---
_id: '3234'
abstract:
- lang: eng
  text: 'The strongest standard security notion for digital signature schemes is unforgeability
    under chosen message attacks. In practice, however, this notion can be insufficient
    due to &quot;side-channel attacks&quot; which exploit leakage of information about
    the secret internal state. In this work we put forward the notion of &quot;leakage-resilient
    signatures,&quot; which strengthens the standard security notion by giving the
    adversary the additional power to learn a bounded amount of arbitrary information
    about the secret state that was accessed during every signature generation. This
    notion naturally implies security against all side-channel attacks as long as
    the amount of information leaked on each invocation is bounded and &quot;only
    computation leaks information.&quot; The main result of this paper is a construction
    which gives a (tree-based, stateful) leakage-resilient signature scheme based
    on any 3-time signature scheme. The amount of information that our scheme can
    safely leak per signature generation is 1/3 of the information the underlying
    3-time signature scheme can leak in total. Signature schemes that remain secure
    even if a bounded total amount of information is leaked were recently constructed,
    hence instantiating our construction with these schemes gives the first constructions
    of provably secure leakage-resilient signature schemes. The above construction
    assumes that the signing algorithm can sample truly random bits, and thus an implementation
    would need some special hardware (randomness gates). Simply generating this randomness
    using a leakage-resilient stream-cipher will in general not work. Our second contribution
    is a sound general principle to replace uniform random bits in any leakage-resilient
    construction with pseudorandom ones: run two leakage-resilient stream-ciphers
    (with independent keys) in parallel and then apply a two-source extractor to their
    outputs. '
alternative_title:
- LNCS
author:
- first_name: Sebastian
  full_name: Faust, Sebastian
  last_name: Faust
- first_name: Eike
  full_name: Kiltz, Eike
  last_name: Kiltz
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
- first_name: Guy
  full_name: Rothblum, Guy N
  last_name: Rothblum
citation:
  ama: 'Faust S, Kiltz E, Pietrzak KZ, Rothblum G. Leakage resilient signatures. In:
    Vol 5978. Springer; 2010:343-360. doi:<a href="https://doi.org/10.1007/978-3-642-11799-2_21">10.1007/978-3-642-11799-2_21</a>'
  apa: 'Faust, S., Kiltz, E., Pietrzak, K. Z., &#38; Rothblum, G. (2010). Leakage
    resilient signatures (Vol. 5978, pp. 343–360). Presented at the TCC: Theory of
    Cryptography Conference, Springer. <a href="https://doi.org/10.1007/978-3-642-11799-2_21">https://doi.org/10.1007/978-3-642-11799-2_21</a>'
  chicago: Faust, Sebastian, Eike Kiltz, Krzysztof Z Pietrzak, and Guy Rothblum. “Leakage
    Resilient Signatures,” 5978:343–60. Springer, 2010. <a href="https://doi.org/10.1007/978-3-642-11799-2_21">https://doi.org/10.1007/978-3-642-11799-2_21</a>.
  ieee: 'S. Faust, E. Kiltz, K. Z. Pietrzak, and G. Rothblum, “Leakage resilient signatures,”
    presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp.
    343–360.'
  ista: 'Faust S, Kiltz E, Pietrzak KZ, Rothblum G. 2010. Leakage resilient signatures.
    TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 343–360.'
  mla: Faust, Sebastian, et al. <i>Leakage Resilient Signatures</i>. Vol. 5978, Springer,
    2010, pp. 343–60, doi:<a href="https://doi.org/10.1007/978-3-642-11799-2_21">10.1007/978-3-642-11799-2_21</a>.
  short: S. Faust, E. Kiltz, K.Z. Pietrzak, G. Rothblum, in:, Springer, 2010, pp.
    343–360.
conference:
  name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:10Z
date_published: 2010-03-26T00:00:00Z
date_updated: 2021-01-12T07:41:59Z
day: '26'
doi: 10.1007/978-3-642-11799-2_21
extern: 1
intvolume: '      5978'
month: '03'
page: 343 - 360
publication_status: published
publisher: Springer
publist_id: '3447'
quality_controlled: 0
status: public
title: Leakage resilient signatures
type: conference
volume: 5978
year: '2010'
...
---
_id: '3235'
abstract:
- lang: eng
  text: 'A cryptographic primitive is leakage-resilient, if it remains secure even
    if an adversary can learn a bounded amount of arbitrary information about the
    computation with every invocation. As a consequence, the physical implementation
    of a leakage-resilient primitive is secure against every side-channel as long
    as the amount of information leaked per invocation is bounded. In this paper we
    prove positive and negative results about the feasibility of constructing leakage-resilient
    pseudorandom functions and permutations (i.e. block-ciphers). Our results are
    three fold: 1. We construct (from any standard PRF) a PRF which satisfies a relaxed
    notion of leakage-resilience where (1) the leakage function is fixed (and not
    adaptively chosen with each query.) and (2) the computation is split into several
    steps which leak individually (a &quot;step&quot; will be the invocation of the
    underlying PRF.) 2. We prove that a Feistel network with a super-logarithmic number
    of rounds, each instantiated with a leakage-resilient PRF, is a leakage resilient
    PRP. This reduction also holds for the non-adaptive notion just discussed, we
    thus get a block-cipher which is leakage-resilient (against non-adaptive leakage).
    3. We propose generic side-channel attacks against Feistel networks. The attacks
    are generic in the sense that they work for any round functions (e.g. uniformly
    random functions) and only require some simple leakage from the inputs to the
    round functions. For example we show how to invert an r round Feistel network
    over 2n bits making 4•(n+1) r-2 forward queries, if with each query we are also
    given as leakage the Hamming weight of the inputs to the r round functions. This
    complements the result from the previous item showing that a super-constant number
    of rounds is necessary.'
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
  full_name: Dodis, Yevgeniy
  last_name: Dodis
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Dodis Y, Pietrzak KZ. Leakage resilient pseudorandom functions and side channel
    attacks on feistel networks. In: Vol 6223. Springer; 2010:21-40. doi:<a href="https://doi.org/10.1007/978-3-642-14623-7_2">10.1007/978-3-642-14623-7_2</a>'
  apa: 'Dodis, Y., &#38; Pietrzak, K. Z. (2010). Leakage resilient pseudorandom functions
    and side channel attacks on feistel networks (Vol. 6223, pp. 21–40). Presented
    at the CRYPTO: International Cryptology Conference, Springer. <a href="https://doi.org/10.1007/978-3-642-14623-7_2">https://doi.org/10.1007/978-3-642-14623-7_2</a>'
  chicago: Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Leakage Resilient Pseudorandom
    Functions and Side Channel Attacks on Feistel Networks,” 6223:21–40. Springer,
    2010. <a href="https://doi.org/10.1007/978-3-642-14623-7_2">https://doi.org/10.1007/978-3-642-14623-7_2</a>.
  ieee: 'Y. Dodis and K. Z. Pietrzak, “Leakage resilient pseudorandom functions and
    side channel attacks on feistel networks,” presented at the CRYPTO: International
    Cryptology Conference, 2010, vol. 6223, pp. 21–40.'
  ista: 'Dodis Y, Pietrzak KZ. 2010. Leakage resilient pseudorandom functions and
    side channel attacks on feistel networks. CRYPTO: International Cryptology Conference,
    LNCS, vol. 6223, 21–40.'
  mla: Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. <i>Leakage Resilient Pseudorandom
    Functions and Side Channel Attacks on Feistel Networks</i>. Vol. 6223, Springer,
    2010, pp. 21–40, doi:<a href="https://doi.org/10.1007/978-3-642-14623-7_2">10.1007/978-3-642-14623-7_2</a>.
  short: Y. Dodis, K.Z. Pietrzak, in:, Springer, 2010, pp. 21–40.
conference:
  name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:10Z
date_published: 2010-09-30T00:00:00Z
date_updated: 2021-01-12T07:42:00Z
day: '30'
doi: 10.1007/978-3-642-14623-7_2
extern: 1
intvolume: '      6223'
month: '09'
page: 21 - 40
publication_status: published
publisher: Springer
publist_id: '3445'
quality_controlled: 0
status: public
title: Leakage resilient pseudorandom functions and side channel attacks on feistel
  networks
type: conference
volume: 6223
year: '2010'
...
---
_id: '3237'
abstract:
- lang: eng
  text: 'Blinding is a popular and well-known countermeasure to protect public-key
    cryptosystems against side-channel attacks. The high level idea is to randomize
    an exponentiation in order to prevent multiple measurements of the same operation
    on different data, as such measurements might allow the adversary to learn the
    secret exponent. Several variants of blinding have been proposed in the literature,
    using additive or multiplicative secret-sharing to blind either the base or the
    exponent. These countermeasures usually aim at preventing particular side-channel
    attacks (mostly power analysis) and come without any formal security guarantee.
    In this work we investigate to which extend blinding can provide provable security
    against a general class of side-channel attacks. Surprisingly, it turns out that
    in the context of public-key encryption some blinding techniques are more suited
    than others. In particular, we consider a multiplicatively blinded version of
    ElGamal public-key encryption where - we prove that the scheme, instantiated over
    bilinear groups of prime order p (where p - 1 is not smooth) is leakage resilient
    in the generic-group model. Here we consider the model of chosen-ciphertext security
    in the presence of continuous leakage, i.e., the scheme remains chosen-ciphertext
    secure even if with every decryption query the adversary can learn a bounded amount
    (roughly log(p)/2 bits) of arbitrary, adversarially chosen information about the
    computation. - we conjecture that the scheme, instantiated over arbitrary groups
    of prime order p (where p - 1 is not smooth) is leakage resilient. Previous to
    this work no encryption scheme secure against continuous leakage was known. Constructing
    a scheme that can be proven secure in the standard model remains an interesting
    open problem. '
alternative_title:
- LNCS
author:
- first_name: Eike
  full_name: Kiltz, Eike
  last_name: Kiltz
- first_name: Krzysztof Z
  full_name: Krzysztof Pietrzak
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Kiltz E, Pietrzak KZ. Leakage resilient ElGamal encryption. In: Vol 6477.
    Springer; 2010:595-612. doi:<a href="https://doi.org/10.1007/978-3-642-17373-8_34">10.1007/978-3-642-17373-8_34</a>'
  apa: 'Kiltz, E., &#38; Pietrzak, K. Z. (2010). Leakage resilient ElGamal encryption
    (Vol. 6477, pp. 595–612). Presented at the ASIACRYPT: Theory and Application of
    Cryptology and Information Security, Springer. <a href="https://doi.org/10.1007/978-3-642-17373-8_34">https://doi.org/10.1007/978-3-642-17373-8_34</a>'
  chicago: Kiltz, Eike, and Krzysztof Z Pietrzak. “Leakage Resilient ElGamal Encryption,”
    6477:595–612. Springer, 2010. <a href="https://doi.org/10.1007/978-3-642-17373-8_34">https://doi.org/10.1007/978-3-642-17373-8_34</a>.
  ieee: 'E. Kiltz and K. Z. Pietrzak, “Leakage resilient ElGamal encryption,” presented
    at the ASIACRYPT: Theory and Application of Cryptology and Information Security,
    2010, vol. 6477, pp. 595–612.'
  ista: 'Kiltz E, Pietrzak KZ. 2010. Leakage resilient ElGamal encryption. ASIACRYPT:
    Theory and Application of Cryptology and Information Security, LNCS, vol. 6477,
    595–612.'
  mla: Kiltz, Eike, and Krzysztof Z. Pietrzak. <i>Leakage Resilient ElGamal Encryption</i>.
    Vol. 6477, Springer, 2010, pp. 595–612, doi:<a href="https://doi.org/10.1007/978-3-642-17373-8_34">10.1007/978-3-642-17373-8_34</a>.
  short: E. Kiltz, K.Z. Pietrzak, in:, Springer, 2010, pp. 595–612.
conference:
  name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
date_created: 2018-12-11T12:02:11Z
date_published: 2010-01-14T00:00:00Z
date_updated: 2021-01-12T07:42:01Z
day: '14'
doi: 10.1007/978-3-642-17373-8_34
extern: 1
intvolume: '      6477'
month: '01'
page: 595 - 612
publication_status: published
publisher: Springer
publist_id: '3444'
quality_controlled: 0
status: public
title: Leakage resilient ElGamal encryption
type: conference
volume: 6477
year: '2010'
...
---
_id: '3294'
abstract:
- lang: eng
  text: 'Olfactory responses of Drosophila undergo pronounced changes after eclosion.
    The flies develop attraction to odors to which they are exposed and aversion to
    other odors. Behavioral adaptation is correlated with changes in the firing pattern
    of olfactory receptor neurons (ORNs). In this article, we present an information-theoretic
    analysis of the firing pattern of ORNs. Flies reared in a synthetic odorless medium
    were transferred after eclosion to three different media: (i) a synthetic medium
    relatively devoid of odor cues, (ii) synthetic medium infused with a single odorant,
    and (iii) complex cornmeal medium rich in odors. Recordings were made from an
    identified sensillum (type II), and the Jensen-Shannon divergence (D(JS)) was
    used to assess quantitatively the differences between ensemble spike responses
    to different odors. Analysis shows that prolonged exposure to ethyl acetate and
    several related esters increases sensitivity to these esters but does not improve
    the ability of the fly to distinguish between them. Flies exposed to cornmeal
    display varied sensitivity to these odorants and at the same time develop greater
    capacity to distinguish between odors. Deprivation of odor experience on an odorless
    synthetic medium leads to a loss of both sensitivity and acuity. Rich olfactory
    experience thus helps to shape the ORNs response and enhances its discriminative
    power. The experiments presented here demonstrate an experience-dependent adaptation
    at the level of the receptor neuron.'
author:
- first_name: Atulya
  full_name: Iyengar, Atulya
  last_name: Iyengar
- first_name: Subhra
  full_name: Chakraborty Tuhin, Subhra
  last_name: Chakraborty Tuhin
- first_name: Sarit
  full_name: Sarit Goswami
  id: 3A578F32-F248-11E8-B48F-1D18A9856A87
  last_name: Goswami
- first_name: Chun
  full_name: Wu, Chun Fang
  last_name: Wu
- first_name: Obaid
  full_name: Siddiqi, Obaid
  last_name: Siddiqi
citation:
  ama: Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. Post eclosion odor
    experience modifies olfactory receptor neuron coding in Drosophila. <i>PNAS</i>.
    2010;107(21):9855-9860. doi:<a href="https://doi.org/10.1073/pnas.1003856107">10.1073/pnas.1003856107</a>
  apa: Iyengar, A., Chakraborty Tuhin, S., Goswami, S., Wu, C., &#38; Siddiqi, O.
    (2010). Post eclosion odor experience modifies olfactory receptor neuron coding
    in Drosophila. <i>PNAS</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.1003856107">https://doi.org/10.1073/pnas.1003856107</a>
  chicago: Iyengar, Atulya, Subhra Chakraborty Tuhin, Sarit Goswami, Chun Wu, and
    Obaid Siddiqi. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron
    Coding in Drosophila.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href="https://doi.org/10.1073/pnas.1003856107">https://doi.org/10.1073/pnas.1003856107</a>.
  ieee: A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, and O. Siddiqi, “Post
    eclosion odor experience modifies olfactory receptor neuron coding in Drosophila,”
    <i>PNAS</i>, vol. 107, no. 21. National Academy of Sciences, pp. 9855–60, 2010.
  ista: Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. 2010. Post eclosion
    odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS.
    107(21), 9855–60.
  mla: Iyengar, Atulya, et al. “Post Eclosion Odor Experience Modifies Olfactory Receptor
    Neuron Coding in Drosophila.” <i>PNAS</i>, vol. 107, no. 21, National Academy
    of Sciences, 2010, pp. 9855–60, doi:<a href="https://doi.org/10.1073/pnas.1003856107">10.1073/pnas.1003856107</a>.
  short: A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, O. Siddiqi, PNAS 107
    (2010) 9855–60.
date_created: 2018-12-11T12:02:31Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:27Z
day: '01'
doi: 10.1073/pnas.1003856107
extern: 1
intvolume: '       107'
issue: '21'
month: '01'
page: 9855 - 60
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3347'
quality_controlled: 0
status: public
title: Post eclosion odor experience modifies olfactory receptor neuron coding in
  Drosophila
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3296'
abstract:
- lang: eng
  text: "Accurate computational representations of highly deformable surfaces are
    indispensable in the fields of computer animation, medical simulation, computer
    vision, digital modeling, and computational physics. The focus of this dissertation
    is on the animation of physics-based phenomena with highly detailed deformable
    surfaces represented by triangle meshes.\r\n \r\nWe first present results from
    an algorithm that generates continuum mechanics animations with intricate surface
    features. This method combines a finite element method with a tetrahedral mesh
    generator and a high resolution surface mesh, and it is orders of magnitude more
    efficient than previous approaches. Next, we present an efficient solution for
    the challenging problem of computing topological changes in detailed dynamic surface
    meshes. We then introduce a new physics-inspired surface tracking algorithm that
    is capable of preserving arbitrarily thin features and reproducing realistic fine-scale
    topological changes like Rayleigh-Plateau instabilities. This physics-inspired
    surface tracking technique also opens the door for a unique coupling between surficial
    finite element methods and volumetric finite difference methods, in order to simulate
    liquid surface tension phenomena more efficiently than any previous method. Due
    to its dramatic increase in computational resolution and efficiency, this method
    yielded the first computer simulations of a fully developed crown splash with
    droplet pinch off."
article_processing_charge: No
author:
- first_name: Christopher J
  full_name: Wojtan, Christopher J
  id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
  last_name: Wojtan
  orcid: 0000-0001-6646-5546
citation:
  ama: Wojtan C. Animating physical phenomena with embedded surface meshes. 2010:1-175.
  apa: Wojtan, C. (2010). <i>Animating physical phenomena with embedded surface meshes</i>.
    Georgia Institute of Technology.
  chicago: Wojtan, Chris. “Animating Physical Phenomena with Embedded Surface Meshes.”
    Georgia Institute of Technology, 2010.
  ieee: C. Wojtan, “Animating physical phenomena with embedded surface meshes,” Georgia
    Institute of Technology, 2010.
  ista: Wojtan C. 2010. Animating physical phenomena with embedded surface meshes.
    Georgia Institute of Technology.
  mla: Wojtan, Chris. <i>Animating Physical Phenomena with Embedded Surface Meshes</i>.
    Georgia Institute of Technology, 2010, pp. 1–175.
  short: C. Wojtan, Animating Physical Phenomena with Embedded Surface Meshes, Georgia
    Institute of Technology, 2010.
date_created: 2018-12-11T12:02:31Z
date_published: 2010-11-17T00:00:00Z
date_updated: 2023-02-23T11:21:00Z
day: '17'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://hdl.handle.net/1853/37256
month: '11'
oa_version: None
page: 1 - 175
publication_status: published
publisher: Georgia Institute of Technology
publist_id: '3345'
status: public
supervisor:
- first_name: Irfan
  full_name: Essa, Irfan
  last_name: Essa
- first_name: Karen
  full_name: Liu, Karen
  last_name: Liu
- first_name: Peter
  full_name: Mucha, Peter
  last_name: Mucha
- first_name: Jarek
  full_name: Rossignac, Jarek
  last_name: Rossignac
title: Animating physical phenomena with embedded surface meshes
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3303'
abstract:
- lang: eng
  text: 'Biological traits result in part from interactions between different genetic
    loci. This can lead to sign epistasis, in which a beneficial adaptation involves
    a combination of individually deleterious or neutral mutations; in this case,
    a population must cross a “fitness valley” to adapt. Recombination can assist
    this process by combining mutations from different individuals or retard it by
    breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
    in which an adaptation requires one mutation at each of two loci to provide a
    fitness benefit. We present a theoretical analysis of the effect of recombination
    on the valley-crossing process across the full spectrum of possible parameter
    regimes. We find that low recombination rates can speed up valley crossing relative
    to the asexual case, while higher recombination rates slow down valley crossing,
    with the transition between the two regimes occurring when the recombination rate
    between the loci is approximately equal to the selective advantage provided by
    the adaptation. In large populations, if the recombination rate is high and selection
    against single mutants is substantial, the time to cross the valley grows exponentially
    with population size, effectively meaning that the population cannot acquire the
    adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
    time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
  Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
  Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
  ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
  for their helpful suggestions. "
author:
- first_name: Daniel
  full_name: Weissman, Daniel
  id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
  last_name: Weissman
- first_name: Marcus
  full_name: Feldman, Marcus
  last_name: Feldman
- first_name: Daniel
  full_name: Fisher, Daniel
  last_name: Fisher
citation:
  ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
    populations. <i>Genetics</i>. 2010;186(4):1389-1410. doi:<a href="https://doi.org/10.1534/genetics.110.123240">10.1534/genetics.110.123240</a>
  apa: Weissman, D., Feldman, M., &#38; Fisher, D. (2010). The rate of fitness-valley
    crossing in sexual populations. <i>Genetics</i>. Genetics Society of America.
    <a href="https://doi.org/10.1534/genetics.110.123240">https://doi.org/10.1534/genetics.110.123240</a>
  chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
    Crossing in Sexual Populations.” <i>Genetics</i>. Genetics Society of America,
    2010. <a href="https://doi.org/10.1534/genetics.110.123240">https://doi.org/10.1534/genetics.110.123240</a>.
  ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
    in sexual populations,” <i>Genetics</i>, vol. 186, no. 4. Genetics Society of
    America, pp. 1389–1410, 2010.
  ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
    in sexual populations. Genetics. 186(4), 1389–1410.
  mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
    <i>Genetics</i>, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
    doi:<a href="https://doi.org/10.1534/genetics.110.123240">10.1534/genetics.110.123240</a>.
  short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
intvolume: '       186'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '250152'
  name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3337'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2010'
...
---
_id: '3306'
abstract:
- lang: eng
  text: We use methods from combinatorics and algebraic statistics to study analogues
    of birth-and-death processes that have as their state space a finite subset of
    the m-dimensional lattice and for which the m matrices that record the transition
    probabilities in each of the lattice directions commute pairwise. One reason such
    processes are of interest is that the transition matrix is straightforward to
    diagonalize, and hence it is easy to compute n step transition probabilities.
    The set of commuting birth-and-death processes decomposes as a union of toric
    varieties, with the main component being the closure of all processes whose nearest
    neighbor transition probabilities are positive. We exhibit an explicit monomial
    parametrization for this main component, and we explore the boundary components
    using primary decomposition.
acknowledgement: Steven N. Evans was supported in part by NSF Grants DMS-04-05778
  and DMS-09-07630. Bernd Sturmfels was supported in part by NSF Grants DMS-04-56960
  and DMS-07-57236. Caroline Uhler was supported by an International Fulbright Science
  and Technology Fellowship.
author:
- first_name: Steven
  full_name: Evans, Steven N
  last_name: Evans
- first_name: Bernd
  full_name: Sturmfels, Bernd
  last_name: Sturmfels
- first_name: Caroline
  full_name: Caroline Uhler
  id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
  last_name: Uhler
  orcid: 0000-0002-7008-0216
citation:
  ama: Evans S, Sturmfels B, Uhler C. Commuting birth and death processes. <i>The
    Annals of Applied Probability</i>. 2010;20:238-266. doi:<a href="https://doi.org/10.1214/09-AAP615">10.1214/09-AAP615</a>
  apa: Evans, S., Sturmfels, B., &#38; Uhler, C. (2010). Commuting birth and death
    processes. <i>The Annals of Applied Probability</i>. Institute of Mathematical
    Statistics. <a href="https://doi.org/10.1214/09-AAP615">https://doi.org/10.1214/09-AAP615</a>
  chicago: Evans, Steven, Bernd Sturmfels, and Caroline Uhler. “Commuting Birth and
    Death Processes.” <i>The Annals of Applied Probability</i>. Institute of Mathematical
    Statistics, 2010. <a href="https://doi.org/10.1214/09-AAP615">https://doi.org/10.1214/09-AAP615</a>.
  ieee: S. Evans, B. Sturmfels, and C. Uhler, “Commuting birth and death processes,”
    <i>The Annals of Applied Probability</i>, vol. 20. Institute of Mathematical Statistics,
    pp. 238–266, 2010.
  ista: Evans S, Sturmfels B, Uhler C. 2010. Commuting birth and death processes.
    The Annals of Applied Probability. 20, 238–266.
  mla: Evans, Steven, et al. “Commuting Birth and Death Processes.” <i>The Annals
    of Applied Probability</i>, vol. 20, Institute of Mathematical Statistics, 2010,
    pp. 238–66, doi:<a href="https://doi.org/10.1214/09-AAP615">10.1214/09-AAP615</a>.
  short: S. Evans, B. Sturmfels, C. Uhler, The Annals of Applied Probability 20 (2010)
    238–266.
date_created: 2018-12-11T12:02:35Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1214/09-AAP615
extern: 1
intvolume: '        20'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/0812.2724
month: '01'
oa: 1
page: 238 - 266
publication: The Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '3334'
quality_controlled: 0
status: public
title: Commuting birth and death processes
type: journal_article
volume: 20
year: '2010'
...
---
_id: '3308'
abstract:
- lang: eng
  text: We study multivariate normal models that are described by linear constraints
    on the inverse of the covariance matrix. Maximum likelihood estimation for such
    models leads to the problem of maximizing the determinant function over a spectrahedron,
    and to the problem of characterizing the image of the positive definite cone under
    an arbitrary linear projection. These problems at the interface of statistics
    and optimization are here examined from the perspective of convex algebraic geometry.
acknowledgement: B. Sturmfels is supported in part by NSF grants DMS-0456960 and DMS-0757236.
  C. Uhler is supported by an International Fulbright Science and Technology Fellowship.
author:
- first_name: Bernd
  full_name: Sturmfels, Bernd
  last_name: Sturmfels
- first_name: Caroline
  full_name: Caroline Uhler
  id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
  last_name: Uhler
  orcid: 0000-0002-7008-0216
citation:
  ama: Sturmfels B, Uhler C. Multivariate Gaussians, semidefinite matrix completion,
    and convex algebraic geometry. <i>Annals of the Institute of Statistical Mathematics</i>.
    2010;62(4):603-638. doi:<a href="https://doi.org/10.1007/s10463-010-0295-4">10.1007/s10463-010-0295-4</a>
  apa: Sturmfels, B., &#38; Uhler, C. (2010). Multivariate Gaussians, semidefinite
    matrix completion, and convex algebraic geometry. <i>Annals of the Institute of
    Statistical Mathematics</i>. Springer. <a href="https://doi.org/10.1007/s10463-010-0295-4">https://doi.org/10.1007/s10463-010-0295-4</a>
  chicago: Sturmfels, Bernd, and Caroline Uhler. “Multivariate Gaussians, Semidefinite
    Matrix Completion, and Convex Algebraic Geometry.” <i>Annals of the Institute
    of Statistical Mathematics</i>. Springer, 2010. <a href="https://doi.org/10.1007/s10463-010-0295-4">https://doi.org/10.1007/s10463-010-0295-4</a>.
  ieee: B. Sturmfels and C. Uhler, “Multivariate Gaussians, semidefinite matrix completion,
    and convex algebraic geometry,” <i>Annals of the Institute of Statistical Mathematics</i>,
    vol. 62, no. 4. Springer, pp. 603–638, 2010.
  ista: Sturmfels B, Uhler C. 2010. Multivariate Gaussians, semidefinite matrix completion,
    and convex algebraic geometry. Annals of the Institute of Statistical Mathematics.
    62(4), 603–638.
  mla: Sturmfels, Bernd, and Caroline Uhler. “Multivariate Gaussians, Semidefinite
    Matrix Completion, and Convex Algebraic Geometry.” <i>Annals of the Institute
    of Statistical Mathematics</i>, vol. 62, no. 4, Springer, 2010, pp. 603–38, doi:<a
    href="https://doi.org/10.1007/s10463-010-0295-4">10.1007/s10463-010-0295-4</a>.
  short: B. Sturmfels, C. Uhler, Annals of the Institute of Statistical Mathematics
    62 (2010) 603–638.
date_created: 2018-12-11T12:02:35Z
date_published: 2010-08-01T00:00:00Z
date_updated: 2021-01-12T07:42:33Z
day: '01'
doi: 10.1007/s10463-010-0295-4
extern: 1
intvolume: '        62'
issue: '4'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/0906.3529
month: '08'
oa: 1
page: 603 - 638
publication: Annals of the Institute of Statistical Mathematics
publication_status: published
publisher: Springer
publist_id: '3332'
quality_controlled: 0
status: public
title: Multivariate Gaussians, semidefinite matrix completion, and convex algebraic
  geometry
type: journal_article
volume: 62
year: '2010'
...
---
_id: '10908'
abstract:
- lang: eng
  text: We present ABC, a software tool for automatically computing symbolic upper
    bounds on the number of iterations of nested program loops. The system combines
    static analysis of programs with symbolic summation techniques to derive loop
    invariant relations between program variables. Iteration bounds are obtained from
    the inferred invariants, by replacing variables with bounds on their greatest
    values. We have successfully applied ABC to a large number of examples. The derived
    symbolic bounds express non-trivial polynomial relations over loop variables.
    We also report on results to automatically infer symbolic expressions over harmonic
    numbers as upper bounds on loop iteration counts.
acknowledgement: This work was supported in part by the Swiss NSF. The fourth author
  is supported by an FWF Hertha Firnberg Research grant (T425-N23).
article_processing_charge: No
author:
- first_name: Régis
  full_name: Blanc, Régis
  last_name: Blanc
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000-0002-2985-7724
- first_name: Thibaud
  full_name: Hottelier, Thibaud
  last_name: Hottelier
- first_name: Laura
  full_name: Kovács, Laura
  last_name: Kovács
citation:
  ama: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation
    for loops. In: Clarke EM, Voronkov A, eds. <i>Logic for Programming, Artificial
    Intelligence, and Reasoning</i>. Vol 6355. LNCS. Berlin, Heidelberg: Springer
    Nature; 2010:103-118. doi:<a href="https://doi.org/10.1007/978-3-642-17511-4_7">10.1007/978-3-642-17511-4_7</a>'
  apa: 'Blanc, R., Henzinger, T. A., Hottelier, T., &#38; Kovács, L. (2010). ABC:
    Algebraic Bound Computation for loops. In E. M. Clarke &#38; A. Voronkov (Eds.),
    <i>Logic for Programming, Artificial Intelligence, and Reasoning</i> (Vol. 6355,
    pp. 103–118). Berlin, Heidelberg: Springer Nature. <a href="https://doi.org/10.1007/978-3-642-17511-4_7">https://doi.org/10.1007/978-3-642-17511-4_7</a>'
  chicago: 'Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács.
    “ABC: Algebraic Bound Computation for Loops.” In <i>Logic for Programming, Artificial
    Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov,
    6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. <a href="https://doi.org/10.1007/978-3-642-17511-4_7">https://doi.org/10.1007/978-3-642-17511-4_7</a>.'
  ieee: 'R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound
    Computation for loops,” in <i>Logic for Programming, Artificial Intelligence,
    and Reasoning</i>, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.'
  ista: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound
    Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning.
    LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS
    vol. 6355, 103–118.'
  mla: 'Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” <i>Logic
    for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund
    M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:<a
    href="https://doi.org/10.1007/978-3-642-17511-4_7">10.1007/978-3-642-17511-4_7</a>.'
  short: R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov
    (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer
    Nature, Berlin, Heidelberg, 2010, pp. 103–118.
conference:
  end_date: 2010-05-01
  location: Dakar, Senegal
  name: 'LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning'
  start_date: 2010-04-25
date_created: 2022-03-21T08:14:35Z
date_published: 2010-05-01T00:00:00Z
date_updated: 2022-06-13T07:44:21Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-17511-4_7
editor:
- first_name: Edmund M
  full_name: Clarke, Edmund M
  last_name: Clarke
- first_name: Andrei
  full_name: Voronkov, Andrei
  last_name: Voronkov
intvolume: '      6355'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://infoscience.epfl.ch/record/186096
month: '05'
oa: 1
oa_version: Submitted Version
page: 103-118
place: Berlin, Heidelberg
publication: Logic for Programming, Artificial Intelligence, and Reasoning
publication_identifier:
  eisbn:
  - '9783642175114'
  eissn:
  - 1611-3349
  isbn:
  - '9783642175107'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: 'ABC: Algebraic Bound Computation for loops'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6355
year: '2010'
...
---
_id: '10909'
abstract:
- lang: eng
  text: We address the problem of localizing homology classes, namely, finding the
    cycle representing a given class with the most concise geometric measure. We focus
    on the volume measure, that is, the 1-norm of a cycle. Two main results are presented.
    First, we prove the problem is NP-hard to approximate within any constant factor.
    Second, we prove that for homology of dimension two or higher, the problem is
    NP-hard to approximate even when the Betti number is O(1). A side effect is the
    inapproximability of the problem of computing the nonbounding cycle with the smallest
    volume, and computing cycles representing a homology basis with the minimal total
    volume. We also discuss other geometric measures (diameter and radius) and show
    their disadvantages in homology localization. Our work is restricted to homology
    over the ℤ2 field.
acknowledgement: Partially supported by the Austrian Science Fund under grantFSP-S9103-N04
  and P20134-N13.
article_processing_charge: No
author:
- first_name: Chao
  full_name: Chen, Chao
  id: 3E92416E-F248-11E8-B48F-1D18A9856A87
  last_name: Chen
- first_name: Daniel
  full_name: Freedman, Daniel
  last_name: Freedman
citation:
  ama: 'Chen C, Freedman D. Hardness results for homology localization. In: <i>Proceedings
    of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for
    Industrial and Applied Mathematics; 2010:1594-1604. doi:<a href="https://doi.org/10.1137/1.9781611973075.129">10.1137/1.9781611973075.129</a>'
  apa: 'Chen, C., &#38; Freedman, D. (2010). Hardness results for homology localization.
    In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>
    (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied
    Mathematics. <a href="https://doi.org/10.1137/1.9781611973075.129">https://doi.org/10.1137/1.9781611973075.129</a>'
  chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
    In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>,
    1594–1604. Society for Industrial and Applied Mathematics, 2010. <a href="https://doi.org/10.1137/1.9781611973075.129">https://doi.org/10.1137/1.9781611973075.129</a>.
  ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” in
    <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>,
    Austin, TX, United States, 2010, pp. 1594–1604.
  ista: 'Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings
    of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium
    on Discrete Algorithms, 1594–1604.'
  mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
    <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>,
    Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:<a href="https://doi.org/10.1137/1.9781611973075.129">10.1137/1.9781611973075.129</a>.
  short: C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium
    on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010,
    pp. 1594–1604.
conference:
  end_date: 2010-01-19
  location: Austin, TX, United States
  name: 'SODA: Symposium on Discrete Algorithms'
  start_date: 2010-01-17
date_created: 2022-03-21T08:24:07Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2023-02-23T11:19:46Z
day: '01'
department:
- _id: HeEd
doi: 10.1137/1.9781611973075.129
language:
- iso: eng
month: '02'
oa_version: None
page: 1594-1604
publication: Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
  eisbn:
  - '9781611973075'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
  record:
  - id: '3267'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Hardness results for homology localization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '11097'
abstract:
- lang: eng
  text: The nuclear envelope (NE) is a highly regulated membrane barrier that separates
    the nucleus from the cytoplasm in eukaryotic cells. It contains a large number
    of different proteins that have been implicated in chromatin organization and
    gene regulation. Although the nuclear membrane enables complex levels of gene
    expression, it also poses a challenge when it comes to cell division. To allow
    access of the mitotic spindle to chromatin, the nucleus of metazoans must completely
    disassemble during mitosis, generating the need to re-establish the nuclear compartment
    at the end of each cell division. Here, I summarize our current understanding
    of the dynamic remodeling of the NE during the cell cycle.
article_processing_charge: No
article_type: original
author:
- 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: Hetzer M. The nuclear envelope. <i>Cold Spring Harbor Perspectives in Biology</i>.
    2010;2(3):a000539-a000539. doi:<a href="https://doi.org/10.1101/cshperspect.a000539">10.1101/cshperspect.a000539</a>
  apa: Hetzer, M. (2010). The nuclear envelope. <i>Cold Spring Harbor Perspectives
    in Biology</i>. Cold Spring Harbor Laboratory. <a href="https://doi.org/10.1101/cshperspect.a000539">https://doi.org/10.1101/cshperspect.a000539</a>
  chicago: Hetzer, Martin. “The Nuclear Envelope.” <i>Cold Spring Harbor Perspectives
    in Biology</i>. Cold Spring Harbor Laboratory, 2010. <a href="https://doi.org/10.1101/cshperspect.a000539">https://doi.org/10.1101/cshperspect.a000539</a>.
  ieee: M. Hetzer, “The nuclear envelope,” <i>Cold Spring Harbor Perspectives in Biology</i>,
    vol. 2, no. 3. Cold Spring Harbor Laboratory, pp. a000539–a000539, 2010.
  ista: Hetzer M. 2010. The nuclear envelope. Cold Spring Harbor Perspectives in Biology.
    2(3), a000539–a000539.
  mla: Hetzer, Martin. “The Nuclear Envelope.” <i>Cold Spring Harbor Perspectives
    in Biology</i>, vol. 2, no. 3, Cold Spring Harbor Laboratory, 2010, pp. a000539–a000539,
    doi:<a href="https://doi.org/10.1101/cshperspect.a000539">10.1101/cshperspect.a000539</a>.
  short: M. Hetzer, Cold Spring Harbor Perspectives in Biology 2 (2010) a000539–a000539.
date_created: 2022-04-07T07:52:49Z
date_published: 2010-02-03T00:00:00Z
date_updated: 2022-07-18T08:53:50Z
day: '03'
doi: 10.1101/cshperspect.a000539
extern: '1'
external_id:
  pmid:
  - '20300205'
intvolume: '         2'
issue: '3'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '02'
oa_version: None
page: a000539-a000539
pmid: 1
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
  issn:
  - 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: The nuclear envelope
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 2
year: '2010'
...
---
_id: '11098'
article_processing_charge: No
article_type: original
author:
- 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: Hetzer M. The role of the nuclear pore complex in aging of post-mitotic cells.
    <i>Aging</i>. 2010;2(2):74-75. doi:<a href="https://doi.org/10.18632/aging.100125">10.18632/aging.100125</a>
  apa: Hetzer, M. (2010). The role of the nuclear pore complex in aging of post-mitotic
    cells. <i>Aging</i>. Impact Journals. <a href="https://doi.org/10.18632/aging.100125">https://doi.org/10.18632/aging.100125</a>
  chicago: Hetzer, Martin. “The Role of the Nuclear Pore Complex in Aging of Post-Mitotic
    Cells.” <i>Aging</i>. Impact Journals, 2010. <a href="https://doi.org/10.18632/aging.100125">https://doi.org/10.18632/aging.100125</a>.
  ieee: M. Hetzer, “The role of the nuclear pore complex in aging of post-mitotic
    cells,” <i>Aging</i>, vol. 2, no. 2. Impact Journals, pp. 74–75, 2010.
  ista: Hetzer M. 2010. The role of the nuclear pore complex in aging of post-mitotic
    cells. Aging. 2(2), 74–75.
  mla: Hetzer, Martin. “The Role of the Nuclear Pore Complex in Aging of Post-Mitotic
    Cells.” <i>Aging</i>, vol. 2, no. 2, Impact Journals, 2010, pp. 74–75, doi:<a
    href="https://doi.org/10.18632/aging.100125">10.18632/aging.100125</a>.
  short: M. Hetzer, Aging 2 (2010) 74–75.
date_created: 2022-04-07T07:52:58Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2022-07-18T08:54:15Z
day: '01'
doi: 10.18632/aging.100125
extern: '1'
external_id:
  pmid:
  - '20354266'
intvolume: '         2'
issue: '2'
keyword:
- Cell Biology
- Aging
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.18632/aging.100125
month: '02'
oa: 1
oa_version: Published Version
page: 74-75
pmid: 1
publication: Aging
publication_identifier:
  issn:
  - 1945-4589
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of the nuclear pore complex in aging of post-mitotic cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 2
year: '2010'
...
---
_id: '11099'
abstract:
- lang: eng
  text: Nuclear pore complexes (NPCs) serve as transport channels across the nuclear
    membrane, a double lipid bilayer that physically separates the nucleoplasm and
    cytoplasm of eukaryotic cells. New evidence suggests that the multiprotein nuclear
    pores also play a role in chromatin organization and gene expression. Given the
    importance of NPC function, it is not surprising that a growing list of human
    diseases and developmental defects have been linked to its malfunction. In order
    to fully understand the functional repertoire of NPCs and their essential role
    for nuclear organization, it is critical to determine the sequence of events that
    lead to the formation of nuclear pores. This is particularly relevant since NPC
    number, and possibly composition, are tightly linked to metabolic activity. Most
    of our knowledge is derived from NPC formation that occurs in dividing cells at
    the end of mitosis when the nuclear envelope (NE) and NPCs reform from disassembled
    precursors. However, NPC assembly also takes place during interphase into an intact
    NE. Importantly, this process is not restricted to dividing cells but also occurs
    during cell differentiation. Here, we will review aspects unique to this process,
    namely the regulation of nuclear expansion and the mechanisms of fusion between
    the outer and inner nuclear membranes. We will then discuss conserved and diverging
    mechanisms between post-mitotic and interphase assembly of the proteinaceous structure
    in light of recently published data.
article_processing_charge: No
article_type: review
author:
- first_name: Christine M.
  full_name: Doucet, Christine M.
  last_name: Doucet
- 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: Doucet CM, Hetzer M. Nuclear pore biogenesis into an intact nuclear envelope.
    <i>Chromosoma</i>. 2010;119:469-477. doi:<a href="https://doi.org/10.1007/s00412-010-0289-2">10.1007/s00412-010-0289-2</a>
  apa: Doucet, C. M., &#38; Hetzer, M. (2010). Nuclear pore biogenesis into an intact
    nuclear envelope. <i>Chromosoma</i>. Springer Nature. <a href="https://doi.org/10.1007/s00412-010-0289-2">https://doi.org/10.1007/s00412-010-0289-2</a>
  chicago: Doucet, Christine M., and Martin Hetzer. “Nuclear Pore Biogenesis into
    an Intact Nuclear Envelope.” <i>Chromosoma</i>. Springer Nature, 2010. <a href="https://doi.org/10.1007/s00412-010-0289-2">https://doi.org/10.1007/s00412-010-0289-2</a>.
  ieee: C. M. Doucet and M. Hetzer, “Nuclear pore biogenesis into an intact nuclear
    envelope,” <i>Chromosoma</i>, vol. 119. Springer Nature, pp. 469–477, 2010.
  ista: Doucet CM, Hetzer M. 2010. Nuclear pore biogenesis into an intact nuclear
    envelope. Chromosoma. 119, 469–477.
  mla: Doucet, Christine M., and Martin Hetzer. “Nuclear Pore Biogenesis into an Intact
    Nuclear Envelope.” <i>Chromosoma</i>, vol. 119, Springer Nature, 2010, pp. 469–77,
    doi:<a href="https://doi.org/10.1007/s00412-010-0289-2">10.1007/s00412-010-0289-2</a>.
  short: C.M. Doucet, M. Hetzer, Chromosoma 119 (2010) 469–477.
date_created: 2022-04-07T07:53:12Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2022-07-18T08:54:20Z
day: '01'
doi: 10.1007/s00412-010-0289-2
extern: '1'
external_id:
  pmid:
  - '20721671'
intvolume: '       119'
keyword:
- Genetics (clinical)
- Genetics
language:
- iso: eng
month: '10'
oa_version: None
page: 469-477
pmid: 1
publication: Chromosoma
publication_identifier:
  eissn:
  - 1432-0886
  issn:
  - 0009-5915
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear pore biogenesis into an intact nuclear envelope
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 119
year: '2010'
...
---
_id: '11101'
abstract:
- lang: eng
  text: In metazoa, nuclear pore complexes (NPCs) assemble from disassembled precursors
    into a reforming nuclear envelope (NE) at the end of mitosis and into growing
    intact NEs during interphase. Here, we show via RNAi-mediated knockdown that ELYS,
    a nucleoporin critical for the recruitment of the essential Nup107/160 complex
    to chromatin, is required for NPC assembly at the end of mitosis but not during
    interphase. Conversely, the transmembrane nucleoporin POM121 is critical for the
    incorporation of the Nup107/160 complex into new assembly sites specifically during
    interphase. Strikingly, recruitment of the Nup107/160 complex to an intact NE
    involves a membrane curvature-sensing domain of its constituent Nup133, which
    is not required for postmitotic NPC formation. Our results suggest that in organisms
    with open mitosis, NPCs assemble via two distinct mechanisms to accommodate cell
    cycle-dependent differences in NE topology.
article_processing_charge: No
article_type: original
author:
- first_name: Christine M.
  full_name: Doucet, Christine M.
  last_name: Doucet
- first_name: Jessica A.
  full_name: Talamas, Jessica A.
  last_name: Talamas
- 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: Doucet CM, Talamas JA, Hetzer M. Cell cycle-dependent differences in nuclear
    pore complex assembly in metazoa. <i>Cell</i>. 2010;141(6):1030-1041. doi:<a href="https://doi.org/10.1016/j.cell.2010.04.036">10.1016/j.cell.2010.04.036</a>
  apa: Doucet, C. M., Talamas, J. A., &#38; Hetzer, M. (2010). Cell cycle-dependent
    differences in nuclear pore complex assembly in metazoa. <i>Cell</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.cell.2010.04.036">https://doi.org/10.1016/j.cell.2010.04.036</a>
  chicago: Doucet, Christine M., Jessica A. Talamas, and Martin Hetzer. “Cell Cycle-Dependent
    Differences in Nuclear Pore Complex Assembly in Metazoa.” <i>Cell</i>. Elsevier,
    2010. <a href="https://doi.org/10.1016/j.cell.2010.04.036">https://doi.org/10.1016/j.cell.2010.04.036</a>.
  ieee: C. M. Doucet, J. A. Talamas, and M. Hetzer, “Cell cycle-dependent differences
    in nuclear pore complex assembly in metazoa,” <i>Cell</i>, vol. 141, no. 6. Elsevier,
    pp. 1030–1041, 2010.
  ista: Doucet CM, Talamas JA, Hetzer M. 2010. Cell cycle-dependent differences in
    nuclear pore complex assembly in metazoa. Cell. 141(6), 1030–1041.
  mla: Doucet, Christine M., et al. “Cell Cycle-Dependent Differences in Nuclear Pore
    Complex Assembly in Metazoa.” <i>Cell</i>, vol. 141, no. 6, Elsevier, 2010, pp.
    1030–41, doi:<a href="https://doi.org/10.1016/j.cell.2010.04.036">10.1016/j.cell.2010.04.036</a>.
  short: C.M. Doucet, J.A. Talamas, M. Hetzer, Cell 141 (2010) 1030–1041.
date_created: 2022-04-07T07:53:29Z
date_published: 2010-06-11T00:00:00Z
date_updated: 2022-07-18T08:54:52Z
day: '11'
doi: 10.1016/j.cell.2010.04.036
extern: '1'
external_id:
  pmid:
  - '20550937'
intvolume: '       141'
issue: '6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cell.2010.04.036
month: '06'
oa: 1
oa_version: Published Version
page: 1030-1041
pmid: 1
publication: Cell
publication_identifier:
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell cycle-dependent differences in nuclear pore complex assembly in metazoa
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 141
year: '2010'
...
---
_id: '11102'
abstract:
- lang: eng
  text: Nuclear pore complexes have recently been shown to play roles in gene activation;
    however their potential involvement in metazoan transcription remains unclear.
    Here we show that the nucleoporins Sec13, Nup98, and Nup88, as well as a group
    of FG-repeat nucleoporins, bind to the Drosophila genome at functionally distinct
    loci that often do not represent nuclear envelope contact sites. Whereas Nup88
    localizes to silent loci, Sec13, Nup98, and a subset of FG-repeat nucleoporins
    bind to developmentally regulated genes undergoing transcription induction. Strikingly,
    RNAi-mediated knockdown of intranuclear Sec13 and Nup98 specifically inhibits
    transcription of their target genes and prevents efficient reactivation of transcription
    after heat shock, suggesting an essential role of NPC components in regulating
    complex gene expression programs of multicellular organisms.
article_processing_charge: No
article_type: original
author:
- first_name: Maya
  full_name: Capelson, Maya
  last_name: Capelson
- first_name: Yun
  full_name: Liang, Yun
  last_name: Liang
- first_name: Roberta
  full_name: Schulte, Roberta
  last_name: Schulte
- first_name: William
  full_name: Mair, William
  last_name: Mair
- first_name: Ulrich
  full_name: Wagner, Ulrich
  last_name: Wagner
- 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, Liang Y, Schulte R, Mair W, Wagner U, Hetzer M. Chromatin-bound
    nuclear pore components regulate gene expression in higher eukaryotes. <i>Cell</i>.
    2010;140(3):372-383. doi:<a href="https://doi.org/10.1016/j.cell.2009.12.054">10.1016/j.cell.2009.12.054</a>
  apa: Capelson, M., Liang, Y., Schulte, R., Mair, W., Wagner, U., &#38; Hetzer, M.
    (2010). Chromatin-bound nuclear pore components regulate gene expression in higher
    eukaryotes. <i>Cell</i>. Elsevier. <a href="https://doi.org/10.1016/j.cell.2009.12.054">https://doi.org/10.1016/j.cell.2009.12.054</a>
  chicago: Capelson, Maya, Yun Liang, Roberta Schulte, William Mair, Ulrich Wagner,
    and Martin Hetzer. “Chromatin-Bound Nuclear Pore Components Regulate Gene Expression
    in Higher Eukaryotes.” <i>Cell</i>. Elsevier, 2010. <a href="https://doi.org/10.1016/j.cell.2009.12.054">https://doi.org/10.1016/j.cell.2009.12.054</a>.
  ieee: M. Capelson, Y. Liang, R. Schulte, W. Mair, U. Wagner, and M. Hetzer, “Chromatin-bound
    nuclear pore components regulate gene expression in higher eukaryotes,” <i>Cell</i>,
    vol. 140, no. 3. Elsevier, pp. 372–383, 2010.
  ista: Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer M. 2010. Chromatin-bound
    nuclear pore components regulate gene expression in higher eukaryotes. Cell. 140(3),
    372–383.
  mla: Capelson, Maya, et al. “Chromatin-Bound Nuclear Pore Components Regulate Gene
    Expression in Higher Eukaryotes.” <i>Cell</i>, vol. 140, no. 3, Elsevier, 2010,
    pp. 372–83, doi:<a href="https://doi.org/10.1016/j.cell.2009.12.054">10.1016/j.cell.2009.12.054</a>.
  short: M. Capelson, Y. Liang, R. Schulte, W. Mair, U. Wagner, M. Hetzer, Cell 140
    (2010) 372–383.
date_created: 2022-04-07T07:53:36Z
date_published: 2010-02-05T00:00:00Z
date_updated: 2022-07-18T08:55:03Z
day: '05'
doi: 10.1016/j.cell.2009.12.054
extern: '1'
external_id:
  pmid:
  - '20144761'
intvolume: '       140'
issue: '3'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cell.2009.12.054
month: '02'
oa: 1
oa_version: Published Version
page: 372-383
pmid: 1
publication: Cell
publication_identifier:
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin-bound nuclear pore components regulate gene expression in higher
  eukaryotes
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 140
year: '2010'
...
---
_id: '11753'
abstract:
- lang: eng
  text: Ferroelectric ceramic materials have a wide range of applications because
    of their piezoelectric and pyroelectric properties. One of their most important
    physical properties is the specific heat. In this study, the specific heats of
    a series of lead-zirconate-titanate (PZT) compositions in the vicinity of the
    morphotropic phase boundary (MPB) were measured. The temperature range was from
    1.8 to 300 K. It is believed that these are the lowest temperature measurements
    ever made on PZT. Differences between the specific heats of the different compositions
    were very small. However, the calculated Debye temperatures were slightly different.
    The results are useful in computing design parameters for technical devices.
article_number: '5568033'
article_processing_charge: No
author:
- first_name: S. B.
  full_name: Lang, S. B.
  last_name: Lang
- first_name: J. C.
  full_name: Lashley, J. C.
  last_name: Lashley
- first_name: Kimberly A
  full_name: Modic, Kimberly A
  id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
  last_name: Modic
  orcid: 0000-0001-9760-3147
- first_name: R. A.
  full_name: Fisher, R. A.
  last_name: Fisher
- first_name: W. M.
  full_name: Zhu, W. M.
  last_name: Zhu
- first_name: Z. G.
  full_name: Ye, Z. G.
  last_name: Ye
citation:
  ama: 'Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. Specific heat of
    a ferroelectric PZT ceramic at the morphotropic phase boundary. In: <i>Proceedings
    of the 2010 IEEE International Conference on Solid Dielectrics</i>. Institute
    of Electrical and Electronics Engineers; 2010. doi:<a href="https://doi.org/10.1109/icsd.2010.5568033">10.1109/icsd.2010.5568033</a>'
  apa: 'Lang, S. B., Lashley, J. C., Modic, K. A., Fisher, R. A., Zhu, W. M., &#38;
    Ye, Z. G. (2010). Specific heat of a ferroelectric PZT ceramic at the morphotropic
    phase boundary. In <i>Proceedings of the 2010 IEEE International Conference on
    Solid Dielectrics</i>. Potsdam, Germany: Institute of Electrical and Electronics
    Engineers. <a href="https://doi.org/10.1109/icsd.2010.5568033">https://doi.org/10.1109/icsd.2010.5568033</a>'
  chicago: Lang, S. B., J. C. Lashley, Kimberly A Modic, R. A. Fisher, W. M. Zhu,
    and Z. G. Ye. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic
    Phase Boundary.” In <i>Proceedings of the 2010 IEEE International Conference on
    Solid Dielectrics</i>. Institute of Electrical and Electronics Engineers, 2010.
    <a href="https://doi.org/10.1109/icsd.2010.5568033">https://doi.org/10.1109/icsd.2010.5568033</a>.
  ieee: S. B. Lang, J. C. Lashley, K. A. Modic, R. A. Fisher, W. M. Zhu, and Z. G.
    Ye, “Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary,”
    in <i>Proceedings of the 2010 IEEE International Conference on Solid Dielectrics</i>,
    Potsdam, Germany, 2010.
  ista: 'Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. 2010. Specific heat
    of a ferroelectric PZT ceramic at the morphotropic phase boundary. Proceedings
    of the 2010 IEEE International Conference on Solid Dielectrics. ICSD: International
    Conference on Solid Dielectrics, 5568033.'
  mla: Lang, S. B., et al. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic
    Phase Boundary.” <i>Proceedings of the 2010 IEEE International Conference on Solid
    Dielectrics</i>, 5568033, Institute of Electrical and Electronics Engineers, 2010,
    doi:<a href="https://doi.org/10.1109/icsd.2010.5568033">10.1109/icsd.2010.5568033</a>.
  short: S.B. Lang, J.C. Lashley, K.A. Modic, R.A. Fisher, W.M. Zhu, Z.G. Ye, in:,
    Proceedings of the 2010 IEEE International Conference on Solid Dielectrics, Institute
    of Electrical and Electronics Engineers, 2010.
conference:
  end_date: 2010-06-09
  location: Potsdam, Germany
  name: 'ICSD: International Conference on Solid Dielectrics'
  start_date: 2010-06-04
date_created: 2022-08-08T09:00:17Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2023-02-21T16:26:58Z
day: '01'
doi: 10.1109/icsd.2010.5568033
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
publication: Proceedings of the 2010 IEEE International Conference on Solid Dielectrics
publication_identifier:
  eissn:
  - 2159-1687
  issn:
  - 1553-5282
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
  record:
  - id: '11754'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '11754'
abstract:
- lang: eng
  text: Ferroelectric ceramic materials have a wide range of applications because
    of their piezoelectric and pyroelectric properties. One of their most important
    physical properties is the specific heat. In this study, the specific heats of
    a series of lead-zirconate-titanate (PZT) compositions in the vicinity of the
    morphotropic phase boundary (MPB) were measured. The temperature range was from
    1.8 to 300 K. It is believed that these are the lowest temperature measurements
    ever made on PZT. Differences between the specific heats of the different compositions
    were very small. However, the calculated Debye temperatures were slightly different.
    The results are useful in computing design parameters for technical devices.
article_number: '5476345'
article_processing_charge: No
author:
- first_name: S.B.
  full_name: Lang, S.B.
  last_name: Lang
- first_name: J.C.
  full_name: Lashley, J.C.
  last_name: Lashley
- first_name: Kimberly A
  full_name: Modic, Kimberly A
  id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
  last_name: Modic
  orcid: 0000-0001-9760-3147
- first_name: R.A.
  full_name: Fisher, R.A.
  last_name: Fisher
- first_name: W.M.
  full_name: Zhu, W.M.
  last_name: Zhu
- first_name: Z.G.
  full_name: Ye, Z.G.
  last_name: Ye
citation:
  ama: 'Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. Specific heat of
    a ferroelectric PZT ceramic at the morphotropic phase boundary. In: <i>15th IEEE
    Mediterranean Electrotechnical Conference</i>. Institute of Electrical and Electronics
    Engineers; 2010. doi:<a href="https://doi.org/10.1109/melcon.2010.5476345">10.1109/melcon.2010.5476345</a>'
  apa: 'Lang, S. B., Lashley, J. C., Modic, K. A., Fisher, R. A., Zhu, W. M., &#38;
    Ye, Z. G. (2010). Specific heat of a ferroelectric PZT ceramic at the morphotropic
    phase boundary. In <i>15th IEEE Mediterranean Electrotechnical Conference</i>.
    Valletta, Malta: Institute of Electrical and Electronics Engineers. <a href="https://doi.org/10.1109/melcon.2010.5476345">https://doi.org/10.1109/melcon.2010.5476345</a>'
  chicago: Lang, S.B., J.C. Lashley, Kimberly A Modic, R.A. Fisher, W.M. Zhu, and
    Z.G. Ye. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic Phase
    Boundary.” In <i>15th IEEE Mediterranean Electrotechnical Conference</i>. Institute
    of Electrical and Electronics Engineers, 2010. <a href="https://doi.org/10.1109/melcon.2010.5476345">https://doi.org/10.1109/melcon.2010.5476345</a>.
  ieee: S. B. Lang, J. C. Lashley, K. A. Modic, R. A. Fisher, W. M. Zhu, and Z. G.
    Ye, “Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary,”
    in <i>15th IEEE Mediterranean Electrotechnical Conference</i>, Valletta, Malta,
    2010.
  ista: 'Lang SB, Lashley JC, Modic KA, Fisher RA, Zhu WM, Ye ZG. 2010. Specific heat
    of a ferroelectric PZT ceramic at the morphotropic phase boundary. 15th IEEE Mediterranean
    Electrotechnical Conference. MELECON: Mediterranean Electrotechnical Conference,
    5476345.'
  mla: Lang, S. B., et al. “Specific Heat of a Ferroelectric PZT Ceramic at the Morphotropic
    Phase Boundary.” <i>15th IEEE Mediterranean Electrotechnical Conference</i>, 5476345,
    Institute of Electrical and Electronics Engineers, 2010, doi:<a href="https://doi.org/10.1109/melcon.2010.5476345">10.1109/melcon.2010.5476345</a>.
  short: S.B. Lang, J.C. Lashley, K.A. Modic, R.A. Fisher, W.M. Zhu, Z.G. Ye, in:,
    15th IEEE Mediterranean Electrotechnical Conference, Institute of Electrical and
    Electronics Engineers, 2010.
conference:
  end_date: 2010-04-28
  location: Valletta, Malta
  name: 'MELECON: Mediterranean Electrotechnical Conference'
  start_date: 2010-04-26
date_created: 2022-08-08T09:11:43Z
date_published: 2010-04-26T00:00:00Z
date_updated: 2023-02-21T16:26:55Z
day: '26'
doi: 10.1109/melcon.2010.5476345
extern: '1'
language:
- iso: eng
month: '04'
oa_version: None
publication: 15th IEEE Mediterranean Electrotechnical Conference
publication_identifier:
  isbn:
  - 978-142445795-3
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
  record:
  - id: '11753'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Specific heat of a ferroelectric PZT ceramic at the morphotropic phase boundary
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '8472'
abstract:
- lang: eng
  text: Characterization of protein dynamics by solid-state NMR spectroscopy requires
    robust and accurate measurement protocols, which are not yet fully developed.
    In this study, we investigate the backbone dynamics of microcrystalline ubiquitin
    using different approaches. A rotational-echo double-resonance type (REDOR-type)
    methodology allows one to accurately measure 1H−15N order parameters in highly
    deuterated samples. We show that the systematic errors in the REDOR experiment
    are as low as 1% or even less, giving access to accurate data for the amplitudes
    of backbone mobility. Combining such dipolar-coupling-derived order parameters
    with autocorrelated and cross-correlated 15N relaxation rates, we are able to
    quantitate amplitudes and correlation times of backbone dynamics on picosecond
    and nanosecond time scales in a residue-resolved manner. While the mobility on
    picosecond time scales appears to have rather uniform amplitude throughout the
    protein, we unambiguously identify and quantitate nanosecond mobility with order
    parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics
    has also been revealed in solution state. The methodology used here, a combination
    of accurate dipolar-coupling measurements and different relaxation parameters,
    yields details about dynamics on different time scales and can be applied to solid
    protein samples such as amyloid fibrils or membrane proteins.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Beat H.
  full_name: Meier, Beat H.
  last_name: Meier
- first_name: Matthias
  full_name: Ernst, Matthias
  last_name: Ernst
citation:
  ama: Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics
    in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the
    American Chemical Society</i>. 2010;132(45):15957-15967. doi:<a href="https://doi.org/10.1021/ja100726a">10.1021/ja100726a</a>
  apa: Schanda, P., Meier, B. H., &#38; Ernst, M. (2010). Quantitative analysis of
    protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy.
    <i>Journal of the American Chemical Society</i>. American Chemical Society. <a
    href="https://doi.org/10.1021/ja100726a">https://doi.org/10.1021/ja100726a</a>
  chicago: Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis
    of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR
    Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical
    Society, 2010. <a href="https://doi.org/10.1021/ja100726a">https://doi.org/10.1021/ja100726a</a>.
  ieee: P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone
    dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” <i>Journal
    of the American Chemical Society</i>, vol. 132, no. 45. American Chemical Society,
    pp. 15957–15967, 2010.
  ista: Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone
    dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal
    of the American Chemical Society. 132(45), 15957–15967.
  mla: Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in
    Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the
    American Chemical Society</i>, vol. 132, no. 45, American Chemical Society, 2010,
    pp. 15957–67, doi:<a href="https://doi.org/10.1021/ja100726a">10.1021/ja100726a</a>.
  short: P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society
    132 (2010) 15957–15967.
date_created: 2020-09-18T10:11:13Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-01-12T08:19:30Z
day: '26'
doi: 10.1021/ja100726a
extern: '1'
intvolume: '       132'
issue: '45'
language:
- iso: eng
month: '10'
oa_version: None
page: 15957-15967
publication: Journal of the American Chemical Society
publication_identifier:
  issn:
  - 0002-7863
  - 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin
  by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2010'
...
---
_id: '8473'
abstract:
- lang: eng
  text: β2-microglobulin (β2m), the light chain of class I major histocompatibility
    complex, is responsible for the dialysis-related amyloidosis and, in patients
    undergoing long term dialysis, the full-length and chemically unmodified β2m converts
    into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily,
    in common to other members of this family, experiences during its folding a long-lived
    intermediate associated to the trans-to-cis isomerization of Pro-32 that has been
    addressed as the precursor of the amyloid fibril formation. In this respect, previous
    studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril
    formation in mild aggregating condition, prompted us to reinvestigate the refolding
    kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The
    analysis, conducted at ambient temperature by the band selective flip angle short
    transient real-time two-dimensional NMR techniques and probing the β2m states
    every 15 s, revealed a more complex folding energy landscape than previously reported
    for wild type β2m, involving more than a single intermediate species, and shedding
    new light into the fibrillogenic pathway. Moreover, a significant difference in
    the kinetic scheme previously characterized by optical spectroscopic methods was
    discovered for the W60G β2m mutant.
article_processing_charge: No
article_type: original
author:
- first_name: Alessandra
  full_name: Corazza, Alessandra
  last_name: Corazza
- first_name: Enrico
  full_name: Rennella, Enrico
  last_name: Rennella
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Maria Chiara
  full_name: Mimmi, Maria Chiara
  last_name: Mimmi
- first_name: Thomas
  full_name: Cutuil, Thomas
  last_name: Cutuil
- first_name: Sara
  full_name: Raimondi, Sara
  last_name: Raimondi
- first_name: Sofia
  full_name: Giorgetti, Sofia
  last_name: Giorgetti
- first_name: Federico
  full_name: Fogolari, Federico
  last_name: Fogolari
- first_name: Paolo
  full_name: Viglino, Paolo
  last_name: Viglino
- first_name: Lucio
  full_name: Frydman, Lucio
  last_name: Frydman
- first_name: Maayan
  full_name: Gal, Maayan
  last_name: Gal
- first_name: Vittorio
  full_name: Bellotti, Vittorio
  last_name: Bellotti
- first_name: Bernhard
  full_name: Brutscher, Bernhard
  last_name: Brutscher
- first_name: Gennaro
  full_name: Esposito, Gennaro
  last_name: Esposito
citation:
  ama: Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates
    along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed
    by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. 2010;285(8):5827-5835.
    doi:<a href="https://doi.org/10.1074/jbc.m109.061168">10.1074/jbc.m109.061168</a>
  apa: Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi,
    S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding
    pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional
    NMR. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry
    &#38; Molecular Biology. <a href="https://doi.org/10.1074/jbc.m109.061168">https://doi.org/10.1074/jbc.m109.061168</a>
  chicago: Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi,
    Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived
    Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin
    Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>.
    American Society for Biochemistry &#38; Molecular Biology, 2010. <a href="https://doi.org/10.1074/jbc.m109.061168">https://doi.org/10.1074/jbc.m109.061168</a>.
  ieee: A. Corazza <i>et al.</i>, “Native-unlike long-lived intermediates along the
    folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time
    two-dimensional NMR,” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8.
    American Society for Biochemistry &#38; Molecular Biology, pp. 5827–5835, 2010.
  ista: Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti
    S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito
    G. 2010. Native-unlike long-lived intermediates along the folding pathway of the
    amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR.
    Journal of Biological Chemistry. 285(8), 5827–5835.
  mla: Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the
    Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time
    Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8,
    American Society for Biochemistry &#38; Molecular Biology, 2010, pp. 5827–35,
    doi:<a href="https://doi.org/10.1074/jbc.m109.061168">10.1074/jbc.m109.061168</a>.
  short: A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi,
    S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher,
    G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.
date_created: 2020-09-18T10:11:23Z
date_published: 2010-02-19T00:00:00Z
date_updated: 2021-01-12T08:19:31Z
day: '19'
doi: 10.1074/jbc.m109.061168
extern: '1'
intvolume: '       285'
issue: '8'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '02'
oa_version: None
page: 5827-5835
publication: Journal of Biological Chemistry
publication_identifier:
  issn:
  - 0021-9258
  - 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic
  protein β2-Microglobulin revealed by real-time two-dimensional NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2010'
...
---
_id: '8506'
article_processing_charge: No
author:
- first_name: Brian R.
  full_name: Hunt, Brian R.
  last_name: Hunt
- first_name: Vadim
  full_name: Kaloshin, Vadim
  id: FE553552-CDE8-11E9-B324-C0EBE5697425
  last_name: Kaloshin
  orcid: 0000-0002-6051-2628
citation:
  ama: 'Hunt BR, Kaloshin V. Prevalence. In: <i>Handbook of Dynamical Systems</i>.
    Vol 3. Elsevier; 2010:43-87. doi:<a href="https://doi.org/10.1016/s1874-575x(10)00310-3">10.1016/s1874-575x(10)00310-3</a>'
  apa: Hunt, B. R., &#38; Kaloshin, V. (2010). Prevalence. In <i>Handbook of Dynamical
    Systems</i> (Vol. 3, pp. 43–87). Elsevier. <a href="https://doi.org/10.1016/s1874-575x(10)00310-3">https://doi.org/10.1016/s1874-575x(10)00310-3</a>
  chicago: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In <i>Handbook of Dynamical
    Systems</i>, 3:43–87. Elsevier, 2010. <a href="https://doi.org/10.1016/s1874-575x(10)00310-3">https://doi.org/10.1016/s1874-575x(10)00310-3</a>.
  ieee: B. R. Hunt and V. Kaloshin, “Prevalence,” in <i>Handbook of Dynamical Systems</i>,
    vol. 3, Elsevier, 2010, pp. 43–87.
  ista: 'Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems.
    vol. 3, 43–87.'
  mla: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” <i>Handbook of Dynamical
    Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87, doi:<a href="https://doi.org/10.1016/s1874-575x(10)00310-3">10.1016/s1874-575x(10)00310-3</a>.
  short: B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010,
    pp. 43–87.
date_created: 2020-09-18T10:47:48Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:45Z
day: '01'
doi: 10.1016/s1874-575x(10)00310-3
extern: '1'
intvolume: '         3'
language:
- iso: eng
month: '01'
oa_version: None
page: 43-87
publication: Handbook of Dynamical Systems
publication_identifier:
  isbn:
  - '9780444531414'
  issn:
  - 1874-575X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Prevalence
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2010'
...
