---
_id: '1234'
abstract:
- lang: eng
  text: We present a new algorithm for the statistical model checking of Markov chains
    with respect to unbounded temporal properties, including full linear temporal
    logic. The main idea is that we monitor each simulation run on the fly, in order
    to detect quickly if a bottom strongly connected component is entered with high
    probability, in which case the simulation run can be terminated early. As a result,
    our simulation runs are often much shorter than required by termination bounds
    that are computed a priori for a desired level of confidence on a large state
    space. In comparison to previous algorithms for statistical model checking our
    method is not only faster in many cases but also requires less information about
    the system, namely, only the minimum transition probability that occurs in the
    Markov chain. In addition, our method can be generalised to unbounded quantitative
    properties such as mean-payoff bounds.
acknowledgement: "This research was funded in part by the European Research Council
  (ERC) under\r\ngrant  agreement  267989  (QUAREM),  the  Austrian  Science  Fund
  \ (FWF)  under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
  the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh
  Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility
  Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation
  under grant agreement P202/12/G061."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
  full_name: Daca, Przemyslaw
  id: 49351290-F248-11E8-B48F-1D18A9856A87
  last_name: Daca
- 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: Jan
  full_name: Kretinsky, Jan
  id: 44CEF464-F248-11E8-B48F-1D18A9856A87
  last_name: Kretinsky
  orcid: 0000-0002-8122-2881
- first_name: Tatjana
  full_name: Petrov, Tatjana
  id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
  last_name: Petrov
  orcid: 0000-0002-9041-0905
citation:
  ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking
    for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:<a
    href="https://doi.org/10.1007/978-3-662-49674-9_7">10.1007/978-3-662-49674-9_7</a>'
  apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Faster
    statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129).
    Presented at the TACAS: Tools and Algorithms for the Construction and Analysis
    of Systems, Eindhoven, The Netherlands: Springer. <a href="https://doi.org/10.1007/978-3-662-49674-9_7">https://doi.org/10.1007/978-3-662-49674-9_7</a>'
  chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
    “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29.
    Springer, 2016. <a href="https://doi.org/10.1007/978-3-662-49674-9_7">https://doi.org/10.1007/978-3-662-49674-9_7</a>.
  ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical
    model checking for unbounded temporal properties,” presented at the TACAS: Tools
    and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands,
    2016, vol. 9636, pp. 112–129.'
  ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model
    checking for unbounded temporal properties. TACAS: Tools and Algorithms for the
    Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.'
  mla: Daca, Przemyslaw, et al. <i>Faster Statistical Model Checking for Unbounded
    Temporal Properties</i>. Vol. 9636, Springer, 2016, pp. 112–29, doi:<a href="https://doi.org/10.1007/978-3-662-49674-9_7">10.1007/978-3-662-49674-9_7</a>.
  short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp.
    112–129.
conference:
  end_date: 2016-04-08
  location: Eindhoven, The Netherlands
  name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
  start_date: 2016-04-02
date_created: 2018-12-11T11:50:51Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1007/978-3-662-49674-9_7
ec_funded: 1
intvolume: '      9636'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1504.05739
month: '01'
oa: 1
oa_version: Preprint
page: 112 - 129
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6099'
quality_controlled: '1'
related_material:
  record:
  - id: '471'
    relation: later_version
    status: public
  - id: '1155'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Faster statistical model checking for unbounded temporal properties
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9636
year: '2016'
...
---
_id: '1235'
abstract:
- lang: eng
  text: 'A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets
    of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute
    a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈
    S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah
    et al. recently constructed the first constrained PRF for inputs of arbitrary
    length whose sets S are decided by Turing machines. They use their CPRF to build
    broadcast encryption and the first ID-based non-interactive key exchange for an
    unbounded number of users. Their constrained keys are obfuscated circuits and
    are therefore large. In this work we drastically reduce the key size and define
    a constrained key for a Turing machine M as a short signature on M. For this,
    we introduce a new signature primitive with constrained signing keys that let
    one only sign certain messages, while forging a signature on others is hard even
    when knowing the coins for key generation.'
acknowledgement: H. Abusalah—Research supported by the European Research Council,
  ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
author:
- first_name: Hamza M
  full_name: Abusalah, Hamza M
  id: 40297222-F248-11E8-B48F-1D18A9856A87
  last_name: Abusalah
- first_name: Georg
  full_name: Fuchsbauer, Georg
  id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
  last_name: Fuchsbauer
citation:
  ama: 'Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short
    keys. In: Vol 9696. Springer; 2016:445-463. doi:<a href="https://doi.org/10.1007/978-3-319-39555-5_24">10.1007/978-3-319-39555-5_24</a>'
  apa: 'Abusalah, H. M., &#38; Fuchsbauer, G. (2016). Constrained PRFs for unbounded
    inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied
    Cryptography and Network Security, Guildford, UK: Springer. <a href="https://doi.org/10.1007/978-3-319-39555-5_24">https://doi.org/10.1007/978-3-319-39555-5_24</a>'
  chicago: Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded
    Inputs with Short Keys,” 9696:445–63. Springer, 2016. <a href="https://doi.org/10.1007/978-3-319-39555-5_24">https://doi.org/10.1007/978-3-319-39555-5_24</a>.
  ieee: 'H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs
    with short keys,” presented at the ACNS: Applied Cryptography and Network Security,
    Guildford, UK, 2016, vol. 9696, pp. 445–463.'
  ista: 'Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with
    short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696,
    445–463.'
  mla: Abusalah, Hamza M., and Georg Fuchsbauer. <i>Constrained PRFs for Unbounded
    Inputs with Short Keys</i>. Vol. 9696, Springer, 2016, pp. 445–63, doi:<a href="https://doi.org/10.1007/978-3-319-39555-5_24">10.1007/978-3-319-39555-5_24</a>.
  short: H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.
conference:
  end_date: 2016-06-22
  location: Guildford, UK
  name: 'ACNS: Applied Cryptography and Network Security'
  start_date: 2016-06-19
date_created: 2018-12-11T11:50:52Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_24
ec_funded: 1
intvolume: '      9696'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2016/279.pdf
month: '01'
oa: 1
oa_version: Submitted Version
page: 445 - 463
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '259668'
  name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6098'
quality_controlled: '1'
related_material:
  record:
  - id: '83'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Constrained PRFs for unbounded inputs with short keys
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9696
year: '2016'
...
---
_id: '1236'
abstract:
- lang: eng
  text: 'A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets
    of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute
    a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while
    even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13
    Boneh and Waters gave a construction which supports the most general set family
    so far. Its keys kc are defined for sets decided by boolean circuits C and enable
    evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF
    input length and the size of the circuits C for which constrained keys can be
    computed must be fixed beforehand during key generation. We construct a constrained
    PRF that has an unbounded input length and whose constrained keys can be defined
    for any set recognized by a Turing machine. The only a priori bound we make is
    on the description size of the machines. We prove our construction secure assuming
    publiccoin differing-input obfuscation. As applications of our constrained PRF
    we build a broadcast encryption scheme where the number of potential receivers
    need not be fixed at setup (in particular, the length of the keys is independent
    of the number of parties) and the first identity-based non-interactive key exchange
    protocol with no bound on the number of parties that can agree on a shared key.'
acknowledgement: Supported by the European Research Council, ERC Starting Grant (259668-PSPC).
alternative_title:
- LNCS
author:
- first_name: Hamza M
  full_name: Abusalah, Hamza M
  id: 40297222-F248-11E8-B48F-1D18A9856A87
  last_name: Abusalah
- first_name: Georg
  full_name: Fuchsbauer, Georg
  id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
  last_name: Fuchsbauer
- first_name: Krzysztof Z
  full_name: Pietrzak, Krzysztof Z
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs.
    In: Vol 9610. Springer; 2016:413-428. doi:<a href="https://doi.org/10.1007/978-3-319-29485-8_24">10.1007/978-3-319-29485-8_24</a>'
  apa: 'Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained
    PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics
    in Cryptology, San Francisco, CA, USA: Springer. <a href="https://doi.org/10.1007/978-3-319-29485-8_24">https://doi.org/10.1007/978-3-319-29485-8_24</a>'
  chicago: Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained
    PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href="https://doi.org/10.1007/978-3-319-29485-8_24">https://doi.org/10.1007/978-3-319-29485-8_24</a>.
  ieee: 'H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for
    unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco,
    CA, USA, 2016, vol. 9610, pp. 413–428.'
  ista: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded
    inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.'
  mla: Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol.
    9610, Springer, 2016, pp. 413–28, doi:<a href="https://doi.org/10.1007/978-3-319-29485-8_24">10.1007/978-3-319-29485-8_24</a>.
  short: H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.
conference:
  end_date: 2016-03-04
  location: San Francisco, CA, USA
  name: 'CT-RSA: Topics in Cryptology'
  start_date: 2016-02-29
date_created: 2018-12-11T11:50:52Z
date_published: 2016-02-02T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '02'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-29485-8_24
ec_funded: 1
file:
- access_level: open_access
  checksum: 3851cee49933ae13b1272e516f213e13
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:05Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '4664'
  file_name: IST-2017-764-v1+1_279.pdf
  file_size: 495176
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '      9610'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 413 - 428
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '259668'
  name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '6097'
pubrep_id: '764'
quality_controlled: '1'
related_material:
  record:
  - id: '83'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Constrained PRFs for unbounded inputs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9610
year: '2016'
...
---
_id: '1238'
abstract:
- lang: eng
  text: The dynamic localization of endosomal compartments labeled with targeted fluorescent
    protein tags is routinely followed by time lapse fluorescence microscopy approaches
    and single particle tracking algorithms. In this way trajectories of individual
    endosomes can be mapped and linked to physiological processes as cell growth.
    However, other aspects of dynamic behavior including endosomal interactions are
    difficult to follow in this manner. Therefore, we characterized the localization
    and dynamic properties of early and late endosomes throughout the entire course
    of root hair formation by means of spinning disc time lapse imaging and post-acquisition
    automated multitracking and quantitative analysis. Our results show differential
    motile behavior of early and late endosomes and interactions of late endosomes
    that may be specified to particular root hair domains. Detailed data analysis
    revealed a particular transient interaction between late endosomes—termed herein
    as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially
    located in the root hair tip interacted as dancing-endosomes and traveled short
    distances during this interaction. Finally, sizes of early and late endosomes
    were addressed by means of super-resolution structured illumination microscopy
    (SIM) to corroborate measurements on the spinning disc. This is a first study
    providing quantitative microscopic data on dynamic spatio-temporal interactions
    of endosomes during root hair tip growth.
acknowledgement: "This work was supported by National Program for Sustainability I
  (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional
  Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help
  with the statistics."
article_number: '1262'
author:
- first_name: Daniel
  full_name: Von Wangenheim, Daniel
  id: 49E91952-F248-11E8-B48F-1D18A9856A87
  last_name: Von Wangenheim
  orcid: 0000-0002-6862-1247
- first_name: Amparo
  full_name: Rosero, Amparo
  last_name: Rosero
- first_name: George
  full_name: Komis, George
  last_name: Komis
- first_name: Olga
  full_name: Šamajová, Olga
  last_name: Šamajová
- first_name: Miroslav
  full_name: Ovečka, Miroslav
  last_name: Ovečka
- first_name: Boris
  full_name: Voigt, Boris
  last_name: Voigt
- first_name: Jozef
  full_name: Šamaj, Jozef
  last_name: Šamaj
citation:
  ama: von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root
    hair growth. <i>Frontiers in Plant Science</i>. 2016;6(JAN2016). doi:<a href="https://doi.org/10.3389/fpls.2015.01262">10.3389/fpls.2015.01262</a>
  apa: von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt,
    B., &#38; Šamaj, J. (2016). Endosomal interactions during root hair growth. <i>Frontiers
    in Plant Science</i>. Frontiers Research Foundation. <a href="https://doi.org/10.3389/fpls.2015.01262">https://doi.org/10.3389/fpls.2015.01262</a>
  chicago: Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav
    Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair
    Growth.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2016.
    <a href="https://doi.org/10.3389/fpls.2015.01262">https://doi.org/10.3389/fpls.2015.01262</a>.
  ieee: D. von Wangenheim <i>et al.</i>, “Endosomal interactions during root hair
    growth,” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016. Frontiers Research
    Foundation, 2016.
  ista: von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj
    J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science.
    6(JAN2016), 1262.
  mla: von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.”
    <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016, 1262, Frontiers Research
    Foundation, 2016, doi:<a href="https://doi.org/10.3389/fpls.2015.01262">10.3389/fpls.2015.01262</a>.
  short: D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt,
    J. Šamaj, Frontiers in Plant Science 6 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2021-01-12T06:49:18Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.3389/fpls.2015.01262
file:
- access_level: open_access
  checksum: 3127eab844d53564bf47e2b6b42f1ca0
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:09:36Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '4760'
  file_name: IST-2016-710-v1+1_fpls-06-01262.pdf
  file_size: 1640550
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '         6'
issue: JAN2016
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6094'
pubrep_id: '710'
quality_controlled: '1'
scopus_import: 1
status: public
title: Endosomal interactions during root hair growth
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1240'
abstract:
- lang: eng
  text: 'Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as
    gene regulators and may ultimately be more numerous than protein-coding genes
    in the human genome. Despite large numbers of reported lncRNAs, reference annotations
    are likely incomplete due to their lower and tighter tissue-specific expression
    compared to mRNAs. An unexplored factor potentially confounding lncRNA identification
    is inter-individual expression variability. Here, we characterize lncRNA natural
    expression variability in human primary granulocytes. Results: We annotate granulocyte
    lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple
    lncRNAs absent from reference annotations, and use this to investigate three known
    features (higher tissue-specificity, lower expression, and reduced splicing efficiency)
    of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals
    sampled three times at 1- or more than 1-month intervals. We show that lncRNAs
    display significantly more inter-individual expression variability compared to
    mRNAs. We confirm this finding in two independent human datasets by analyzing
    multiple tissues from the GTEx project and lymphoblastoid cell lines from the
    GEUVADIS project. Using the latter dataset we also show that including more human
    donors into the transcriptome annotation pipeline allows identification of an
    increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions:
    A comprehensive annotation of lncRNAs is known to require an approach that is
    sensitive to low and tight tissue-specific expression. Here we show that increased
    inter-individual expression variability is an additional general lncRNA feature
    to consider when creating a comprehensive annotation of human lncRNAs or proposing
    their use as prognostic or disease markers.'
acknowledgement: "This study was partly funded by the Austrian Science Fund (FWF F43-B09,
  FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of
  Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth
  Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the
  CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe
  Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing
  and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions,
  Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript."
article_number: '14'
author:
- first_name: Aleksandra
  full_name: Kornienko, Aleksandra
  last_name: Kornienko
- first_name: Christoph
  full_name: Dotter, Christoph
  id: 4C66542E-F248-11E8-B48F-1D18A9856A87
  last_name: Dotter
- first_name: Philipp
  full_name: Guenzl, Philipp
  last_name: Guenzl
- first_name: Heinz
  full_name: Gisslinger, Heinz
  last_name: Gisslinger
- first_name: Bettina
  full_name: Gisslinger, Bettina
  last_name: Gisslinger
- first_name: Ciara
  full_name: Cleary, Ciara
  last_name: Cleary
- first_name: Robert
  full_name: Kralovics, Robert
  last_name: Kralovics
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
- first_name: Denise
  full_name: Barlow, Denise
  last_name: Barlow
citation:
  ama: Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher
    natural expression variation than protein-coding genes in healthy humans. <i>Genome
    Biology</i>. 2016;17(1). doi:<a href="https://doi.org/10.1186/s13059-016-0873-8">10.1186/s13059-016-0873-8</a>
  apa: Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary,
    C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression
    variation than protein-coding genes in healthy humans. <i>Genome Biology</i>.
    BioMed Central. <a href="https://doi.org/10.1186/s13059-016-0873-8">https://doi.org/10.1186/s13059-016-0873-8</a>
  chicago: Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger,
    Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise
    Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than
    Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>. BioMed Central,
    2016. <a href="https://doi.org/10.1186/s13059-016-0873-8">https://doi.org/10.1186/s13059-016-0873-8</a>.
  ieee: A. Kornienko <i>et al.</i>, “Long non-coding RNAs display higher natural expression
    variation than protein-coding genes in healthy humans,” <i>Genome Biology</i>,
    vol. 17, no. 1. BioMed Central, 2016.
  ista: Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics
    R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression
    variation than protein-coding genes in healthy humans. Genome Biology. 17(1),
    14.
  mla: Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural
    Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>,
    vol. 17, no. 1, 14, BioMed Central, 2016, doi:<a href="https://doi.org/10.1186/s13059-016-0873-8">10.1186/s13059-016-0873-8</a>.
  short: A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary,
    R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '29'
ddc:
- '576'
department:
- _id: GaNo
doi: 10.1186/s13059-016-0873-8
file:
- access_level: open_access
  checksum: a268beee1a690801c83ec6729f9ebc5b
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:10:05Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '4789'
  file_name: IST-2016-709-v1+1_s13059-016-0873-8.pdf
  file_size: 2914601
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '        17'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '6093'
pubrep_id: '709'
quality_controlled: '1'
scopus_import: 1
status: public
title: Long non-coding RNAs display higher natural expression variation than protein-coding
  genes in healthy humans
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1241'
abstract:
- lang: eng
  text: 'How likely is it that a population escapes extinction through adaptive evolution?
    The answer to this question is of great relevance in conservation biology, where
    we aim at species’ rescue and the maintenance of biodiversity, and in agriculture
    and medicine, where we seek to hamper the emergence of pesticide or drug resistance.
    By reshuffling the genome, recombination has two antagonistic effects on the probability
    of evolutionary rescue: It generates and it breaks up favorable gene combinations.
    Which of the two effects prevails depends on the fitness effects of mutations
    and on the impact of stochasticity on the allele frequencies. In this article,
    we analyze a mathematical model for rescue after a sudden environmental change
    when adaptation is contingent on mutations at two loci. The analysis reveals a
    complex nonlinear dependence of population survival on recombination. We moreover
    find that, counterintuitively, a fast eradication of the wild type can promote
    rescue in the presence of recombination. The model also shows that two-step rescue
    is not unlikely to happen and can even be more likely than single-step rescue
    (where adaptation relies on a single mutation), depending on the circumstances.'
acknowledgement: This work was made possible by a “For Women in Science” fellowship
  (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations
  Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences
  with financial support from the Federal Ministry for Science and Research Austria)
  and European Research Council grant 250152 (to Nick Barton).
author:
- first_name: Hildegard
  full_name: Uecker, Hildegard
  id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
  last_name: Uecker
  orcid: 0000-0001-9435-2813
- first_name: Joachim
  full_name: Hermisson, Joachim
  last_name: Hermisson
citation:
  ama: Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>.
    2016;202(2):721-732. doi:<a href="https://doi.org/10.1534/genetics.115.180299">10.1534/genetics.115.180299</a>
  apa: Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary
    rescue. <i>Genetics</i>. Genetics Society of America. <a href="https://doi.org/10.1534/genetics.115.180299">https://doi.org/10.1534/genetics.115.180299</a>
  chicago: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in
    Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href="https://doi.org/10.1534/genetics.115.180299">https://doi.org/10.1534/genetics.115.180299</a>.
  ieee: H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,”
    <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.
  ista: Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue.
    Genetics. 202(2), 721–732.
  mla: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary
    Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016,
    pp. 721–32, doi:<a href="https://doi.org/10.1534/genetics.115.180299">10.1534/genetics.115.180299</a>.
  short: H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2023-02-21T10:24:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.115.180299
ec_funded: 1
intvolume: '       202'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://biorxiv.org/content/early/2015/07/06/022020.abstract
month: '02'
oa: 1
oa_version: Preprint
page: 721 - 732
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '250152'
  name: Limits to selection in biology and in evolutionary computation
- _id: 25B67606-B435-11E9-9278-68D0E5697425
  name: L'OREAL Fellowship
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6091'
quality_controlled: '1'
scopus_import: 1
status: public
title: The role of recombination in evolutionary rescue
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1242'
abstract:
- lang: eng
  text: A crucial step in the regulation of gene expression is binding of transcription
    factor (TF) proteins to regulatory sites along the DNA. But transcription factors
    act at nanomolar concentrations, and noise due to random arrival of these molecules
    at their binding sites can severely limit the precision of regulation. Recent
    work on the optimization of information flow through regulatory networks indicates
    that the lower end of the dynamic range of concentrations is simply inaccessible,
    overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain
    proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest
    a scheme in which transcription factors also act as indirect translational regulators,
    binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule
    acts as an independent sensor of the input concentration, and averaging over these
    multiple sensors reduces the noise. We analyze information flow through this scheme
    and identify conditions under which it outperforms direct transcriptional regulation.
    Our results suggest that the dual role of homeodomain proteins is not just a historical
    accident, but a solution to a crucial physics problem in the regulation of gene
    expression.
acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions.
  This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370
  from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W.
  acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561.
  G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S."
article_number: '022404'
author:
- first_name: Thomas R
  full_name: Sokolowski, Thomas R
  id: 3E999752-F248-11E8-B48F-1D18A9856A87
  last_name: Sokolowski
  orcid: 0000-0002-1287-3779
- first_name: Aleksandra
  full_name: Walczak, Aleksandra
  last_name: Walczak
- first_name: William
  full_name: Bialek, William
  last_name: Bialek
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
citation:
  ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of
    transcription factor action by translational regulation. <i>Physical Review E
    Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href="https://doi.org/10.1103/PhysRevE.93.022404">10.1103/PhysRevE.93.022404</a>
  apa: Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending
    the dynamic range of transcription factor action by translational regulation.
    <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American
    Institute of Physics. <a href="https://doi.org/10.1103/PhysRevE.93.022404">https://doi.org/10.1103/PhysRevE.93.022404</a>
  chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik.
    “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”
    <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American
    Institute of Physics, 2016. <a href="https://doi.org/10.1103/PhysRevE.93.022404">https://doi.org/10.1103/PhysRevE.93.022404</a>.
  ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic
    range of transcription factor action by translational regulation,” <i>Physical
    Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American
    Institute of Physics, 2016.
  ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic
    range of transcription factor action by translational regulation. Physical Review
    E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
  mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription
    Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear
    and Soft Matter Physics</i>, vol. 93, no. 2, 022404, American Institute of Physics,
    2016, doi:<a href="https://doi.org/10.1103/PhysRevE.93.022404">10.1103/PhysRevE.93.022404</a>.
  short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical
    Nonlinear and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-04T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '04'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.93.022404
intvolume: '        93'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1507.02562
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28844-B27
  name: Biophysics of information processing in gene regulation
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6088'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extending the dynamic range of transcription factor action by translational
  regulation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1244'
abstract:
- lang: eng
  text: Cell polarity refers to a functional spatial organization of proteins that
    is crucial for the control of essential cellular processes such as growth and
    division. To establish polarity, cells rely on elaborate regulation networks that
    control the distribution of proteins at the cell membrane. In fission yeast cells,
    a microtubule-dependent network has been identified that polarizes the distribution
    of signaling proteins that restricts growth to cell ends and targets the cytokinetic
    machinery to the middle of the cell. Although many molecular components have been
    shown to play a role in this network, it remains unknown which molecular functionalities
    are minimally required to establish a polarized protein distribution in this system.
    Here we show that a membrane-binding protein fragment, which distributes homogeneously
    in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching
    it to a cytoplasmic microtubule end-binding protein. This concentration results
    in a polarized pattern of chimera proteins with a spatial extension that is very
    reminiscent of natural polarity patterns in fission yeast. However, chimera levels
    fluctuate in response to microtubule dynamics, and disruption of microtubules
    leads to disappearance of the pattern. Numerical simulations confirm that the
    combined functionality of membrane anchoring and microtubule tip affinity is in
    principle sufficient to create polarized patterns. Our chimera protein may thus
    represent a simple molecular functionality that is able to polarize the membrane,
    onto which additional layers of molecular complexity may be built to provide the
    temporal robustness that is typical of natural polarity patterns.
acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian
  Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong
  Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions;
  and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the
  manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor
  Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse
  organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”"
author:
- first_name: Pierre
  full_name: Recouvreux, Pierre
  last_name: Recouvreux
- first_name: Thomas R
  full_name: Sokolowski, Thomas R
  id: 3E999752-F248-11E8-B48F-1D18A9856A87
  last_name: Sokolowski
  orcid: 0000-0002-1287-3779
- first_name: Aristea
  full_name: Grammoustianou, Aristea
  last_name: Grammoustianou
- first_name: Pieter
  full_name: Tenwolde, Pieter
  last_name: Tenwolde
- first_name: Marileen
  full_name: Dogterom, Marileen
  last_name: Dogterom
citation:
  ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera
    proteins with affinity for membranes and microtubule tips polarize in the membrane
    of fission yeast cells. <i>PNAS</i>. 2016;113(7):1811-1816. doi:<a href="https://doi.org/10.1073/pnas.1419248113">10.1073/pnas.1419248113</a>
  apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &#38;
    Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule
    tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. National Academy
    of Sciences. <a href="https://doi.org/10.1073/pnas.1419248113">https://doi.org/10.1073/pnas.1419248113</a>
  chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter
    Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes
    and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>.
    National Academy of Sciences, 2016. <a href="https://doi.org/10.1073/pnas.1419248113">https://doi.org/10.1073/pnas.1419248113</a>.
  ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom,
    “Chimera proteins with affinity for membranes and microtubule tips polarize in
    the membrane of fission yeast cells,” <i>PNAS</i>, vol. 113, no. 7. National Academy
    of Sciences, pp. 1811–1816, 2016.
  ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016.
    Chimera proteins with affinity for membranes and microtubule tips polarize in
    the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
  mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and
    Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>,
    vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:<a href="https://doi.org/10.1073/pnas.1419248113">10.1073/pnas.1419248113</a>.
  short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom,
    PNAS 113 (2016) 1811–1816.
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-16T00:00:00Z
date_updated: 2021-01-12T06:49:21Z
day: '16'
department:
- _id: GaTk
doi: 10.1073/pnas.1419248113
intvolume: '       113'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/
month: '02'
oa: 1
oa_version: Submitted Version
page: 1811 - 1816
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6085'
quality_controlled: '1'
scopus_import: 1
status: public
title: Chimera proteins with affinity for membranes and microtubule tips polarize
  in the membrane of fission yeast cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1246'
abstract:
- lang: eng
  text: Near-field imaging is a powerful tool to investigate the complex structure
    of light at the nanoscale. Recent advances in near-field imaging have indicated
    the possibility for the complete reconstruction of both electric and magnetic
    components of the evanescent field. Here we study the electro-magnetic field structure
    of surface plasmon polariton waves propagating along subwavelength gold nanowires
    by performing phase- and polarization-resolved near-field microscopy in collection
    mode. By applying the optical reciprocity theorem, we describe the signal collected
    by the probe as an overlap integral of the nanowire's evanescent field and the
    probe's response function. As a result, we find that the probe's sensitivity to
    the magnetic field is approximately equal to its sensitivity to the electric field.
    Through rigorous modeling of the nanowire mode as well as the aperture probe response
    function, we obtain a good agreement between experimentally measured signals and
    a numerical model. Our findings provide a better understanding of aperture-based
    near-field imaging of the nanoscopic plasmonic and photonic structures and are
    helpful for the interpretation of future near-field experiments.
acknowledgement: 'This work is supported part of the research program of the Netherlands
  Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization
  for Scientific Research (NWO), and part of this work has been funded by the project
  ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging
  Technologies (FET) program within the Seventh Framework Programme for Research of
  the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges
  funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).'
article_number: '22665'
author:
- first_name: Irina
  full_name: Kabakova, Irina
  last_name: Kabakova
- first_name: Anouk
  full_name: De Hoogh, Anouk
  last_name: De Hoogh
- first_name: Ruben
  full_name: Van Der Wel, Ruben
  last_name: Van Der Wel
- first_name: Matthias
  full_name: Wulf, Matthias
  id: 45598606-F248-11E8-B48F-1D18A9856A87
  last_name: Wulf
  orcid: 0000-0001-6613-1378
- first_name: Boris
  full_name: Le Feber, Boris
  last_name: Le Feber
- first_name: Laurens
  full_name: Kuipers, Laurens
  last_name: Kuipers
citation:
  ama: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging
    of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>.
    2016;6. doi:<a href="https://doi.org/10.1038/srep22665">10.1038/srep22665</a>
  apa: Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &#38;
    Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires.
    <i>Scientific Reports</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/srep22665">https://doi.org/10.1038/srep22665</a>
  chicago: Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris
    Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic
    Nanowires.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href="https://doi.org/10.1038/srep22665">https://doi.org/10.1038/srep22665</a>.
  ieee: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers,
    “Imaging of electric and magnetic fields near plasmonic nanowires,” <i>Scientific
    Reports</i>, vol. 6. Nature Publishing Group, 2016.
  ista: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016.
    Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
    6, 22665.
  mla: Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic
    Nanowires.” <i>Scientific Reports</i>, vol. 6, 22665, Nature Publishing Group,
    2016, doi:<a href="https://doi.org/10.1038/srep22665">10.1038/srep22665</a>.
  short: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers,
    Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:55Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '07'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1038/srep22665
file:
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  creator: system
  date_created: 2018-12-12T10:14:11Z
  date_updated: 2020-07-14T12:44:41Z
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  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '         6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6082'
pubrep_id: '707'
quality_controlled: '1'
scopus_import: 1
status: public
title: Imaging of electric and magnetic fields near plasmonic nanowires
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1247'
abstract:
- lang: eng
  text: The shaping of organs in plants depends on the intercellular flow of the phytohormone
    auxin, of which the directional signaling is determined by the polar subcellular
    localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics
    of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID
    kinase, which act antagonistically to mediate their apical-basal polar delivery.
    Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase
    activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting
    from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding
    for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant
    phenotypes [i.e., reduced apical dominance, primary root length, lateral root
    emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia;
    decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems;
    hypergravitropic root growth and response; increased IAA levels in shoot apices;
    and reduced auxin accumulation in root meristems] support a role for RON3 in auxin
    biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3
    might act in PIN transporter trafficking. Indeed, pharmacological interference
    with vesicle trafficking processes revealed that single ron3-2 and double ron3-2
    rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our
    data indicate that RON3 contributes to auxin-mediated development by playing a
    role in PIN recycling and polarity establishment through regulation of the PP2A
    complex activity.
acknowledgement: "This work was supported by the Ghent University Special Research
  Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP)
  (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted
  to the Agency for Science and Technology for\r\na predoctoral fellowship."
author:
- first_name: Michael
  full_name: Karampelias, Michael
  last_name: Karampelias
- first_name: Pia
  full_name: Neyt, Pia
  last_name: Neyt
- first_name: Steven
  full_name: De Groeve, Steven
  last_name: De Groeve
- first_name: Stijn
  full_name: Aesaert, Stijn
  last_name: Aesaert
- first_name: Griet
  full_name: Coussens, Griet
  last_name: Coussens
- first_name: Jakub
  full_name: Rolčík, Jakub
  last_name: Rolčík
- first_name: Leonardo
  full_name: Bruno, Leonardo
  last_name: Bruno
- first_name: Nancy
  full_name: De Winne, Nancy
  last_name: De Winne
- first_name: Annemie
  full_name: Van Minnebruggen, Annemie
  last_name: Van Minnebruggen
- first_name: Marc
  full_name: Van Montagu, Marc
  last_name: Van Montagu
- first_name: Maria
  full_name: Ponce, Maria
  last_name: Ponce
- first_name: José
  full_name: Micol, José
  last_name: Micol
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Geert
  full_name: De Jaeger, Geert
  last_name: De Jaeger
- first_name: Mieke
  full_name: Van Lijsebettens, Mieke
  last_name: Van Lijsebettens
citation:
  ama: Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development
    by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>.
    2016;113(10):2768-2773. doi:<a href="https://doi.org/10.1073/pnas.1501343112">10.1073/pnas.1501343112</a>
  apa: Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík,
    J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase
    2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. National Academy
    of Sciences. <a href="https://doi.org/10.1073/pnas.1501343112">https://doi.org/10.1073/pnas.1501343112</a>
  chicago: Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet
    Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development
    by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>.
    National Academy of Sciences, 2016. <a href="https://doi.org/10.1073/pnas.1501343112">https://doi.org/10.1073/pnas.1501343112</a>.
  ieee: M. Karampelias <i>et al.</i>, “ROTUNDA3 function in plant development by phosphatase
    2A-mediated regulation of auxin transporter recycling,” <i>PNAS</i>, vol. 113,
    no. 10. National Academy of Sciences, pp. 2768–2773, 2016.
  ista: Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno
    L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De
    Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by
    phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10),
    2768–2773.
  mla: Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase
    2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>, vol. 113,
    no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:<a href="https://doi.org/10.1073/pnas.1501343112">10.1073/pnas.1501343112</a>.
  short: M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík,
    L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol,
    J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-08T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '08'
department:
- _id: JiFr
doi: 10.1073/pnas.1501343112
ec_funded: 1
intvolume: '       113'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/
month: '03'
oa: 1
oa_version: Submitted Version
page: 2768 - 2773
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '282300'
  name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6081'
quality_controlled: '1'
scopus_import: 1
status: public
title: ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation
  of auxin transporter recycling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1248'
abstract:
- lang: eng
  text: Life depends as much on the flow of information as on the flow of energy.
    Here we review the many efforts to make this intuition precise. Starting with
    the building blocks of information theory, we explore examples where it has been
    possible to measure, directly, the flow of information in biological networks,
    or more generally where information-theoretic ideas have been used to guide the
    analysis of experiments. Systems of interest range from single molecules (the
    sequence diversity in families of proteins) to groups of organisms (the distribution
    of velocities in flocks of birds), and all scales in between. Many of these analyses
    are motivated by the idea that biological systems may have evolved to optimize
    the gathering and representation of information, and we review the experimental
    evidence for this optimization, again across a wide range of scales.
acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation
  (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651),
  by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations."
author:
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
- first_name: William
  full_name: Bialek, William
  last_name: Bialek
citation:
  ama: Tkačik G, Bialek W. Information processing in living systems. <i>Annual Review
    of Condensed Matter Physics</i>. 2016;7:89-117. doi:<a href="https://doi.org/10.1146/annurev-conmatphys-031214-014803">10.1146/annurev-conmatphys-031214-014803</a>
  apa: Tkačik, G., &#38; Bialek, W. (2016). Information processing in living systems.
    <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews. <a href="https://doi.org/10.1146/annurev-conmatphys-031214-014803">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>
  chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
    <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews, 2016. <a href="https://doi.org/10.1146/annurev-conmatphys-031214-014803">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>.
  ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” <i>Annual
    Review of Condensed Matter Physics</i>, vol. 7. Annual Reviews, pp. 89–117, 2016.
  ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual
    Review of Condensed Matter Physics. 7, 89–117.
  mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
    <i>Annual Review of Condensed Matter Physics</i>, vol. 7, Annual Reviews, 2016,
    pp. 89–117, doi:<a href="https://doi.org/10.1146/annurev-conmatphys-031214-014803">10.1146/annurev-conmatphys-031214-014803</a>.
  short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016)
    89–117.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '10'
department:
- _id: GaTk
doi: 10.1146/annurev-conmatphys-031214-014803
intvolume: '         7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1412.8752
month: '03'
oa: 1
oa_version: Preprint
page: 89 - 117
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P 25651-N26
  name: Sensitivity to higher-order statistics in natural scenes
publication: Annual Review of Condensed Matter Physics
publication_status: published
publisher: Annual Reviews
publist_id: '6080'
quality_controlled: '1'
scopus_import: 1
status: public
title: Information processing in living systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1249'
abstract:
- lang: eng
  text: 'Actin and myosin assemble into a thin layer of a highly dynamic network underneath
    the membrane of eukaryotic cells. This network generates the forces that drive
    cell- and tissue-scale morphogenetic processes. The effective material properties
    of this active network determine large-scale deformations and other morphogenetic
    events. For example, the characteristic time of stress relaxation (the Maxwell
    time τM) in the actomyosin sets the timescale of large-scale deformation of the
    cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic
    length λ) sets the length scale of slow deformations, and a large hydrodynamic
    length is a prerequisite for long-ranged cortical flows. Here we introduce a method
    to determine physical parameters of the actomyosin cortical layer in vivo directly
    from laser ablation experiments. For this we investigate the cortical response
    to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the
    gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained
    physical description of the cortex in terms of a two-dimensional thin film of
    an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic
    length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated
    the response to laser ablation in two different ways: by quantifying flow and
    density fields as a function of space and time, and by determining the time evolution
    of the shape of the ablated region. Importantly, both methods provide best-fit
    physical parameters that are in close agreement with each other and that are similar
    to previous estimates in the two systems. Our method provides an accurate and
    robust means for measuring physical parameters of the actomyosin cortical layer.
    It can be useful for investigations of actomyosin mechanics at the cellular-scale,
    but also for providing insights into the active mechanics processes that govern
    tissue-scale morphogenesis.'
acknowledgement: S.W.G. acknowledges support by grant no. 281903 from the European
  Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft.
  S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung
  der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20).
  We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We
  thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.
author:
- first_name: Arnab
  full_name: Saha, Arnab
  last_name: Saha
- first_name: Masatoshi
  full_name: Nishikawa, Masatoshi
  last_name: Nishikawa
- first_name: Martin
  full_name: Behrndt, Martin
  id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
  last_name: Behrndt
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
- first_name: Frank
  full_name: Julicher, Frank
  last_name: Julicher
- first_name: Stephan
  full_name: Grill, Stephan
  last_name: Grill
citation:
  ama: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining
    physical properties of the cell cortex. <i>Biophysical Journal</i>. 2016;110(6):1421-1429.
    doi:<a href="https://doi.org/10.1016/j.bpj.2016.02.013">10.1016/j.bpj.2016.02.013</a>
  apa: Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., &#38;
    Grill, S. (2016). Determining physical properties of the cell cortex. <i>Biophysical
    Journal</i>. Biophysical Society. <a href="https://doi.org/10.1016/j.bpj.2016.02.013">https://doi.org/10.1016/j.bpj.2016.02.013</a>
  chicago: Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg,
    Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell
    Cortex.” <i>Biophysical Journal</i>. Biophysical Society, 2016. <a href="https://doi.org/10.1016/j.bpj.2016.02.013">https://doi.org/10.1016/j.bpj.2016.02.013</a>.
  ieee: A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S.
    Grill, “Determining physical properties of the cell cortex,” <i>Biophysical Journal</i>,
    vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016.
  ista: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016.
    Determining physical properties of the cell cortex. Biophysical Journal. 110(6),
    1421–1429.
  mla: Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical
    Journal</i>, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:<a href="https://doi.org/10.1016/j.bpj.2016.02.013">10.1016/j.bpj.2016.02.013</a>.
  short: A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill,
    Biophysical Journal 110 (2016) 1421–1429.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-29T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '29'
ddc:
- '572'
- '576'
department:
- _id: CaHe
doi: 10.1016/j.bpj.2016.02.013
file:
- access_level: open_access
  checksum: c408cf2e25a25c8d711cffea524bda55
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:10:54Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '4845'
  file_name: IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf
  file_size: 1965645
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '       110'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1421 - 1429
project:
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I 930-B20
  name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '6079'
pubrep_id: '706'
quality_controlled: '1'
scopus_import: 1
status: public
title: Determining physical properties of the cell cortex
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2016'
...
---
_id: '1250'
abstract:
- lang: eng
  text: In bacteria, replicative aging manifests as a difference in growth or survival
    between the two cells emerging from division. One cell can be regarded as an aging
    mother with a decreased potential for future survival and division, the other
    as a rejuvenated daughter. Here, we aimed at investigating some of the processes
    involved in aging in the bacterium Escherichia coli, where the two types of cells
    can be distinguished by the age of their cell poles. We found that certain changes
    in the regulation of the carbohydrate metabolism can affect aging. A mutation
    in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative
    lifespan; csrA mutants stop dividing once their pole exceeds an age of about five
    divisions. These old-pole cells accumulate glycogen at their old cell poles; after
    their last division, they do not contain a chromosome, presumably because of spatial
    exclusion by the glycogen aggregates. The new-pole daughters produced by these
    aging mothers are born young; they only express the deleterious phenotype once
    their pole is old. These results demonstrate how manipulations of nutrient allocation
    can lead to the exclusion of the chromosome and limit replicative lifespan in
    E. coli, and illustrate how mutations can have phenotypic effects that are specific
    for cells with old poles. This raises the question how bacteria can avoid the
    accumulation of such mutations in their genomes over evolutionary times, and how
    they can achieve the long replicative lifespans that have recently been reported.
acknowledgement: This manuscript is dedicated to the memory of Alex Böhm, who was
  a great friend and a passionate biologist. Alex passed away after the initial submission
  of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für
  Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and
  Nela Nikolic for helpful discussions. This work was supported by the Swiss National
  Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).
article_number: e1005974
author:
- first_name: Alex
  full_name: Boehm, Alex
  last_name: Boehm
- first_name: Markus
  full_name: Arnoldini, Markus
  last_name: Arnoldini
- first_name: Tobias
  full_name: Bergmiller, Tobias
  id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
  last_name: Bergmiller
  orcid: 0000-0001-5396-4346
- first_name: Thomas
  full_name: Röösli, Thomas
  last_name: Röösli
- first_name: Colette
  full_name: Bigosch, Colette
  last_name: Bigosch
- first_name: Martin
  full_name: Ackermann, Martin
  last_name: Ackermann
citation:
  ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic
    manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS
    Genetics</i>. 2016;12(4). doi:<a href="https://doi.org/10.1371/journal.pgen.1005974">10.1371/journal.pgen.1005974</a>
  apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann,
    M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan
    in E coli. <i>PLoS Genetics</i>. Public Library of Science. <a href="https://doi.org/10.1371/journal.pgen.1005974">https://doi.org/10.1371/journal.pgen.1005974</a>
  chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
    Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects
    Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>. Public Library of Science,
    2016. <a href="https://doi.org/10.1371/journal.pgen.1005974">https://doi.org/10.1371/journal.pgen.1005974</a>.
  ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
    “Genetic manipulation of glycogen allocation affects replicative lifespan in E
    coli,” <i>PLoS Genetics</i>, vol. 12, no. 4. Public Library of Science, 2016.
  ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
    Genetic manipulation of glycogen allocation affects replicative lifespan in E
    coli. PLoS Genetics. 12(4), e1005974.
  mla: Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative
    Lifespan in E Coli.” <i>PLoS Genetics</i>, vol. 12, no. 4, e1005974, Public Library
    of Science, 2016, doi:<a href="https://doi.org/10.1371/journal.pgen.1005974">10.1371/journal.pgen.1005974</a>.
  short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
    PLoS Genetics 12 (2016).
date_created: 2018-12-11T11:50:56Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2023-02-23T14:11:39Z
day: '19'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974
file:
- access_level: open_access
  checksum: 53d22b2b39e5adc243d34f18b2615a85
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:14:17Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '5067'
  file_name: IST-2016-705-v1+1_journal.pgen.1005974.PDF
  file_size: 6273249
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '        12'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6077'
pubrep_id: '705'
quality_controlled: '1'
related_material:
  record:
  - id: '9873'
    relation: research_data
    status: public
scopus_import: 1
status: public
title: Genetic manipulation of glycogen allocation affects replicative lifespan in
  E coli
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '1251'
abstract:
- lang: eng
  text: Plant growth and architecture is regulated by the polar distribution of the
    hormone auxin. Polarity and flexibility of this process is provided by constant
    cycling of auxin transporter vesicles along actin filaments, coordinated by a
    positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling
    are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic
    acid (NPA), counteracting the effect of auxin; however, underlying targets and
    mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis
    thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant,
    although likely indirect, TWD1 interactor, and show TWD1-dependent regulation
    of actin filament organization and dynamics and that TWD1 is required for NPA-mediated
    actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence
    of efflux transporters, and as a consequence act7 and twd1 share developmental
    and physiological phenotypes indicative of defects in auxin transport. These can
    be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide
    evidence that TWD1 determines downstreamlocations of auxin efflux transporters
    by adjusting actin filament debundling and dynamizing processes and mediating
    NPA action on the latter. This function appears to be evolutionary conserved since
    TWD1 expression in budding yeast alters actin polarization and cell polarity and
    provides NPA sensitivity.
acknowledgement: ' This work was supported by grants from the European Social Fund
  (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F.
  and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under
  the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and
  Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program
  for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the
  Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all
  to M.G.). '
author:
- first_name: Jinsheng
  full_name: Zhu, Jinsheng
  last_name: Zhu
- first_name: Aurélien
  full_name: Bailly, Aurélien
  last_name: Bailly
- first_name: Marta
  full_name: Zwiewka, Marta
  last_name: Zwiewka
- first_name: Valpuri
  full_name: Sovero, Valpuri
  last_name: Sovero
- first_name: Martin
  full_name: Di Donato, Martin
  last_name: Di Donato
- first_name: Pei
  full_name: Ge, Pei
  last_name: Ge
- first_name: Jacqueline
  full_name: Oehri, Jacqueline
  last_name: Oehri
- first_name: Bibek
  full_name: Aryal, Bibek
  last_name: Aryal
- first_name: Pengchao
  full_name: Hao, Pengchao
  last_name: Hao
- first_name: Miriam
  full_name: Linnert, Miriam
  last_name: Linnert
- first_name: Noelia
  full_name: Burgardt, Noelia
  last_name: Burgardt
- first_name: Christian
  full_name: Lücke, Christian
  last_name: Lücke
- first_name: Matthias
  full_name: Weiwad, Matthias
  last_name: Weiwad
- first_name: Max
  full_name: Michel, Max
  last_name: Michel
- first_name: Oliver
  full_name: Weiergräber, Oliver
  last_name: Weiergräber
- first_name: Stephan
  full_name: Pollmann, Stephan
  last_name: Pollmann
- first_name: Elisa
  full_name: Azzarello, Elisa
  last_name: Azzarello
- first_name: Stefano
  full_name: Mancuso, Stefano
  last_name: Mancuso
- first_name: Noel
  full_name: Ferro, Noel
  last_name: Ferro
- first_name: Yoichiro
  full_name: Fukao, Yoichiro
  last_name: Fukao
- first_name: Céline
  full_name: Hoffmann, Céline
  last_name: Hoffmann
- first_name: Roland
  full_name: Wedlich Söldner, Roland
  last_name: Wedlich Söldner
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Clément
  full_name: Thomas, Clément
  last_name: Thomas
- first_name: Markus
  full_name: Geisler, Markus
  last_name: Geisler
citation:
  ama: Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin
    transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. 2016;28(4):930-948.
    doi:<a href="https://doi.org/10.1105/tpc.15.00726">10.1105/tpc.15.00726</a>
  apa: Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler,
    M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on
    actin cytoskeleton dynamics. <i>Plant Cell</i>. American Society of Plant Biologists.
    <a href="https://doi.org/10.1105/tpc.15.00726">https://doi.org/10.1105/tpc.15.00726</a>
  chicago: Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di
    Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of
    Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>.
    American Society of Plant Biologists, 2016. <a href="https://doi.org/10.1105/tpc.15.00726">https://doi.org/10.1105/tpc.15.00726</a>.
  ieee: J. Zhu <i>et al.</i>, “TWISTED DWARF1 mediates the action of auxin transport
    inhibitors on actin cytoskeleton dynamics,” <i>Plant Cell</i>, vol. 28, no. 4.
    American Society of Plant Biologists, pp. 930–948, 2016.
  ista: Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B,
    Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann
    S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml
    J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport
    inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.
  mla: Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport
    Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>, vol. 28, no. 4,
    American Society of Plant Biologists, 2016, pp. 930–48, doi:<a href="https://doi.org/10.1105/tpc.15.00726">10.1105/tpc.15.00726</a>.
  short: J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri,
    B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O.
    Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann,
    R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.
date_created: 2018-12-11T11:50:57Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:49:24Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.15.00726
intvolume: '        28'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/
month: '04'
oa: 1
oa_version: Submitted Version
page: 930 - 948
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6078'
quality_controlled: '1'
scopus_import: 1
status: public
title: TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton
  dynamics
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '1252'
abstract:
- lang: eng
  text: We study the homomorphism induced in homology by a closed correspondence between
    topological spaces, using projections from the graph of the correspondence to
    its domain and codomain. We provide assumptions under which the homomorphism induced
    by an outer approximation of a continuous map coincides with the homomorphism
    induced in homology by the map. In contrast to more classical results we do not
    require that the projection to the domain have acyclic preimages. Moreover, we
    show that it is possible to retrieve correct homological information from a correspondence
    even if some data is missing or perturbed. Finally, we describe an application
    to combinatorial maps that are either outer approximations of continuous maps
    or reconstructions of such maps from a finite set of data points.
acknowledgement: "The authors gratefully acknowledge the support of the Lorenz Center
  which\r\nprovided an opportunity for us to discuss in depth the work of this paper.
  Research leading to these results has received funding from Fundo Europeu de Desenvolvimento
  Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade
  (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia
  e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645
  (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie
  Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013)
  under REA grant agreement no. 622033 (supporting PP). The work of the first and
  third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019,
  1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second
  author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029),
  Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Shaun
  full_name: Harker, Shaun
  last_name: Harker
- first_name: Hiroshi
  full_name: Kokubu, Hiroshi
  last_name: Kokubu
- first_name: Konstantin
  full_name: Mischaikow, Konstantin
  last_name: Mischaikow
- first_name: Pawel
  full_name: Pilarczyk, Pawel
  id: 3768D56A-F248-11E8-B48F-1D18A9856A87
  last_name: Pilarczyk
citation:
  ama: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from
    a correspondence. <i>Proceedings of the American Mathematical Society</i>. 2016;144(4):1787-1801.
    doi:<a href="https://doi.org/10.1090/proc/12812">10.1090/proc/12812</a>
  apa: Harker, S., Kokubu, H., Mischaikow, K., &#38; Pilarczyk, P. (2016). Inducing
    a map on homology from a correspondence. <i>Proceedings of the American Mathematical
    Society</i>. American Mathematical Society. <a href="https://doi.org/10.1090/proc/12812">https://doi.org/10.1090/proc/12812</a>
  chicago: Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk.
    “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American
    Mathematical Society</i>. American Mathematical Society, 2016. <a href="https://doi.org/10.1090/proc/12812">https://doi.org/10.1090/proc/12812</a>.
  ieee: S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on
    homology from a correspondence,” <i>Proceedings of the American Mathematical Society</i>,
    vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.
  ista: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology
    from a correspondence. Proceedings of the American Mathematical Society. 144(4),
    1787–1801.
  mla: Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings
    of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical
    Society, 2016, pp. 1787–801, doi:<a href="https://doi.org/10.1090/proc/12812">10.1090/proc/12812</a>.
  short: S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American
    Mathematical Society 144 (2016) 1787–1801.
date_created: 2018-12-11T11:50:57Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2022-05-24T09:35:58Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/12812
ec_funded: 1
external_id:
  arxiv:
  - '1411.7563'
intvolume: '       144'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1411.7563
month: '04'
oa: 1
oa_version: Preprint
page: 1787 - 1801
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '622033'
  name: Persistent Homology - Images, Data and Maps
publication: Proceedings of the American Mathematical Society
publication_identifier:
  issn:
  - 1088-6826
publication_status: published
publisher: American Mathematical Society
publist_id: '6075'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inducing a map on homology from a correspondence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2016'
...
---
_id: '1253'
abstract:
- lang: eng
  text: This article provides an introduction to the role of microRNAs in the nervous
    system and outlines their potential involvement in the pathophysiology of schizophrenia,
    which is hypothesized to arise owing to environmental factors and genetic predisposition.
article_processing_charge: No
author:
- first_name: Lihuei
  full_name: Tsai, Lihuei
  last_name: Tsai
- first_name: Sandra
  full_name: Siegert, Sandra
  id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
  last_name: Siegert
  orcid: 0000-0001-8635-0877
citation:
  ama: Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. <i>JAMA
    Psychiatry</i>. 2016;73(4):409-410. doi:<a href="https://doi.org/10.1001/jamapsychiatry.2015.3144">10.1001/jamapsychiatry.2015.3144</a>
  apa: Tsai, L., &#38; Siegert, S. (2016). How MicroRNAs Are involved in splitting
    the mind. <i>JAMA Psychiatry</i>. American Medical Association. <a href="https://doi.org/10.1001/jamapsychiatry.2015.3144">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>
  chicago: Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting
    the Mind.” <i>JAMA Psychiatry</i>. American Medical Association, 2016. <a href="https://doi.org/10.1001/jamapsychiatry.2015.3144">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>.
  ieee: L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,”
    <i>JAMA Psychiatry</i>, vol. 73, no. 4. American Medical Association, pp. 409–410,
    2016.
  ista: Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind.
    JAMA Psychiatry. 73(4), 409–410.
  mla: Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting
    the Mind.” <i>JAMA Psychiatry</i>, vol. 73, no. 4, American Medical Association,
    2016, pp. 409–10, doi:<a href="https://doi.org/10.1001/jamapsychiatry.2015.3144">10.1001/jamapsychiatry.2015.3144</a>.
  short: L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2024-02-14T12:07:22Z
day: '01'
ddc:
- '576'
- '610'
department:
- _id: SaSi
doi: 10.1001/jamapsychiatry.2015.3144
external_id:
  pmid:
  - '26963490'
file:
- access_level: open_access
  checksum: 649aee381f30f7ef7e9efa912d41c2e3
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:17:24Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '5278'
  file_name: IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf
  file_size: 601679
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: '        73'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 409 - 410
pmid: 1
publication: JAMA Psychiatry
publication_identifier:
  issn:
  - 2168-622X
publication_status: published
publisher: American Medical Association
publist_id: '6074'
pubrep_id: '981'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How MicroRNAs Are involved in splitting the mind
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2016'
...
---
_id: '1254'
abstract:
- lang: eng
  text: We use rigorous numerical techniques to compute a lower bound for the exponent
    of expansivity outside a neighborhood of the critical point for thousands of intervals
    of parameter values in the quadratic family. We first compute a radius of the
    critical neighborhood outside which the map is uniformly expanding. This radius
    is taken as small as possible, yet large enough for our numerical procedure to
    succeed in proving that the expansivity exponent outside this neighborhood is
    positive. Then, for each of the intervals, we compute a lower bound for this expansivity
    exponent, valid for all the parameters in that interval. We illustrate and study
    the distribution of the radii and the expansivity exponents. The results of our
    computations are mathematically rigorous. The source code of the software and
    the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.
acknowledgement: "AG and PP were partially supported by Abdus Salam International
  Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS,
  and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento
  Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade
  (POFC) and from the Portuguese national funds through Fundação para a Ciência e
  a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645
  (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions)
  of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
  agreement no. 622033. The  authors  gratefully  acknowledge  the  Department  of\r\nMathematics
  \ of  Kyoto  University  for  providing  access\r\nto  their  server  for  conducting
  \ computations  for  this\r\nproject."
author:
- first_name: Ali
  full_name: Golmakani, Ali
  last_name: Golmakani
- first_name: Stefano
  full_name: Luzzatto, Stefano
  last_name: Luzzatto
- first_name: Pawel
  full_name: Pilarczyk, Pawel
  id: 3768D56A-F248-11E8-B48F-1D18A9856A87
  last_name: Pilarczyk
citation:
  ama: Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical
    neighborhood in the quadratic family. <i>Experimental Mathematics</i>. 2016;25(2):116-124.
    doi:<a href="https://doi.org/10.1080/10586458.2015.1048011">10.1080/10586458.2015.1048011</a>
  apa: Golmakani, A., Luzzatto, S., &#38; Pilarczyk, P. (2016). Uniform expansivity
    outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>.
    Taylor and Francis. <a href="https://doi.org/10.1080/10586458.2015.1048011">https://doi.org/10.1080/10586458.2015.1048011</a>
  chicago: Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity
    Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>.
    Taylor and Francis, 2016. <a href="https://doi.org/10.1080/10586458.2015.1048011">https://doi.org/10.1080/10586458.2015.1048011</a>.
  ieee: A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside
    a critical neighborhood in the quadratic family,” <i>Experimental Mathematics</i>,
    vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.
  ista: Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a
    critical neighborhood in the quadratic family. Experimental Mathematics. 25(2),
    116–124.
  mla: Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood
    in the Quadratic Family.” <i>Experimental Mathematics</i>, vol. 25, no. 2, Taylor
    and Francis, 2016, pp. 116–24, doi:<a href="https://doi.org/10.1080/10586458.2015.1048011">10.1080/10586458.2015.1048011</a>.
  short: A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016)
    116–124.
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-02T00:00:00Z
date_updated: 2021-01-12T06:49:25Z
day: '02'
department:
- _id: HeEd
doi: 10.1080/10586458.2015.1048011
ec_funded: 1
intvolume: '        25'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1504.00116
month: '04'
oa: 1
oa_version: Preprint
page: 116 - 124
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '622033'
  name: Persistent Homology - Images, Data and Maps
publication: Experimental Mathematics
publication_status: published
publisher: Taylor and Francis
publist_id: '6071'
quality_controlled: '1'
scopus_import: 1
status: public
title: Uniform expansivity outside a critical neighborhood in the quadratic family
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '1255'
abstract:
- lang: eng
  text: Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital
    neuronal functions although the role it plays in insect and crustacean immunity
    is less well understood. In this study, we combine different approaches to understand
    the roles that Dscam1 plays in fitness-related contexts in two model insect species.
    Contrary to our expectations, we found no short-term modulation of Dscam1 gene
    expression after haemocoelic or oral bacterial exposure in Tribolium castaneum,
    or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore,
    RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce
    T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion
    defects, as well as dramatically reduced fecundity in males and females. We suggest
    that Dscam1 does not always play a straightforward role in immunity, but strongly
    influences behaviour and fecundity. This study takes a step towards understanding
    more about the role of this intriguing gene from different phenotypic perspectives.
acknowledgement: "We thank Dietmar Schmucker for reading a draft of this manuscript
  and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert,
  Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions.
  We also thank two anonymous reviewers for their comments. This study was supported
  by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.)
  and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2
  to R.P. and J.K.)."
article_number: '160138'
author:
- first_name: Robert
  full_name: Peuß, Robert
  last_name: Peuß
- first_name: Kristina
  full_name: Wensing, Kristina
  last_name: Wensing
- first_name: Luisa
  full_name: Woestmann, Luisa
  last_name: Woestmann
- first_name: Hendrik
  full_name: Eggert, Hendrik
  last_name: Eggert
- first_name: Barbara
  full_name: Milutinovic, Barbara
  id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
  last_name: Milutinovic
  orcid: 0000-0002-8214-4758
- first_name: Marlene
  full_name: Sroka, Marlene
  last_name: Sroka
- first_name: Jörn
  full_name: Scharsack, Jörn
  last_name: Scharsack
- first_name: Joachim
  full_name: Kurtz, Joachim
  last_name: Kurtz
- first_name: Sophie
  full_name: Armitage, Sophie
  last_name: Armitage
citation:
  ama: 'Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule
    1: Testing for a role in insect immunity, behaviour and reproduction. <i>Royal
    Society Open Science</i>. 2016;3(4). doi:<a href="https://doi.org/10.1098/rsos.160138">10.1098/rsos.160138</a>'
  apa: 'Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka,
    M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for
    a role in insect immunity, behaviour and reproduction. <i>Royal Society Open Science</i>.
    Royal Society, The. <a href="https://doi.org/10.1098/rsos.160138">https://doi.org/10.1098/rsos.160138</a>'
  chicago: 'Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara
    Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage.
    “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity,
    Behaviour and Reproduction.” <i>Royal Society Open Science</i>. Royal Society,
    The, 2016. <a href="https://doi.org/10.1098/rsos.160138">https://doi.org/10.1098/rsos.160138</a>.'
  ieee: 'R. Peuß <i>et al.</i>, “Down syndrome cell adhesion molecule 1: Testing for
    a role in insect immunity, behaviour and reproduction,” <i>Royal Society Open
    Science</i>, vol. 3, no. 4. Royal Society, The, 2016.'
  ista: 'Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack
    J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing
    for a role in insect immunity, behaviour and reproduction. Royal Society Open
    Science. 3(4), 160138.'
  mla: 'Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for
    a Role in Insect Immunity, Behaviour and Reproduction.” <i>Royal Society Open
    Science</i>, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:<a href="https://doi.org/10.1098/rsos.160138">10.1098/rsos.160138</a>.'
  short: R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J.
    Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016).
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:49:25Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rsos.160138
file:
- access_level: open_access
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  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:14:01Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '5049'
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  file_size: 627377
  relation: main_file
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has_accepted_license: '1'
intvolume: '         3'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_status: published
publisher: Royal Society, The
publist_id: '6070'
pubrep_id: '704'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity,
  behaviour and reproduction'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2016'
...
---
_id: '1256'
abstract:
- lang: eng
  text: Simulink is widely used for model driven development (MDD) of industrial software
    systems. Typically, the Simulink based development is initiated from Stateflow
    modeling, followed by simulation, validation and code generation mapped to physical
    execution platforms. However, recent industrial trends have raised the demands
    of rigorous verification on safety-critical applications, which is unfortunately
    challenging for Simulink. In this paper, we present an approach to bridge the
    Stateflow based model driven development and a well- defined rigorous verification.
    First, we develop a self- contained toolkit to translate Stateflow model into
    timed automata, where major advanced modeling features in Stateflow are supported.
    Taking advantage of the strong verification capability of Uppaal, we can not only
    find bugs in Stateflow models which are missed by Simulink Design Verifier, but
    also check more important temporal properties. Next, we customize a runtime verifier
    for the generated nonintrusive VHDL and C code of Stateflow model for monitoring.
    The major strength of the customization is the flexibility to collect and analyze
    runtime properties with a pure software monitor, which opens more opportunities
    for engineers to achieve high reliability of the target system compared with the
    traditional act that only relies on Simulink Polyspace. We incorporate these two
    parts into original Stateflow based MDD seamlessly. In this way, safety-critical
    properties are both verified at the model level, and at the consistent system
    implementation level with physical execution environment in consideration. We
    apply our approach on a train controller design, and the verified implementation
    is tested and deployed on a real hardware platform.
acknowledgement: This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886,
  NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302.
article_number: '7461337'
author:
- first_name: Yu
  full_name: Jiang, Yu
  last_name: Jiang
- first_name: Yixiao
  full_name: Yang, Yixiao
  last_name: Yang
- first_name: Han
  full_name: Liu, Han
  last_name: Liu
- first_name: Hui
  full_name: Kong, Hui
  id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
  last_name: Kong
  orcid: 0000-0002-3066-6941
- first_name: Ming
  full_name: Gu, Ming
  last_name: Gu
- first_name: Jiaguang
  full_name: Sun, Jiaguang
  last_name: Sun
- first_name: Lui
  full_name: Sha, Lui
  last_name: Sha
citation:
  ama: 'Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation:
    A verification approach and a real-time train controller design. In: IEEE; 2016.
    doi:<a href="https://doi.org/10.1109/RTAS.2016.7461337">10.1109/RTAS.2016.7461337</a>'
  apa: 'Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., &#38; Sha, L. (2016).
    From stateflow simulation to verified implementation: A verification approach
    and a real-time train controller design. Presented at the RTAS: Real-time and
    Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. <a href="https://doi.org/10.1109/RTAS.2016.7461337">https://doi.org/10.1109/RTAS.2016.7461337</a>'
  chicago: 'Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and
    Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification
    Approach and a Real-Time Train Controller Design.” IEEE, 2016. <a href="https://doi.org/10.1109/RTAS.2016.7461337">https://doi.org/10.1109/RTAS.2016.7461337</a>.'
  ieee: 'Y. Jiang <i>et al.</i>, “From stateflow simulation to verified implementation:
    A verification approach and a real-time train controller design,” presented at
    the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna,
    Austria, 2016.'
  ista: 'Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow
    simulation to verified implementation: A verification approach and a real-time
    train controller design. RTAS: Real-time and Embedded Technology and Applications
    Symposium, 7461337.'
  mla: 'Jiang, Yu, et al. <i>From Stateflow Simulation to Verified Implementation:
    A Verification Approach and a Real-Time Train Controller Design</i>. 7461337,
    IEEE, 2016, doi:<a href="https://doi.org/10.1109/RTAS.2016.7461337">10.1109/RTAS.2016.7461337</a>.'
  short: Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016.
conference:
  end_date: 2016-04-14
  location: Vienna, Austria
  name: 'RTAS: Real-time and Embedded Technology and Applications Symposium'
  start_date: 2016-04-11
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-27T00:00:00Z
date_updated: 2021-01-12T06:49:26Z
day: '27'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1109/RTAS.2016.7461337
file:
- access_level: open_access
  checksum: 42f0462911cc9957f2356b12fb33b4b6
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:12:31Z
  date_updated: 2020-07-14T12:44:41Z
  file_id: '4949'
  file_name: IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf
  file_size: 1293599
  relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '6069'
pubrep_id: '780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'From stateflow simulation to verified implementation: A verification approach
  and a real-time train controller design'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1257'
abstract:
- lang: eng
  text: We consider products of random matrices that are small, independent identically
    distributed perturbations of a fixed matrix (Formula presented.). Focusing on
    the eigenvalues of (Formula presented.) of a particular size we obtain a limit
    to a SDE in a critical scaling. Previous results required (Formula presented.)
    to be a (conjugated) unitary matrix so it could not have eigenvalues of different
    modulus. From the result we can also obtain a limit SDE for the Markov process
    given by the action of the random products on the flag manifold. Applying the
    result to random Schrödinger operators we can improve some results by Valko and
    Virag showing GOE statistics for the rescaled eigenvalue process of a sequence
    of Anderson models on long boxes. In particular, we solve a problem posed in their
    work.
acknowledgement: Open access funding provided by Institute of Science and Technology
  (IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010
  RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework
  Programme FP7/2007-2013, REA Grant 291734.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christian
  full_name: Sadel, Christian
  id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
  last_name: Sadel
  orcid: 0000-0001-8255-3968
- first_name: Bálint
  full_name: Virág, Bálint
  last_name: Virág
citation:
  ama: Sadel C, Virág B. A central limit theorem for products of random matrices and
    GOE statistics for the Anderson model on long boxes. <i>Communications in Mathematical
    Physics</i>. 2016;343(3):881-919. doi:<a href="https://doi.org/10.1007/s00220-016-2600-4">10.1007/s00220-016-2600-4</a>
  apa: Sadel, C., &#38; Virág, B. (2016). A central limit theorem for products of
    random matrices and GOE statistics for the Anderson model on long boxes. <i>Communications
    in Mathematical Physics</i>. Springer. <a href="https://doi.org/10.1007/s00220-016-2600-4">https://doi.org/10.1007/s00220-016-2600-4</a>
  chicago: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products
    of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” <i>Communications
    in Mathematical Physics</i>. Springer, 2016. <a href="https://doi.org/10.1007/s00220-016-2600-4">https://doi.org/10.1007/s00220-016-2600-4</a>.
  ieee: C. Sadel and B. Virág, “A central limit theorem for products of random matrices
    and GOE statistics for the Anderson model on long boxes,” <i>Communications in
    Mathematical Physics</i>, vol. 343, no. 3. Springer, pp. 881–919, 2016.
  ista: Sadel C, Virág B. 2016. A central limit theorem for products of random matrices
    and GOE statistics for the Anderson model on long boxes. Communications in Mathematical
    Physics. 343(3), 881–919.
  mla: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of
    Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” <i>Communications
    in Mathematical Physics</i>, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:<a
    href="https://doi.org/10.1007/s00220-016-2600-4">10.1007/s00220-016-2600-4</a>.
  short: C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919.
date_created: 2018-12-11T11:50:59Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T06:49:26Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: LaEr
doi: 10.1007/s00220-016-2600-4
ec_funded: 1
file:
- access_level: open_access
  checksum: 4fb2411d9c2f56676123165aad46c828
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:15:02Z
  date_updated: 2020-07-14T12:44:42Z
  file_id: '5119'
  file_name: IST-2016-703-v1+1_s00220-016-2600-4.pdf
  file_size: 800792
  relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: '       343'
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 881 - 919
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
  name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6067'
pubrep_id: '703'
quality_controlled: '1'
scopus_import: 1
status: public
title: A central limit theorem for products of random matrices and GOE statistics
  for the Anderson model on long boxes
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2016'
...