1016/j.jmb.2005.12.065">10.1016/j.jmb.2005.12.065</a>
  apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., &#38; Gaub, H. (2006).
    Bacteriorhodopsin folds into the membrane against an external force. <i>Journal
    of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2005.12.065">https://doi.org/10.1016/j.jmb.2005.12.065</a>
  chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann
    Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” <i>Journal
    of Molecular Biology</i>. Elsevier, 2006. <a href="https://doi.org/10.1016/j.jmb.2005.12.065">https://doi.org/10.1016/j.jmb.2005.12.065</a>.
  ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin
    folds into the membrane against an external force,” <i>Journal of Molecular Biology</i>,
    vol. 357, no. 2. Elsevier, pp. 644–654, 2006.
  ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin
    folds into the membrane against an external force. Journal of Molecular Biology.
    357(2), 644–654.
  mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an
    External Force.” <i>Journal of Molecular Biology</i>, vol. 357, no. 2, Elsevier,
    2006, pp. 644–54, doi:<a href="https://doi.org/10.1016/j.jmb.2005.12.065">10.1016/j.jmb.2005.12.065</a>.
  short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of
    Molecular Biology 357 (2006) 644–654.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-03-24T00:00:00Z
date_updated: 2021-01-12T07:43:18Z
day: '24'
doi: 10.1016/j.jmb.2005.12.065
extern: 1
intvolume: '       357'
issue: '2'
month: '03'
page: 644 - 654
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2988'
quality_controlled: 0
status: public
title: Bacteriorhodopsin folds into the membrane against an external force
type: journal_article
volume: 357
year: '2006'
...
---
_id: '3414'
abstract:
- lang: eng
  text: Mechanisms of folding and misfolding of membrane proteins are of interest
    in cell biology. Recently, we have established single-molecule force spectroscopy
    to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia
    coli in vitro. Here, we improved this approach significantly to track the folding
    intermediates of asingle NhaA polypeptide forming structural segments such as
    the Na+-binding site, transmembrane α-helices, and helical pairs. The folding
    rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed
    insight into a distinct folding hierarchy of an unfolded polypeptide into the
    native membrane protein structure. In some cases, however, the folding chain formed
    stable and kinetically trapped non-native structures, which could be assigned
    to misfolding events of the antiporter.
author:
- first_name: Alexej
  full_name: Kedrov, Alexej
  last_name: Kedrov
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Christine
  full_name: Ziegler,  Christine
  last_name: Ziegler
- first_name: Werner
  full_name: Kühlbrandt, Werner
  last_name: Kühlbrandt
- first_name: Daniel
  full_name: Mueller, Daniel J
  last_name: Mueller
citation:
  ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding
    pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.
    <i>Journal of Molecular Biology</i>. 2006;355(1):2-8. doi:<a href="https://doi.org/10.1016/j.jmb.2005.10.028">10.1016/j.jmb.2005.10.028</a>
  apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., &#38; Mueller, D.
    (2006). Observing folding pathways and kinetics of a single sodium-proton antiporter
    from Escherichia coli. <i>Journal of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2005.10.028">https://doi.org/10.1016/j.jmb.2005.10.028</a>
  chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt,
    and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton
    Antiporter from Escherichia Coli.” <i>Journal of Molecular Biology</i>. Elsevier,
    2006. <a href="https://doi.org/10.1016/j.jmb.2005.10.028">https://doi.org/10.1016/j.jmb.2005.10.028</a>.
  ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing
    folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
    coli,” <i>Journal of Molecular Biology</i>, vol. 355, no. 1. Elsevier, pp. 2–8,
    2006.
  ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing
    folding pathways and kinetics of a single sodium-proton antiporter from Escherichia
    coli. Journal of Molecular Biology. 355(1), 2–8.
  mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single
    Sodium-Proton Antiporter from Escherichia Coli.” <i>Journal of Molecular Biology</i>,
    vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:<a href="https://doi.org/10.1016/j.jmb.2005.10.028">10.1016/j.jmb.2005.10.028</a>.
  short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal
    of Molecular Biology 355 (2006) 2–8.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-06T00:00:00Z
date_updated: 2021-01-12T07:43:19Z
day: '06'
doi: 10.1016/j.jmb.2005.10.028
extern: 1
intvolume: '       355'
issue: '1'
month: '01'
page: 2 - 8
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2987'
quality_controlled: 0
status: public
title: Observing folding pathways and kinetics of a single sodium-proton antiporter
  from Escherichia coli
type: journal_article
volume: 355
year: '2006'
...
---
_id: '3415'
author:
- first_name: Harald L
  full_name: Harald Janovjak
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
- first_name: Alexej
  full_name: Kedrov, Alexej
  last_name: Kedrov
- first_name: David
  full_name: Cisneros, David
  last_name: Cisneros
- first_name: Tanuj
  full_name: Sapra, Tanuj K
  last_name: Sapra
- first_name: Jens
  full_name: Struckmeier, Jens
  last_name: Struckmeier
- first_name: Daniel
  full_name: Mueller, Daniel J
  last_name: Mueller
citation:
  ama: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging
    and detecting molecular interactions of single membrane proteins. <i>Neurobiology
    of Aging</i>. 2006;27:546-561. doi:<a href="https://doi.org/10.1016/j.neurobiolaging.2005.03.031">10.1016/j.neurobiolaging.2005.03.031</a>
  apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., &#38;
    Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane
    proteins. <i>Neurobiology of Aging</i>. Elsevier. <a href="https://doi.org/10.1016/j.neurobiolaging.2005.03.031">https://doi.org/10.1016/j.neurobiolaging.2005.03.031</a>
  chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier,
    and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane
    Proteins.” <i>Neurobiology of Aging</i>. Elsevier, 2006. <a href="https://doi.org/10.1016/j.neurobiolaging.2005.03.031">https://doi.org/10.1016/j.neurobiolaging.2005.03.031</a>.
  ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller,
    “Imaging and detecting molecular interactions of single membrane proteins,” <i>Neurobiology
    of Aging</i>, vol. 27. Elsevier, pp. 546–561, 2006.
  ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006.
    Imaging and detecting molecular interactions of single membrane proteins. Neurobiology
    of Aging. 27, 546–561.
  mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of
    Single Membrane Proteins.” <i>Neurobiology of Aging</i>, vol. 27, Elsevier, 2006,
    pp. 546–61, doi:<a href="https://doi.org/10.1016/j.neurobiolaging.2005.03.031">10.1016/j.neurobiolaging.2005.03.031</a>.
  short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller,
    Neurobiology of Aging 27 (2006) 546–561.
date_created: 2018-12-11T12:03:12Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:27Z
day: '01'
doi: 10.1016/j.neurobiolaging.2005.03.031
extern: 1
intvolume: '        27'
month: '01'
page: 546 - 561
publication: Neurobiology of Aging
publication_status: published
publisher: Elsevier
publist_id: '2986'
quality_controlled: 0
status: public
title: Imaging and detecting molecular interactions of single membrane proteins
type: review
volume: 27
year: '2006'
...
---
_id: '3431'
abstract:
- lang: eng
  text: Ising models with pairwise interactions are the least structured, or maximum-entropy,
    probability distributions that exactly reproduce measured pairwise correlations
    between spins. Here we use this equivalence to construct Ising models that describe
    the correlated spiking activity of populations of 40 neurons in the retina, and
    show that pairwise interactions account for observed higher-order correlations.
    By first finding a representative ensemble for observed networks we can create
    synthetic networks of 120 neurons, and find that with increasing size the networks
    operate closer to a critical point and start exhibiting collective behaviors reminiscent
    of spin glasses.
author:
- first_name: Gasper
  full_name: Gasper Tkacik
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
- first_name: E.
  full_name: Schneidman, E.
  last_name: Schneidman
- first_name: M.
  full_name: Berry, M. J.
  last_name: Berry
- first_name: William
  full_name: Bialek, William S
  last_name: Bialek
citation:
  ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real
    neurons. <i>ArXiv</i>. 2006:1-4.
  apa: Tkačik, G., Schneidman, E., Berry, M., &#38; Bialek, W. (2006). Ising models
    for networks of real neurons. <i>ArXiv</i>. ArXiv.
  chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models
    for Networks of Real Neurons.” <i>ArXiv</i>. ArXiv, 2006.
  ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks
    of real neurons,” <i>ArXiv</i>. ArXiv, pp. 1–4, 2006.
  ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks
    of real neurons. ArXiv, 1–4, .
  mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” <i>ArXiv</i>,
    ArXiv, 2006, pp. 1–4.
  short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.
date_created: 2018-12-11T12:03:18Z
date_published: 2006-11-22T00:00:00Z
date_updated: 2021-01-12T07:43:25Z
day: '22'
extern: 1
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/q-bio/0611072
month: '11'
oa: 1
page: 1 - 4
publication: ArXiv
publication_status: published
publisher: ArXiv
publist_id: '2969'
quality_controlled: 0
status: public
title: Ising models for networks of real neurons
type: preprint
year: '2006'
...
---
_id: '3437'
abstract:
- lang: eng
  text: The mutational landscape model is a theoretical model describing sequence
    evolution in natural populations. However, recent experimental work has begun
    to test its predictions in laboratory populations of microbes. Several of these
    studies have focused on testing the prediction that the effects of beneficial
    mutations should be roughly exponentially distributed. The prediction appears
    to be borne out by most of these studies, at least qualitatively. Another study
    showed that a modified version of the model was able to predict, with reasonable
    accuracy, which of a ranked set of beneficial alleles will be fixed next. Although
    it remains to be seen whether the mutational landscape model adequately describes
    adaptation in organisms other than microbes, together these studies suggest that
    adaptive evolution has surprisingly general properties that can be successfully
    captured by theoretical models.
author:
- first_name: Andrea
  full_name: Betancourt, Andrea J
  last_name: Betancourt
- first_name: Jonathan P
  full_name: Jonathan Bollback
  id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
  last_name: Bollback
  orcid: 0000-0002-4624-4612
citation:
  ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational
    landscape model in experimental evolution. <i>Current Opinion in Genetics &#38;
    Development</i>. 2006;16(6):618-623. doi:<a href="https://doi.org/10.1016/j.gde.2006.10.006">10.1016/j.gde.2006.10.006</a>'
  apa: 'Betancourt, A., &#38; Bollback, J. P. (2006). Fitness effects of beneficial
    mutations: the mutational landscape model in experimental evolution. <i>Current
    Opinion in Genetics &#38; Development</i>. Elsevier. <a href="https://doi.org/10.1016/j.gde.2006.10.006">https://doi.org/10.1016/j.gde.2006.10.006</a>'
  chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial
    Mutations: The Mutational Landscape Model in Experimental Evolution.” <i>Current
    Opinion in Genetics &#38; Development</i>. Elsevier, 2006. <a href="https://doi.org/10.1016/j.gde.2006.10.006">https://doi.org/10.1016/j.gde.2006.10.006</a>.'
  ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations:
    the mutational landscape model in experimental evolution,” <i>Current Opinion
    in Genetics &#38; Development</i>, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.'
  ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations:
    the mutational landscape model in experimental evolution. Current Opinion in Genetics
    &#38; Development. 16(6), 618–623.'
  mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial
    Mutations: The Mutational Landscape Model in Experimental Evolution.” <i>Current
    Opinion in Genetics &#38; Development</i>, vol. 16, no. 6, Elsevier, 2006, pp.
    618–23, doi:<a href="https://doi.org/10.1016/j.gde.2006.10.006">10.1016/j.gde.2006.10.006</a>.'
  short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics &#38; Development
    16 (2006) 618–623.
date_created: 2018-12-11T12:03:19Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:43:27Z
day: '01'
doi: 10.1016/j.gde.2006.10.006
extern: 1
intvolume: '        16'
issue: '6'
month: '12'
page: 618 - 623
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '2963'
quality_controlled: 0
status: public
title: 'Fitness effects of beneficial mutations: the mutational landscape model in
  experimental evolution'
type: journal_article
volume: 16
year: '2006'
...
---
_id: '3449'
abstract:
- lang: eng
  text: We argue that games are expressive enough to encompass (history-based) access
    control, (resource) usage control (e.g., dynamic adaptive access control of reputation
    systems), accountability based controls (e.g., insurance), controls derived from
    rationality assumptions on participants (e.g., network mechanisms), and their
    composition. Building on the extensive research into games, we demonstrate that
    this expressive power coexists with a formal analysis framework comparable to
    that available for access control.
author:
- first_name: Krishnendu
  full_name: Krishnendu Chatterjee
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Rhada
  full_name: Jagadeesan, Rhada
  last_name: Jagadeesan
- first_name: Corin
  full_name: Pitcher, Corin
  last_name: Pitcher
citation:
  ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82.
    doi:<a href="https://doi.org/10.1109/CSFW.2006.14">10.1109/CSFW.2006.14</a>'
  apa: 'Chatterjee, K., Jagadeesan, R., &#38; Pitcher, C. (2006). Games for controls
    (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. <a href="https://doi.org/10.1109/CSFW.2006.14">https://doi.org/10.1109/CSFW.2006.14</a>'
  chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for
    Controls,” 70–82. IEEE, 2006. <a href="https://doi.org/10.1109/CSFW.2006.14">https://doi.org/10.1109/CSFW.2006.14</a>.
  ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented
    at the CSF: Computer Security Foundations, 2006, pp. 70–82.'
  ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer
    Security Foundations, 70–82.'
  mla: Chatterjee, Krishnendu, et al. <i>Games for Controls</i>. IEEE, 2006, pp. 70–82,
    doi:<a href="https://doi.org/10.1109/CSFW.2006.14">10.1109/CSFW.2006.14</a>.
  short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.
conference:
  name: 'CSF: Computer Security Foundations'
date_created: 2018-12-11T12:03:23Z
date_published: 2006-07-31T00:00:00Z
date_updated: 2021-01-12T07:43:32Z
day: '31'
doi: 10.1109/CSFW.2006.14
extern: 1
month: '07'
page: 70 - 82
publication_status: published
publisher: IEEE
publist_id: '2938'
quality_controlled: 0
status: public
title: Games for controls
type: conference
year: '2006'
...
---
_id: '3463'
abstract:
- lang: eng
  text: It is widely accepted that the hippocampus plays a major role in learning
    and memory. The mossy fiber synapse between granule cells in the dentate gyrus
    and pyramidal neurons in the CA3 region is a key component of the hippocampal
    trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp
    recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms
    of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+)
    channel density in mossy fiber boutons leads to a large amplitude of the presynaptic
    action potential. Together with the fast gating of presynaptic Ca(2+) channels,
    this generates a large and brief presynaptic Ca(2+) influx, which can trigger
    transmitter release with high efficiency and temporal precision. The large number
    of release sites, the large size of the releasable pool of vesicles, and the huge
    extent of presynaptic plasticity confer unique strength to this synapse, suggesting
    a large impact onto the CA3 pyramidal cell network under specific behavioral conditions.
    The characteristic properties of the hippocampal mossy fiber synapse may be important
    for pattern separation and information storage in the dentate gyrus-CA3 cell network.
author:
- first_name: Joseph
  full_name: Bischofberger, Joseph
  last_name: Bischofberger
- first_name: Dominique
  full_name: Engel, Dominique
  last_name: Engel
- first_name: Michael
  full_name: Frotscher, Michael
  last_name: Frotscher
- first_name: Peter M
  full_name: Peter Jonas
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
citation:
  ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter
    release at mossy fiber synapses in the hippocampal network. (Review). <i>Pflugers
    Archiv : European Journal of Physiology</i>. 2006;453(3):361-372. doi:<a href="https://doi.org/10.1007/s00424-006-0093-2">10.1007/s00424-006-0093-2</a>'
  apa: 'Bischofberger, J., Engel, D., Frotscher, M., &#38; Jonas, P. M. (2006). Timing
    and efficacy of transmitter release at mossy fiber synapses in the hippocampal
    network. (Review). <i>Pflugers Archiv : European Journal of Physiology</i>. Springer.
    <a href="https://doi.org/10.1007/s00424-006-0093-2">https://doi.org/10.1007/s00424-006-0093-2</a>'
  chicago: 'Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M
    Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in
    the Hippocampal Network. (Review).” <i>Pflugers Archiv : European Journal of Physiology</i>.
    Springer, 2006. <a href="https://doi.org/10.1007/s00424-006-0093-2">https://doi.org/10.1007/s00424-006-0093-2</a>.'
  ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy
    of transmitter release at mossy fiber synapses in the hippocampal network. (Review),”
    <i>Pflugers Archiv : European Journal of Physiology</i>, vol. 453, no. 3. Springer,
    pp. 361–372, 2006.'
  ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy
    of transmitter release at mossy fiber synapses in the hippocampal network. (Review).
    Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.'
  mla: 'Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release
    at Mossy Fiber Synapses in the Hippocampal Network. (Review).” <i>Pflugers Archiv :
    European Journal of Physiology</i>, vol. 453, no. 3, Springer, 2006, pp. 361–72,
    doi:<a href="https://doi.org/10.1007/s00424-006-0093-2">10.1007/s00424-006-0093-2</a>.'
  short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv :
    European Journal of Physiology 453 (2006) 361–372.'
date_created: 2018-12-11T12:03:28Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2019-04-26T07:22:28Z
day: '01'
doi: 10.1007/s00424-006-0093-2
extern: 1
intvolume: '       453'
issue: '3'
month: '12'
page: 361 - 372
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_status: published
publisher: Springer
publist_id: '2924'
quality_controlled: 0
status: public
title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal
  network. (Review)
type: review
volume: 453
year: '2006'
...
---
_id: '3499'
abstract:
- lang: eng
  text: 'We study infinite stochastic games played by n-players on a finite graph
    with goals specified by sets of infinite traces. The games are concurrent (each
    player simultaneously and independently chooses an action at each round), stochastic
    (the next state is determined by a probability distribution depending on the current
    state and the chosen actions), infinite (the game continues for an infinite number
    of rounds), nonzero-sum (the players’ goals are not necessarily conflicting),
    and undiscounted. We show that if each player has an upward-closed objective,
    then there exists an ε-Nash equilibrium in memoryless strategies, for every ε&gt;0;
    and exact Nash equilibria need not exist. Upward-closure of an objective means
    that if a set Z of infinitely repeating states is winning, then all supersets
    of Z of infinitely repeating states are also winning. Memoryless strategies are
    strategies that are independent of history of plays and depend only on the current
    state. We also study the complexity of finding values (payoff profile) of an ε-Nash
    equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent
    games with upward-closed objectives for all players can be computed by computing
    ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives
    for all players and a polynomial procedure. As a consequence we establish that
    values of an ε-Nash equilibrium can be computed in TFNP (total functional NP),
    and hence in EXPTIME. '
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
  and CCR- 0234690, and by the SNSF under the Indo-Swiss Joint Research Programme.
alternative_title:
- 'LNCS '
author:
- first_name: Krishnendu
  full_name: Krishnendu Chatterjee
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
citation:
  ama: 'Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207.
    Springer; 2006:271-286. doi:<a href="https://doi.org/10.1007/11874683_18">10.1007/11874683_18</a>'
  apa: 'Chatterjee, K. (2006). Nash equilibrium for upward-closed objectives (Vol.
    4207, pp. 271–286). Presented at the CSL: Computer Science Logic, Springer. <a
    href="https://doi.org/10.1007/11874683_18">https://doi.org/10.1007/11874683_18</a>'
  chicago: Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,”
    4207:271–86. Springer, 2006. <a href="https://doi.org/10.1007/11874683_18">https://doi.org/10.1007/11874683_18</a>.
  ieee: 'K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented
    at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.'
  ista: 'Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer
    Science Logic, LNCS , vol. 4207, 271–286.'
  mla: Chatterjee, Krishnendu. <i>Nash Equilibrium for Upward-Closed Objectives</i>.
    Vol. 4207, Springer, 2006, pp. 271–86, doi:<a href="https://doi.org/10.1007/11874683_18">10.1007/11874683_18</a>.
  short: K. Chatterjee, in:, Springer, 2006, pp. 271–286.
conference:
  name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:03:39Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:52Z
day: '28'
doi: 10.1007/11874683_18
extern: 1
intvolume: '      4207'
month: '09'
page: 271 - 286
publication_status: published
publisher: Springer
publist_id: '2888'
quality_controlled: 0
status: public
title: Nash equilibrium for upward-closed objectives
type: conference
volume: 4207
year: '2006'
...
---
_id: '3500'
abstract:
- lang: eng
  text: The classical algorithm for solving Bu ̈chi games requires time O(n · m) for
    game graphs with n states and m edges. For game graphs with constant outdegree,
    the best known algorithm has running time O(n2/logn). We present two new algorithms
    for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more
    work than the classical algorithm, but runs in time O(n) on infinitely many graphs
    of constant outdegree on which the classical algorithm requires time O(n2). Second,
    we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n)
    ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically
    better than the classical algorithm if δ(n) = O(log n).
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
  and the NSF ITR grant CCR-0225610 and the SNSF under the Indo-Swiss Joint Research
  Programme.
author:
- first_name: Krishnendu
  full_name: Krishnendu Chatterjee
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Thomas Henzinger
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Nir
  full_name: Piterman, Nir
  last_name: Piterman
citation:
  ama: 'Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM;
    2006.'
  apa: 'Chatterjee, K., Henzinger, T. A., &#38; Piterman, N. (2006). Algorithms for
    Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.'
  chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms
    for Büchi Games.” ACM, 2006.
  ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,”
    presented at the GDV: Games in Design and Verification, 2006.'
  ista: 'Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games.
    GDV: Games in Design and Verification.'
  mla: Chatterjee, Krishnendu, et al. <i>Algorithms for Büchi Games</i>. ACM, 2006.
  short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006.
conference:
  name: 'GDV: Games in Design and Verification'
date_created: 2018-12-11T12:03:39Z
date_published: 2006-08-21T00:00:00Z
date_updated: 2021-01-12T07:43:53Z
day: '21'
extern: 1
main_file_link:
- open_access: '0'
  url: http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf
month: '08'
publication_status: published
publisher: ACM
publist_id: '2887'
quality_controlled: 0
status: public
title: Algorithms for Büchi Games
type: conference
year: '2006'
...
---
_id: '3510'
abstract:
- lang: eng
  text: Embodiments automatically generate an accurate network of watertight NURBS
    patches from polygonal models of objects while automatically detecting and preserving
    character lines thereon. These embodiments generate from an initial triangulation
    of the surface, a hierarchy of progressively coarser triangulations of the surface
    by performing a sequence of edge contractions using a greedy algorithm that selects
    edge contractions by their numerical properties. Operations are also performed
    to connect the triangulations in the hierarchy using homeomorphisms that preserve
    the topology of the initial triangulation in the coarsest triangulation. A desired
    quadrangulation of the surface can then be generated by homeomorphically mapping
    edges of a coarsest triangulation in the hierarchy back to the initial triangulation.
    This quadrangulation is topologically consistent with the initial triangulation
    and is defined by a plurality of quadrangular patches. These quadrangular patches
    are linked together by a (U, V) mesh that is guaranteed to be continuous at patch
    boundaries. A grid is then preferably fit to each of the quadrangles in the resulting
    quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles.
    A watertight NURBS model may be generated from the resulting quadrangulation.
applicant:
- Raindrop Geomagic, Inc.
article_processing_charge: No
author:
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Ping
  full_name: Fu, Ping
  last_name: Fu
- first_name: Dmitry
  full_name: Nekhayev, Dmitry
  last_name: Nekhayev
- first_name: Michael
  full_name: Facello, Michael
  last_name: Facello
- first_name: Steven
  full_name: Williams, Steven
  last_name: Williams
citation:
  ama: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus
    and computer program products for automatically generating NURBS models of triangulated
    surfaces using homeomorphism. 2006.
  apa: Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., &#38; Williams, S. (2006).
    Method, apparatus and computer program products for automatically generating NURBS
    models of triangulated surfaces using homeomorphism.
  chicago: Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven
    Williams. “Method, Apparatus and Computer Program Products for Automatically Generating
    NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006.
  ieee: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method,
    apparatus and computer program products for automatically generating NURBS models
    of triangulated surfaces using homeomorphism.” 2006.
  ista: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus
    and computer program products for automatically generating NURBS models of triangulated
    surfaces using homeomorphism.
  mla: Edelsbrunner, Herbert, et al. <i>Method, Apparatus and Computer Program Products
    for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism</i>.
    2006.
  short: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006).
date_created: 2018-12-11T12:03:42Z
date_published: 2006-02-07T00:00:00Z
date_updated: 2022-01-05T12:58:26Z
day: '07'
extern: '1'
ipc: G06F 7/60 ; G06F 17/10 ; G06F 101/00
ipn: US6996505B1
main_file_link:
- open_access: '1'
  url: https://patents.google.com/patent/US6996505
month: '02'
oa: 1
oa_version: Published Version
publication_date: 2006-02-07
publist_id: '2877'
status: public
title: Method, apparatus and computer program products for automatically generating
  NURBS models of triangulated surfaces using homeomorphism
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2006'
...
