---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9662'
abstract:
- lang: eng
text: Fractionation of isotopes among distinct molecules or phases is a quantum
effect which is often exploited to obtain insights on reaction mechanisms, biochemical,
geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios
in atomistic simulations is challenging, because one needs to perform a thermodynamic
integration with respect to the isotope mass, along with time-consuming path integral
calculations. By re-formulating the problem as a particle exchange in the ring
polymer partition function, we derive new estimators giving direct access to the
differential partitioning of isotopes, which can simplify the calculations by
avoiding thermodynamic integration. We demonstrate the efficiency of these estimators
by applying them to investigate the isotope fractionation ratios in the gas-phase
Zundel cation, and in a few simple hydrocarbons.
article_number: '244112'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293
apa: Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope
fractionation ratios. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4904293
chicago: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators
for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP
Publishing, 2014. https://doi.org/10.1063/1.4904293.
ieee: B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation
ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing,
2014.
ista: Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 141(24), 244112.
mla: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for
Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141,
no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).
date_created: 2021-07-15T09:22:49Z
date_published: 2014-12-28T00:00:00Z
date_updated: 2021-08-09T12:32:24Z
day: '28'
doi: 10.1063/1.4904293
extern: '1'
external_id:
arxiv:
- '1412.1308'
pmid:
- '25554138'
intvolume: ' 141'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1308
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct path integral estimators for isotope fractionation ratios
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 141
year: '2014'
...
---
_id: '97'
abstract:
- lang: eng
text: The distribution of Coulomb blockade peak heights as a function of magnetic
field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit
coupling in this hole-gas system leads to antilocalization of Coulomb blockade
peaks, consistent with theory. In particular, the peak height distribution has
its maximum away from zero at zero magnetic field, with an average that decreases
with increasing field. Magnetoconductance in the open-wire regime places a bound
on the spin-orbit length (lso < 20 nm), consistent with values extracted in the
Coulomb blockade regime (lso < 25 nm).
acknowledgement: Research supported by the Danish National Research Foundation, the
Office of Science at the U.S. Department of Energy, the National Science Foundation
(PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST
Program.
article_number: '216806'
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Thorvald
full_name: Larsen, Thorvald
last_name: Larsen
- first_name: Mattias
full_name: Fitzpatrick, Mattias
last_name: Fitzpatrick
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Hao
full_name: Yan, Hao
last_name: Yan
- first_name: Charles
full_name: Lieber, Charles
last_name: Lieber
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade
in a Ge/Si nanowire. APS Physics, Physical Review Letters. 2014;112(21).
doi:10.1103/PhysRevLett.112.216806
apa: Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan,
H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire.
APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.216806
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick,
Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb
Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters. American
Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.216806.
ieee: A. P. Higginbotham et al., “Antilocalization of coulomb blockade in
a Ge/Si nanowire,” APS Physics, Physical Review Letters, vol. 112, no.
21. American Physical Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber
C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS
Physics, Physical Review Letters. 112(21), 216806.
mla: Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a
Ge/Si Nanowire.” APS Physics, Physical Review Letters, vol. 112, no. 21,
216806, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.216806.
short: A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan,
C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-05-29T00:00:00Z
date_updated: 2021-01-12T08:22:19Z
day: '29'
doi: 10.1103/PhysRevLett.112.216806
extern: '1'
external_id:
arxiv:
- '1401.2948'
intvolume: ' 112'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.2948
month: '05'
oa: 1
oa_version: None
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7957'
quality_controlled: '1'
status: public
title: Antilocalization of coulomb blockade in a Ge/Si nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '2004'
abstract:
- lang: eng
text: We have assembled a network of cell-fate determining transcription factors
that play a key role in the specification of the ventral neuronal subtypes of
the spinal cord on the basis of published transcriptional interactions. Asynchronous
Boolean modelling of the network was used to compare simulation results with reported
experimental observations. Such comparison highlighted the need to include additional
regulatory connections in order to obtain the fixed point attractors of the model
associated with the five known progenitor cell types located in the ventral spinal
cord. The revised gene regulatory network reproduced previously observed cell
state switches between progenitor cells observed in knock-out animal models or
in experiments where the transcription factors were overexpressed. Furthermore
the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was
tested experimentally. Our results provide evidence for the existence of an as
yet undescribed inhibitory connection which could potentially have significance
beyond the ventral spinal cord. The work presented in this paper demonstrates
the strength of Boolean modelling for identifying gene regulatory networks.
article_number: e111430
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen
full_name: Byrne, Helen
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory
connections between transcription factors orchestrating the development of the
ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács,
K. (2014). Boolean modelling reveals new regulatory connections between transcription
factors orchestrating the development of the ventral spinal cord. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0111430
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András
Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections
between Transcription Factors Orchestrating the Development of the Ventral Spinal
Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.
ieee: A. Lovrics et al., “Boolean modelling reveals new regulatory connections
between transcription factors orchestrating the development of the ventral spinal
cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean
modelling reveals new regulatory connections between transcription factors orchestrating
the development of the ventral spinal cord. PLoS One. 9(11), e111430.
mla: Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections
between Transcription Factors Orchestrating the Development of the Ventral Spinal
Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014,
doi:10.1371/journal.pone.0111430.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács,
PLoS One 9 (2014).
date_created: 2018-12-11T11:55:09Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T14:06:14Z
day: '14'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430
ec_funded: 1
file:
- access_level: open_access
checksum: a2289b843f7463eb1233f9ce45e6a943
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:58Z
date_updated: 2020-07-14T12:45:24Z
file_id: '4850'
file_name: IST-2016-435-v1+1_journal.pone.0111430.pdf
file_size: 829363
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5072'
pubrep_id: '435'
quality_controlled: '1'
related_material:
record:
- id: '9722'
relation: research_data
status: public
scopus_import: 1
status: public
title: Boolean modelling reveals new regulatory connections between transcription
factors orchestrating the development of the ventral spinal cord
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '9722'
article_processing_charge: No
author:
- first_name: Anna
full_name: Lovrics, Anna
last_name: Lovrics
- first_name: Yu
full_name: Gao, Yu
last_name: Gao
- first_name: Bianka
full_name: Juhász, Bianka
last_name: Juhász
- first_name: István
full_name: Bock, István
last_name: Bock
- first_name: Helen M.
full_name: Byrne, Helen M.
last_name: Byrne
- first_name: András
full_name: Dinnyés, András
last_name: Dinnyés
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
citation:
ama: Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression
states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006
apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &
Kovács, K. (2014). Transition probability between TF expression states when Dbx2
inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006
chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András
Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.
ieee: A. Lovrics et al., “Transition probability between TF expression states
when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.
ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition
probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library
of Science, 10.1371/journal.pone.0111430.s006.
mla: Lovrics, Anna, et al. Transition Probability between TF Expression States
When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.
short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács,
(2014).
date_created: 2021-07-26T14:35:00Z
date_published: 2014-11-14T00:00:00Z
date_updated: 2023-02-23T10:24:07Z
day: '14'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0111430.s006
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2004'
relation: used_in_publication
status: public
status: public
title: Transition probability between TF expression states when Dbx2 inhibits Nkx2.2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '2039'
abstract:
- lang: eng
text: 'A fundamental question in biology is the following: what is the time scale
that is needed for evolutionary innovations? There are many results that characterize
single steps in terms of the fixation time of new mutants arising in populations
of certain size and structure. But here we ask a different question, which is
concerned with the much longer time scale of evolutionary trajectories: how long
does it take for a population exploring a fitness landscape to find target sequences
that encode new biological functions? Our key variable is the length, (Formula
presented.) of the genetic sequence that undergoes adaptation. In computer science
there is a crucial distinction between problems that require algorithms which
take polynomial or exponential time. The latter are considered to be intractable.
Here we develop a theoretical approach that allows us to estimate the time of
evolution as function of (Formula presented.) We show that adaptation on many
fitness landscapes takes time that is exponential in (Formula presented.) even
if there are broad selection gradients and many targets uniformly distributed
in sequence space. These negative results lead us to search for specific mechanisms
that allow evolution to work on polynomial time scales. We study a regeneration
process and show that it enables evolution to work in polynomial time.'
article_number: 7p
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary
innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time
scale of evolutionary innovation. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1003818
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak.
“The Time Scale of Evolutionary Innovation.” PLoS Computational Biology.
Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of
evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public
Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary
innovation. PLoS Computational Biology. 10(9), 7p.
mla: Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.”
PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science,
2014, doi:10.1371/journal.pcbi.1003818.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology
10 (2014).
date_created: 2018-12-11T11:55:22Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T14:06:36Z
day: '11'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818
ec_funded: 1
file:
- access_level: open_access
checksum: 712d4c5787ddf97809cfc962507f0738
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:35Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4890'
file_name: IST-2016-440-v1+1_journal.pcbi.1003818.pdf
file_size: 1399093
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5012'
pubrep_id: '440'
quality_controlled: '1'
related_material:
record:
- id: '9739'
relation: research_data
status: public
scopus_import: 1
status: public
title: The time scale of evolutionary innovation
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '2161'
abstract:
- lang: eng
text: 'Repeated pathogen exposure is a common threat in colonies of social insects,
posing selection pressures on colony members to respond with improved disease-defense
performance. We here tested whether experience gained by repeated tending of low-level
fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary
brood care in the clonal ant, Platythyrea punctata. We trained ants individually
over nine consecutive trials to either sham-treated or fungus-exposed larvae.
We then compared the larval grooming behavior of naive and trained ants and measured
how effectively they removed infectious fungal conidiospores from the fungus-exposed
larvae. We found that the ants changed the duration of larval grooming in response
to both, larval treatment and their level of experience: (1) sham-treated larvae
received longer grooming than the fungus-exposed larvae and (2) trained ants performed
less self-grooming but longer larval grooming than naive ants, which was true
for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants
that groomed the fungus-exposed larvae for longer periods removed a higher number
of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced
ants performed longer larval grooming, they were more effective in fungal removal,
thus making them better caretakers under pathogen attack of the colony. By studying
this clonal ant, we can thus conclude that even in the absence of genetic variation
between colony members, differences in experience levels of brood care may affect
performance of sanitary brood care in social insects.'
acknowledgement: "We thank Katrin Kellner for colony establishment and characterization,
Mike Bidochka for the fungal strain, Meghan Vyleta for fungal strain characterization,
Martina Klatt and Simon Tragust for help in the laboratory, Dimitri Missoh for developing
the software BioLogic, and Mark Brown and Raphaël Jeanson for discussion and help
with data analysis. The study was funded by the European Research Council (ERC Starting
Grant to SC; Marie Curie IEF to LVU) and the German Research Foundation DFG (to
SC and to JH), and CW received funding by the doctoral school Diversité du Vivant
(Cotutelle project to CD and SC).\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Claudia
full_name: Westhus, Claudia
id: ca9c6ca9-e8aa-11ec-a586-b9471ede0494
last_name: Westhus
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Edouard
full_name: Tourdot, Edouard
last_name: Tourdot
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Claudie
full_name: Doums, Claudie
last_name: Doums
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Increased grooming
after repeated brood care provides sanitary benefits in a clonal ant. Behavioral
Ecology and Sociobiology. 2014;68(10):1701-1710. doi:10.1007/s00265-014-1778-8
apa: Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer,
S. (2014). Increased grooming after repeated brood care provides sanitary benefits
in a clonal ant. Behavioral Ecology and Sociobiology. Springer. https://doi.org/10.1007/s00265-014-1778-8
chicago: Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie
Doums, and Sylvia Cremer. “Increased Grooming after Repeated Brood Care Provides
Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology.
Springer, 2014. https://doi.org/10.1007/s00265-014-1778-8.
ieee: C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer,
“Increased grooming after repeated brood care provides sanitary benefits in a
clonal ant,” Behavioral Ecology and Sociobiology, vol. 68, no. 10. Springer,
pp. 1701–1710, 2014.
ista: Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2014. Increased
grooming after repeated brood care provides sanitary benefits in a clonal ant.
Behavioral Ecology and Sociobiology. 68(10), 1701–1710.
mla: Westhus, Claudia, et al. “Increased Grooming after Repeated Brood Care Provides
Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology,
vol. 68, no. 10, Springer, 2014, pp. 1701–10, doi:10.1007/s00265-014-1778-8.
short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, Behavioral
Ecology and Sociobiology 68 (2014) 1701–1710.
date_created: 2018-12-11T11:56:03Z
date_published: 2014-07-23T00:00:00Z
date_updated: 2023-02-23T14:06:46Z
day: '23'
department:
- _id: SyCr
doi: 10.1007/s00265-014-1778-8
ec_funded: 1
intvolume: ' 68'
issue: '10'
language:
- iso: eng
month: '07'
oa_version: None
page: 1701 - 1710
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Behavioral Ecology and Sociobiology
publication_identifier:
issn:
- 0340-5443
publication_status: published
publisher: Springer
publist_id: '4823'
quality_controlled: '1'
related_material:
record:
- id: '9742'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Increased grooming after repeated brood care provides sanitary benefits in
a clonal ant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2014'
...
---
_id: '2036'
abstract:
- lang: eng
text: ' In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments. '
acknowledgement: The project was supported by Leverhulme Trust.
article_number: '20141679'
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses. Proceedings
of the Royal Society of London Series B Biological Sciences. 2014;281(1794).
doi:10.1098/rspb.2014.1679
apa: Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. Proceedings
of the Royal Society of London Series B Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rspb.2014.1679
chicago: Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic
Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings
of the Royal Society of London Series B Biological Sciences. Royal Society,
The, 2014. https://doi.org/10.1098/rspb.2014.1679.
ieee: M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 281, no.
1794. Royal Society, The, 2014.
ista: Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses. Proceedings of
the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.
mla: Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact
Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 281, no. 1794,
20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.
short: M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London
Series B Biological Sciences 281 (2014).
date_created: 2018-12-11T11:55:21Z
date_published: 2014-09-17T00:00:00Z
date_updated: 2023-02-23T14:06:44Z
day: '17'
department:
- _id: CaGu
doi: 10.1098/rspb.2014.1679
intvolume: ' 281'
issue: '1794'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/
month: '09'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '5019'
quality_controlled: '1'
related_material:
record:
- id: '9741'
relation: research_data
status: public
scopus_import: 1
status: public
title: Selection history and epistatic interactions impact dynamics of adaptation
to novel environmental stresses
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2014'
...
---
_id: '9740'
abstract:
- lang: eng
text: The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens.
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc'
apa: 'Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from:
Anti-pathogen protection versus survival costs mediated by an ectosymbiont in
an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc'
chicago: 'Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data
from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont
in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.'
ieee: 'M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host.”
Dryad, 2014.'
ista: 'Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad,
10.5061/dryad.vm0vc.'
mla: 'Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival
Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.'
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).
date_created: 2021-07-28T08:38:40Z
date_published: 2014-11-13T00:00:00Z
date_updated: 2023-02-23T10:23:32Z
day: '13'
department:
- _id: SyCr
doi: 10.5061/dryad.vm0vc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.vm0vc
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1993'
relation: used_in_publication
status: public
status: public
title: 'Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9741'
abstract:
- lang: eng
text: In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: 'Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. 2014.
doi:10.5061/dryad.85dn7'
apa: 'Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history
and epistatic interactions impact dynamics of adaptation to novel environmental
stresses. Dryad. https://doi.org/10.5061/dryad.85dn7'
chicago: 'Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History
and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental
Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.'
ieee: 'M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and
epistatic interactions impact dynamics of adaptation to novel environmental stresses.”
Dryad, 2014.'
ista: 'Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses, Dryad,
10.5061/dryad.85dn7.'
mla: 'Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions
Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014,
doi:10.5061/dryad.85dn7.'
short: M. Lagator, N. Colegrave, P. Neve, (2014).
date_created: 2021-07-28T08:48:06Z
date_published: 2014-08-21T00:00:00Z
date_updated: 2023-02-23T10:25:31Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.85dn7
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.85dn7
month: '08'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2036'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selection history and epistatic interactions impact dynamics of
adaptation to novel environmental stresses'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9739'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Novak, Martin
last_name: Novak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time
scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed
proofs for “The time scale of evolutionary innovation.” Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003818.s001
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak.
“Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library
of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for
‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for
“The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.
mla: Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary
Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).
date_created: 2021-07-28T08:13:57Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T10:25:37Z
day: '11'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2039'
relation: used_in_publication
status: public
status: public
title: Detailed proofs for “The time scale of evolutionary innovation”
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '2170'
abstract:
- lang: eng
text: ' Short-read sequencing technologies have in principle made it feasible to
draw detailed inferences about the recent history of any organism. In practice,
however, this remains challenging due to the difficulty of genome assembly in
most organisms and the lack of statistical methods powerful enough to discriminate
between recent, nonequilibrium histories. We address both the assembly and inference
challenges. We develop a bioinformatic pipeline for generating outgroup-rooted
alignments of orthologous sequence blocks from de novo low-coverage short-read
data for a small number of genomes, and show how such sequence blocks can be used
to fit explicit models of population divergence and admixture in a likelihood
framework. To illustrate our approach, we reconstruct the Pleistocene history
of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common
with many other taxa, was restricted during Pleistocene ice ages to a longitudinal
series of southern refugia spanning the Western Palaearctic. Our analysis of sequence
blocks sampled from a single genome from each of three major glacial refugia reveals
support for an unexpected history dominated by recent admixture. Despite the fact
that 80% of the genome is affected by admixture during the last glacial cycle,
we are able to infer the deeper divergence history of these populations. These
inferences are robust to variation in block length, mutation model and the sampling
location of individual genomes within refugia. This combination of de novo assembly
and numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.'
acknowledgement: This work was funded by NERC grants to G Stone, J Nicholls, K Lohse
and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
- first_name: James
full_name: Nicholls, James
last_name: Nicholls
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
citation:
ama: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578
apa: Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse,
K. (2014). Likelihood-based inference of population history from low-coverage
de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578
chicago: Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H
Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell,
2014. https://doi.org/10.1111/mec.12578.
ieee: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse,
“Likelihood-based inference of population history from low-coverage de novo genome
assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211,
2014.
ista: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 23(1), 198–211.
mla: Hearn, Jack, et al. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no.
1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.
short: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular
Ecology 23 (2014) 198–211.
date_created: 2018-12-11T11:56:07Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T14:07:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.12578
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date_updated: 2020-07-14T12:45:31Z
file_id: '4651'
file_name: IST-2016-559-v1+1_Hearn_et_al.pdf
file_size: 807444
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checksum: 01a8073e071c088500425f910b0f1f71
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date_updated: 2020-07-14T12:45:31Z
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file_name: IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf
file_size: 1518088
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has_accepted_license: '1'
intvolume: ' 23'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 198 - 211
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4814'
pubrep_id: '559'
quality_controlled: '1'
related_material:
record:
- id: '9754'
relation: research_data
status: public
scopus_import: 1
status: public
title: Likelihood-based inference of population history from low-coverage de novo
genome assemblies
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2014'
...
---
_id: '9753'
abstract:
- lang: eng
text: 'Background: The brood of ants and other social insects is highly susceptible
to pathogens, particularly those that penetrate the soft larval and pupal cuticle.
We here test whether the presence of a pupal cocoon, which occurs in some ant
species but not in others, affects the sanitary brood care and fungal infection
patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We
use a) a comparative approach analysing four species with either naked or cocooned
pupae and b) a within-species analysis of a single ant species, in which both
pupal types co-exist in the same colony. Results: We found that the presence of
a cocoon did not compromise fungal pathogen detection by the ants and that species
with cocooned pupae increased brood grooming after pathogen exposure. All tested
ant species further removed brood from their nests, which was predominantly expressed
towards larvae and naked pupae treated with the live fungal pathogen. In contrast,
cocooned pupae exposed to live fungus were not removed at higher rates than cocooned
pupae exposed to dead fungus or a sham control. Consistent with this, exposure
to the live fungus caused high numbers of infections and fungal outgrowth in larvae
and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed
the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion:
Our study suggests that the pupal cocoon has a protective effect against fungal
infection, causing an adaptive change in sanitary behaviours by the ants. It further
demonstrates that brood removal - originally described for honeybees as “hygienic
behaviour” – is a widespread sanitary behaviour in ants, which likely has important
implications on disease dynamics in social insect colonies.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons
affect sanitary brood care and limit fungal infections in ant colonies. 2014.
doi:10.5061/dryad.nc0gc'
apa: 'Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2014).
Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies. Dryad. https://doi.org/10.5061/dryad.nc0gc'
chicago: 'Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia
Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal
Infections in Ant Colonies.” Dryad, 2014. https://doi.org/10.5061/dryad.nc0gc.'
ieee: 'S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data
from: Pupal cocoons affect sanitary brood care and limit fungal infections in
ant colonies.” Dryad, 2014.'
ista: 'Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from:
Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,
Dryad, 10.5061/dryad.nc0gc.'
mla: 'Tragust, Simon, et al. Data from: Pupal Cocoons Affect Sanitary Brood Care
and Limit Fungal Infections in Ant Colonies. Dryad, 2014, doi:10.5061/dryad.nc0gc.'
short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).
date_created: 2021-07-30T08:24:11Z
date_published: 2014-10-08T00:00:00Z
date_updated: 2023-02-23T10:36:17Z
day: '08'
department:
- _id: SyCr
doi: 10.5061/dryad.nc0gc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.nc0gc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2284'
relation: used_in_publication
status: public
status: public
title: 'Data from: Pupal cocoons affect sanitary brood care and limit fungal infections
in ant colonies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '9752'
abstract:
- lang: eng
text: Redundancies and correlations in the responses of sensory neurons may seem
to waste neural resources, but they can also carry cues about structured stimuli
and may help the brain to correct for response errors. To investigate the effect
of stimulus structure on redundancy in retina, we measured simultaneous responses
from populations of retinal ganglion cells presented with natural and artificial
stimuli that varied greatly in correlation structure; these stimuli and recordings
are publicly available online. Responding to spatio-temporally structured stimuli
such as natural movies, pairs of ganglion cells were modestly more correlated
than in response to white noise checkerboards, but they were much less correlated
than predicted by a non-adapting functional model of retinal response. Meanwhile,
responding to stimuli with purely spatial correlations, pairs of ganglion cells
showed increased correlations consistent with a static, non-adapting receptive
field and nonlinearity. We found that in response to spatio-temporally correlated
stimuli, ganglion cells had faster temporal kernels and tended to have stronger
surrounds. These properties of individual cells, along with gain changes that
opposed changes in effective contrast at the ganglion cell input, largely explained
the pattern of pairwise correlations across stimuli where receptive field measurements
were possible.
article_processing_charge: No
author:
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Jan
full_name: Homann, Jan
last_name: Homann
- first_name: Heather
full_name: Yee, Heather
last_name: Yee
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Philip
full_name: Nelson, Philip
last_name: Nelson
- first_name: Vijay
full_name: Balasubramanian, Vijay
last_name: Balasubramanian
citation:
ama: 'Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus
correlations by the retina. 2014. doi:10.5061/dryad.246qg'
apa: 'Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., …
Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations
by the retina. Dryad. https://doi.org/10.5061/dryad.246qg'
chicago: 'Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather
Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation
of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg.'
ieee: 'K. Simmons et al., “Data from: Transformation of stimulus correlations
by the retina.” Dryad, 2014.'
ista: 'Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian
V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad,
10.5061/dryad.246qg.'
mla: 'Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations
by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.'
short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson,
V. Balasubramanian, (2014).
date_created: 2021-07-30T08:13:52Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-02-23T10:35:57Z
day: '07'
department:
- _id: GaTk
doi: 10.5061/dryad.246qg
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.246qg
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2277'
relation: used_in_publication
status: public
status: public
title: 'Data from: Transformation of stimulus correlations by the retina'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '978'
abstract:
- lang: eng
text: The newly discovered topological crystalline insulators feature a complex
band structure involving multiple Dirac cones, and are potentially highly tunable
by external electric field, temperature or strain. Theoretically, it has been
predicted that the various Dirac cones, which are offset in energy and momentum,
might harbour vastly different orbital character. However, their orbital texture,
which is of immense importance in determining a variety of a materialâ €™ s properties
remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical
topological crystalline insulator. By using Fourier-transform scanning tunnelling
spectroscopy we measure the interference patterns produced by the scattering of
surface-state electrons. We discover that the intensity and energy dependences
of the Fourier transforms show distinct characteristics, which can be directly
attributed to orbital effects. Our experiments reveal a complex band topology
involving two Lifshitz transitions and establish the orbital nature of the Dirac
bands, which could provide an alternative pathway towards future quantum applications.
acknowledgement: V.M. gratefully acknowledges funding from the US Department of Energy,
Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support
of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105
for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern
University is supported by the US Department of Energy grant number DE-FG02-07ER46352,
and benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231.
W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009.
W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University
is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C.
acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Chengyi
full_name: Huang, Chengyi
last_name: Huang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Wei
full_name: Tsai, Wei-Feng
last_name: Tsai
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture
in topological crystalline insulators. Nature Physics. 2014;10(8):572-577.
doi:10.1038/nphys3012
apa: Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2014). Mapping the unconventional orbital texture in topological crystalline
insulators. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3012
chicago: Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital
Texture in Topological Crystalline Insulators.” Nature Physics. Nature
Publishing Group, 2014. https://doi.org/10.1038/nphys3012.
ieee: I. Zeljkovic et al., “Mapping the unconventional orbital texture in
topological crystalline insulators,” Nature Physics, vol. 10, no. 8. Nature
Publishing Group, pp. 572–577, 2014.
ista: Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou
F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional
orbital texture in topological crystalline insulators. Nature Physics. 10(8),
572–577.
mla: Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological
Crystalline Insulators.” Nature Physics, vol. 10, no. 8, Nature Publishing
Group, 2014, pp. 572–77, doi:10.1038/nphys3012.
short: I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn,
F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics
10 (2014) 572–577.
date_created: 2018-12-11T11:49:30Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '01'
doi: 10.1038/nphys3012
extern: 1
intvolume: ' 10'
issue: '8'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.0164
month: '08'
oa: 1
page: 572 - 577
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6423'
quality_controlled: 0
status: public
title: Mapping the unconventional orbital texture in topological crystalline insulators
type: journal_article
volume: 10
year: '2014'
...
---
_id: '979'
abstract:
- lang: eng
text: In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te,
Se), crystal symmetry and electronic topology intertwine to create topological
surface states with many interesting features including Lifshitz transition, Van-Hove
singularity, and fermion mass generation. These surface states are protected by
mirror symmetry with respect to the (110) plane. In this work we present a comprehensive
study of the effects of different mirror-symmetry-breaking perturbations on the
(001) surface band structure. Pristine (001) surface states have four branches
of Dirac fermions at low energy. We show that ferroelectric-type structural distortion
generates a mass and gaps out some or all of these Dirac points, while strain
shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the
surface state gapless, but introduces asymmetry between Dirac points. Finally,
an out-of-plane magnetic field leads to discrete Landau levels. We show that the
Landau level spectrum has an unusual pattern of degeneracy and interesting features
due to the unique underlying band structure. This suggests that Landau level spectroscopy
can detect and distinguish between different mechanisms of symmetry breaking in
topological crystalline insulators.
acknowledgement: We thank V. Madhavan and Y. Okada for related collaborations, and
P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR
1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division
of Materials Sciences and Engineering under award DE-SC0010526.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
citation:
ama: Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline
insulators. Physical Review B - Condensed Matter and Materials Physics.
2014;90(3). doi:10.1103/PhysRevB.90.035402
apa: Serbyn, M., & Fu, L. (2014). Symmetry breaking and Landau quantization
in topological crystalline insulators. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.035402
chicago: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization
in Topological Crystalline Insulators.” Physical Review B - Condensed Matter
and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.035402.
ieee: M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological
crystalline insulators,” Physical Review B - Condensed Matter and Materials
Physics, vol. 90, no. 3. American Physical Society, 2014.
ista: Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological
crystalline insulators. Physical Review B - Condensed Matter and Materials Physics.
90(3).
mla: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in
Topological Crystalline Insulators.” Physical Review B - Condensed Matter and
Materials Physics, vol. 90, no. 3, American Physical Society, 2014, doi:10.1103/PhysRevB.90.035402.
short: M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics
90 (2014).
date_created: 2018-12-11T11:49:31Z
date_published: 2014-07-03T00:00:00Z
date_updated: 2021-01-12T08:22:23Z
day: '03'
doi: 10.1103/PhysRevB.90.035402
extern: 1
intvolume: ' 90'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.8153
month: '07'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6422'
quality_controlled: 0
status: public
title: Symmetry breaking and Landau quantization in topological crystalline insulators
type: journal_article
volume: 90
year: '2014'
...
---
_id: '9931'
abstract:
- lang: eng
text: Gene duplication is important in evolution, because it provides new raw material
for evolutionary adaptations. Several existing hypotheses about the causes of
duplicate retention and diversification differ in their emphasis on gene dosage,
subfunctionalization, and neofunctionalization. Little experimental data exist
on the relative importance of gene expression changes and changes in coding regions
for the evolution of duplicate genes. Furthermore, we do not know how strongly
the environment could affect this importance. To address these questions, we performed
evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to
study the initial stages of duplicate gene evolution in the laboratory. We mimicked
tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid.
We then subjected these copies to repeated cycles of mutagenesis and selection
in various environments that contained antibiotics in different combinations and
concentrations. Our experiments showed that gene dosage is the most important
factor in the initial stages of duplicate gene evolution, and overshadows the
importance of point mutations in the coding region.
acknowledgement: We thank the Functional Genomics Center Zurich for its service in
generating sequencing data, M. Ackermann and E. Hayden for helpful discussions,
A. de Visser for comments on earlier versions of this manuscript, and M. Moser for
help with quantitative PCR. This work was supported by Swiss National Science Foundation
(grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and
the University Priority Research Program in Systems Biology at the University of
Zurich. RD acknowledges support from the Forschungskredit program of the University
of Zurich. The authors declare no conflict of interest.
article_processing_charge: No
article_type: original
author:
- first_name: Riddhiman
full_name: Dhar, Riddhiman
last_name: Dhar
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Andreas
full_name: Wagner, Andreas
last_name: Wagner
citation:
ama: Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role
in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution.
2014;68(6):1775-1791. doi:10.1111/evo.12373
apa: Dhar, R., Bergmiller, T., & Wagner, A. (2014). Increased gene dosage plays
a predominant role in the initial stages of evolution of duplicate TEM-1 beta
lactamase genes. Evolution. Wiley. https://doi.org/10.1111/evo.12373
chicago: Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene
Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate
TEM-1 Beta Lactamase Genes.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12373.
ieee: R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,”
Evolution, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.
ista: Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.
Evolution. 68(6), 1775–1791.
mla: Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in
the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution,
vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:10.1111/evo.12373.
short: R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.
date_created: 2021-08-17T09:03:09Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2023-02-23T14:13:27Z
day: '03'
department:
- _id: CaGu
doi: 10.1111/evo.12373
external_id:
pmid:
- '24495000'
intvolume: ' 68'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1775-1791
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9932'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Increased gene dosage plays a predominant role in the initial stages of evolution
of duplicate TEM-1 beta lactamase genes
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 68
year: '2014'
...
---
_id: '9932'
abstract:
- lang: eng
text: Gene duplication is important in evolution, because it provides new raw material
for evolutionary adaptations. Several existing hypotheses about the causes of
duplicate retention and diversification differ in their emphasis on gene dosage,
sub-functionalization, and neo-functionalization. Little experimental data exists
on the relative importance of gene expression changes and changes in coding regions
for the evolution of duplicate genes. Furthermore, we do not know how strongly
the environment could affect this importance. To address these questions, we performed
evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the
initial stages of duplicate gene evolution in the laboratory. We mimicked tandem
duplication by inserting two copies of the TEM-1 gene on the same plasmid. We
then subjected these copies to repeated cycles of mutagenesis and selection in
various environments that contained antibiotics in different combinations and
concentrations. Our experiments showed that gene dosage is the most important
factor in the initial stages of duplicate gene evolution, and overshadows the
importance of point mutations in the coding region.
article_processing_charge: No
author:
- first_name: Riddhiman
full_name: Dhar, Riddhiman
last_name: Dhar
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Andreas
full_name: Wagner, Andreas
last_name: Wagner
citation:
ama: 'Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant
role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.
2014. doi:10.5061/dryad.jc402'
apa: 'Dhar, R., Bergmiller, T., & Wagner, A. (2014). Data from: Increased gene
dosage plays a predominant role in the initial stages of evolution of duplicate
TEM-1 beta lactamase genes. Dryad. https://doi.org/10.5061/dryad.jc402'
chicago: 'Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased
Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate
TEM-1 Beta Lactamase Genes.” Dryad, 2014. https://doi.org/10.5061/dryad.jc402.'
ieee: 'R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage
plays a predominant role in the initial stages of evolution of duplicate TEM-1
beta lactamase genes.” Dryad, 2014.'
ista: 'Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays
a predominant role in the initial stages of evolution of duplicate TEM-1 beta
lactamase genes, Dryad, 10.5061/dryad.jc402.'
mla: 'Dhar, Riddhiman, et al. Data from: Increased Gene Dosage Plays a Predominant
Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.
Dryad, 2014, doi:10.5061/dryad.jc402.'
short: R. Dhar, T. Bergmiller, A. Wagner, (2014).
date_created: 2021-08-17T09:11:40Z
date_published: 2014-01-27T00:00:00Z
date_updated: 2023-02-23T14:13:24Z
day: '27'
department:
- _id: CaGu
doi: 10.5061/dryad.jc402
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.jc402
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9931'
relation: used_in_publication
status: public
status: public
title: 'Data from: Increased gene dosage plays a predominant role in the initial stages
of evolution of duplicate TEM-1 beta lactamase genes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '12637'
abstract:
- lang: eng
text: The performance of glaciohydrological models which simulate catchment response
to climate variability depends to a large degree on the data used to force the
models. The forcing data become increasingly important in high-elevation, glacierized
catchments where the interplay between extreme topography, climate, and the cryosphere
is complex. It is challenging to generate a reliable forcing data set that captures
this spatial heterogeneity. In this paper, we analyze the results of a 1 year
field campaign focusing on air temperature and precipitation observations in the
Langtang valley in the Nepalese Himalayas. We use the observed time series to
characterize both temperature lapse rates (LRs) and precipitation gradients (PGs).
We study their spatial and temporal variability, and we attempt to identify possible
controlling factors. We show that very clear LRs exist in the valley and that
there are strong seasonal differences related to the water vapor content in the
atmosphere. Results also show that the LRs are generally shallower than the commonly
used environmental lapse rates. The analysis of the precipitation observations
reveals that there is great variability in precipitation over short horizontal
distances. A uniform valley wide PG cannot be established, and several scale-dependent
mechanisms may explain our observations. We complete our analysis by showing the
impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological
model. We conclude that LRs and PGs have a very large impact on the water balance
composition and that short-term monitoring campaigns have the potential to improve
model quality considerably.
article_processing_charge: No
article_type: original
author:
- first_name: W. W.
full_name: Immerzeel, W. W.
last_name: Immerzeel
- first_name: L.
full_name: Petersen, L.
last_name: Petersen
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. The importance of observed
gradients of air temperature and precipitation for modeling runoff from a glacierized
watershed in the Nepalese Himalayas. Water Resources Research. 2014;50(3):2212-2226.
doi:10.1002/2013wr014506
apa: Immerzeel, W. W., Petersen, L., Ragettli, S., & Pellicciotti, F. (2014).
The importance of observed gradients of air temperature and precipitation for
modeling runoff from a glacierized watershed in the Nepalese Himalayas. Water
Resources Research. American Geophysical Union. https://doi.org/10.1002/2013wr014506
chicago: Immerzeel, W. W., L. Petersen, S. Ragettli, and Francesca Pellicciotti.
“The Importance of Observed Gradients of Air Temperature and Precipitation for
Modeling Runoff from a Glacierized Watershed in the Nepalese Himalayas.” Water
Resources Research. American Geophysical Union, 2014. https://doi.org/10.1002/2013wr014506.
ieee: W. W. Immerzeel, L. Petersen, S. Ragettli, and F. Pellicciotti, “The importance
of observed gradients of air temperature and precipitation for modeling runoff
from a glacierized watershed in the Nepalese Himalayas,” Water Resources Research,
vol. 50, no. 3. American Geophysical Union, pp. 2212–2226, 2014.
ista: Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. 2014. The importance
of observed gradients of air temperature and precipitation for modeling runoff
from a glacierized watershed in the Nepalese Himalayas. Water Resources Research.
50(3), 2212–2226.
mla: Immerzeel, W. W., et al. “The Importance of Observed Gradients of Air Temperature
and Precipitation for Modeling Runoff from a Glacierized Watershed in the Nepalese
Himalayas.” Water Resources Research, vol. 50, no. 3, American Geophysical
Union, 2014, pp. 2212–26, doi:10.1002/2013wr014506.
short: W.W. Immerzeel, L. Petersen, S. Ragettli, F. Pellicciotti, Water Resources
Research 50 (2014) 2212–2226.
date_created: 2023-02-20T08:17:01Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-02-24T08:28:23Z
day: '01'
doi: 10.1002/2013wr014506
extern: '1'
intvolume: ' 50'
issue: '3'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2013WR014506
month: '03'
oa: 1
oa_version: Published Version
page: 2212-2226
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: The importance of observed gradients of air temperature and precipitation for
modeling runoff from a glacierized watershed in the Nepalese Himalayas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '12636'
abstract:
- lang: eng
text: Himalayan glacier tongues are commonly debris covered and they are an important
source of melt water. However, they remain relatively unstudied because of the
inaccessibility of the terrain and the difficulties in field work caused by the
thick debris mantles. Observations of debris-covered glaciers are therefore scarce
and airborne remote sensing may bridge the gap between scarce field observations
and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned
Aerial Vehicle (UAV) before and after the melt and monsoon season (May and October
2013) over the debris-covered tongue of the Lirung Glacier in Nepal. Based on
stereo-imaging and the structure for motion algorithm we derive highly detailed
ortho-mosaics and digital elevation models (DEMs), which we geometrically correct
using differential GPS observations collected in the field. Based on DEM differencing
and manual feature tracking we derive the mass loss and the surface velocity of
the glacier at a high spatial accuracy. On average, mass loss is limited and the
surface velocity is very small. However, the spatial variability of melt rates
is very high, and ice cliffs and supra-glacial ponds show mass losses that can
be an order of magnitude higher than the average. We suggest that future research
should focus on the interaction between supra-glacial ponds, ice cliffs and englacial
hydrology to further understand the dynamics of debris-covered glaciers. Finally,
we conclude that UAV deployment has large potential in glaciology and it may revolutionize
methods currently applied in studying glacier surface features.
article_processing_charge: No
article_type: original
author:
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: P.D.A.
full_name: Kraaijenbrink, P.D.A.
last_name: Kraaijenbrink
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: A.B.
full_name: Shrestha, A.B.
last_name: Shrestha
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M.F.P.
full_name: Bierkens, M.F.P.
last_name: Bierkens
- first_name: S.M.
full_name: de Jong, S.M.
last_name: de Jong
citation:
ama: Immerzeel WW, Kraaijenbrink PDA, Shea JM, et al. High-resolution monitoring
of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing
of Environment. 2014;150(7):93-103. doi:10.1016/j.rse.2014.04.025
apa: Immerzeel, W. W., Kraaijenbrink, P. D. A., Shea, J. M., Shrestha, A. B., Pellicciotti,
F., Bierkens, M. F. P., & de Jong, S. M. (2014). High-resolution monitoring
of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing
of Environment. Elsevier. https://doi.org/10.1016/j.rse.2014.04.025
chicago: Immerzeel, W.W., P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, Francesca
Pellicciotti, M.F.P. Bierkens, and S.M. de Jong. “High-Resolution Monitoring of
Himalayan Glacier Dynamics Using Unmanned Aerial Vehicles.” Remote Sensing
of Environment. Elsevier, 2014. https://doi.org/10.1016/j.rse.2014.04.025.
ieee: W. W. Immerzeel et al., “High-resolution monitoring of Himalayan glacier
dynamics using unmanned aerial vehicles,” Remote Sensing of Environment,
vol. 150, no. 7. Elsevier, pp. 93–103, 2014.
ista: Immerzeel WW, Kraaijenbrink PDA, Shea JM, Shrestha AB, Pellicciotti F, Bierkens
MFP, de Jong SM. 2014. High-resolution monitoring of Himalayan glacier dynamics
using unmanned aerial vehicles. Remote Sensing of Environment. 150(7), 93–103.
mla: Immerzeel, W. W., et al. “High-Resolution Monitoring of Himalayan Glacier Dynamics
Using Unmanned Aerial Vehicles.” Remote Sensing of Environment, vol. 150,
no. 7, Elsevier, 2014, pp. 93–103, doi:10.1016/j.rse.2014.04.025.
short: W.W. Immerzeel, P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, F. Pellicciotti,
M.F.P. Bierkens, S.M. de Jong, Remote Sensing of Environment 150 (2014) 93–103.
date_created: 2023-02-20T08:16:56Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-02-24T08:32:39Z
day: '01'
doi: 10.1016/j.rse.2014.04.025
extern: '1'
intvolume: ' 150'
issue: '7'
keyword:
- Computers in Earth Sciences
- Geology
- Soil Science
language:
- iso: eng
month: '07'
oa_version: None
page: 93-103
publication: Remote Sensing of Environment
publication_identifier:
issn:
- 0034-4257
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial
vehicles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 150
year: '2014'
...
---
_id: '12635'
abstract:
- lang: eng
text: 'Switzerland is one of the countries with some of the longest and best glaciological
data sets. Its glaciers and their changes in response to climate have been extensively
investigated, and the number and quality of related studies are notable. However,
a comprehensive review of glacier changes and their impact on the hydrology of
glacierised catchments for Switzerland is missing and we use the opportunity provided
by the EU-FP7 ACQWA project to review the current state of knowledge about past
changes and future projections. We examine the type of models that have been applied
to infer glacier evolution and identify knowledge gaps that should be addressed
in future research in addition to those indicated in previous publications. Common
characteristics in long-term series of projected future glacier runoff are an
initial peak followed by a decline, associated with shifts in seasonality, earlier
melt onset and reduced summer runoff. However, the quantitative predictions are
difficult to compare, as studies differ in terms of model structure, calibration
strategies, input data, temporal and spatial resolution as well as future scenarios
used for impact studies. We identify two sources of uncertainties among those
emerging from recent research, and use simulations over four glaciers to: i) quantify
the importance of the correct extrapolation of air temperature, and ii) point
at the key role played by debris cover in modulating glacier response.'
article_processing_charge: No
article_type: review
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: R.
full_name: Bordoy, R.
last_name: Bordoy
- first_name: M.
full_name: Stoffel, M.
last_name: Stoffel
citation:
ama: 'Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. Changes in glaciers in the
Swiss Alps and impact on basin hydrology: Current state of the art and future
research. Science of The Total Environment. 2014;493:1152-1170. doi:10.1016/j.scitotenv.2014.04.022'
apa: 'Pellicciotti, F., Carenzo, M., Bordoy, R., & Stoffel, M. (2014). Changes
in glaciers in the Swiss Alps and impact on basin hydrology: Current state of
the art and future research. Science of The Total Environment. Elsevier.
https://doi.org/10.1016/j.scitotenv.2014.04.022'
chicago: 'Pellicciotti, Francesca, M. Carenzo, R. Bordoy, and M. Stoffel. “Changes
in Glaciers in the Swiss Alps and Impact on Basin Hydrology: Current State of
the Art and Future Research.” Science of The Total Environment. Elsevier,
2014. https://doi.org/10.1016/j.scitotenv.2014.04.022.'
ieee: 'F. Pellicciotti, M. Carenzo, R. Bordoy, and M. Stoffel, “Changes in glaciers
in the Swiss Alps and impact on basin hydrology: Current state of the art and
future research,” Science of The Total Environment, vol. 493. Elsevier,
pp. 1152–1170, 2014.'
ista: 'Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. 2014. Changes in glaciers
in the Swiss Alps and impact on basin hydrology: Current state of the art and
future research. Science of The Total Environment. 493, 1152–1170.'
mla: 'Pellicciotti, Francesca, et al. “Changes in Glaciers in the Swiss Alps and
Impact on Basin Hydrology: Current State of the Art and Future Research.” Science
of The Total Environment, vol. 493, Elsevier, 2014, pp. 1152–70, doi:10.1016/j.scitotenv.2014.04.022.'
short: F. Pellicciotti, M. Carenzo, R. Bordoy, M. Stoffel, Science of The Total
Environment 493 (2014) 1152–1170.
date_created: 2023-02-20T08:16:51Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2023-02-24T08:36:04Z
day: '15'
doi: 10.1016/j.scitotenv.2014.04.022
extern: '1'
intvolume: ' 493'
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '09'
oa_version: None
page: 1152-1170
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current
state of the art and future research'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 493
year: '2014'
...
---
_id: '12632'
abstract:
- lang: eng
text: We investigate the performance of five glacier melt models over a multi-decadal
period in order to assess their ability to model future glacier response. The
models range from a simple degree-day model, based solely on air temperature,
to more-sophisticated models, including the full shortwave radiation balance.
In addition to the empirical models, the performance of a physically based energy-balance
(EB) model is examined. The melt models are coupled to an accumulation and a surface
evolution model and applied in a distributed manner to Rhonegletscher, Switzerland,
over the period 1929–2012 at hourly resolution. For calibration, seasonal mass-balance
measurements (2006–12) are used. Decadal ice volume changes for six periods in
the years 1929–2012 serve for model validation. Over the period 2006–12, there
are almost no differences in performance between the models, except for EB, which
is less consistent with observations, likely due to lack of meteorological in
situ data. However, simulations over the long term (1929–2012) reveal that models
which include a separate term for shortwave radiation agree best with the observed
ice volume changes, indicating that their melt relationships are robust in time
and thus suitable for long-term modelling, in contrast to more empirical approaches
that are oversensitive to temperature fluctuations.
article_processing_charge: No
article_type: original
author:
- first_name: Jeannette
full_name: Gabbi, Jeannette
last_name: Gabbi
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Andreas
full_name: Bauder, Andreas
last_name: Bauder
- first_name: Martin
full_name: Funk, Martin
last_name: Funk
citation:
ama: Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. A comparison of empirical
and physically based glacier surface melt models for long-term simulations of
glacier response. Journal of Glaciology. 2014;60(224):1140-1154. doi:10.3189/2014jog14j011
apa: Gabbi, J., Carenzo, M., Pellicciotti, F., Bauder, A., & Funk, M. (2014).
A comparison of empirical and physically based glacier surface melt models for
long-term simulations of glacier response. Journal of Glaciology. International
Glaciological Society. https://doi.org/10.3189/2014jog14j011
chicago: Gabbi, Jeannette, Marco Carenzo, Francesca Pellicciotti, Andreas Bauder,
and Martin Funk. “A Comparison of Empirical and Physically Based Glacier Surface
Melt Models for Long-Term Simulations of Glacier Response.” Journal of Glaciology.
International Glaciological Society, 2014. https://doi.org/10.3189/2014jog14j011.
ieee: J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, and M. Funk, “A comparison
of empirical and physically based glacier surface melt models for long-term simulations
of glacier response,” Journal of Glaciology, vol. 60, no. 224. International
Glaciological Society, pp. 1140–1154, 2014.
ista: Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. 2014. A comparison of
empirical and physically based glacier surface melt models for long-term simulations
of glacier response. Journal of Glaciology. 60(224), 1140–1154.
mla: Gabbi, Jeannette, et al. “A Comparison of Empirical and Physically Based Glacier
Surface Melt Models for Long-Term Simulations of Glacier Response.” Journal
of Glaciology, vol. 60, no. 224, International Glaciological Society, 2014,
pp. 1140–54, doi:10.3189/2014jog14j011.
short: J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, M. Funk, Journal of Glaciology
60 (2014) 1140–1154.
date_created: 2023-02-20T08:16:34Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-02-24T08:56:35Z
day: '01'
doi: 10.3189/2014jog14j011
extern: '1'
intvolume: ' 60'
issue: '224'
keyword:
- Earth-Surface Processes
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2014JoG14J011
month: '08'
oa: 1
oa_version: Published Version
page: 1140-1154
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of empirical and physically based glacier surface melt models
for long-term simulations of glacier response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2014'
...
---
_id: '12634'
abstract:
- lang: eng
text: 'Glaciers in the Andes of Chile seem to be shrinking and possibly loosing
mass, but the number and types of studies conducted, constrained mainly by data
availability, are not sufficient to provide a synopsis of glacier changes for
the past or future or explain in an explicit way causes of the observed changes.
In this paper, we provide a systematic review of changes in glaciers for the entire
country, followed by a discussion of the studies that have provided evidence of
such changes. We identify a missing type of work in distributed, physically-oriented
modelling studies that are needed to bridge the gap between the numerous remote
sensing studies and the specific, point scale works focused on process understanding.
We use an advanced mass balance model applied to one of the best monitored glaciers
in the region to investigate four main research issues that should be addressed
in modelling studies for a sound assessment of glacier changes: 1) the use of
physically-based models of glacier ablation (energy balance models) versus more
empirical models (enhanced temperature index approaches); 2) the importance of
the correct extrapolation of air temperature forcing on glaciers and in high elevation
areas and the large uncertainty in model outputs associated with it; 3) the role
played by snow gravitational redistribution; and 4) the uncertainty associated
with future climate scenarios. We quantify differences in model outputs associated
with each of these choices, and conclude with suggestions for future work directions.'
article_processing_charge: No
article_type: review
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: J.
full_name: McPhee, J.
last_name: McPhee
citation:
ama: Pellicciotti F, Ragettli S, Carenzo M, McPhee J. Changes of glaciers in the
Andes of Chile and priorities for future work. Science of The Total Environment.
2014;493:1197-1210. doi:10.1016/j.scitotenv.2013.10.055
apa: Pellicciotti, F., Ragettli, S., Carenzo, M., & McPhee, J. (2014). Changes
of glaciers in the Andes of Chile and priorities for future work. Science of
The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2013.10.055
chicago: Pellicciotti, Francesca, S. Ragettli, M. Carenzo, and J. McPhee. “Changes
of Glaciers in the Andes of Chile and Priorities for Future Work.” Science
of The Total Environment. Elsevier, 2014. https://doi.org/10.1016/j.scitotenv.2013.10.055.
ieee: F. Pellicciotti, S. Ragettli, M. Carenzo, and J. McPhee, “Changes of glaciers
in the Andes of Chile and priorities for future work,” Science of The Total
Environment, vol. 493. Elsevier, pp. 1197–1210, 2014.
ista: Pellicciotti F, Ragettli S, Carenzo M, McPhee J. 2014. Changes of glaciers
in the Andes of Chile and priorities for future work. Science of The Total Environment.
493, 1197–1210.
mla: Pellicciotti, Francesca, et al. “Changes of Glaciers in the Andes of Chile
and Priorities for Future Work.” Science of The Total Environment, vol.
493, Elsevier, 2014, pp. 1197–210, doi:10.1016/j.scitotenv.2013.10.055.
short: F. Pellicciotti, S. Ragettli, M. Carenzo, J. McPhee, Science of The Total
Environment 493 (2014) 1197–1210.
date_created: 2023-02-20T08:16:46Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2023-02-24T08:37:57Z
day: '15'
doi: 10.1016/j.scitotenv.2013.10.055
extern: '1'
intvolume: ' 493'
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '09'
oa_version: None
page: 1197-1210
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Changes of glaciers in the Andes of Chile and priorities for future work
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 493
year: '2014'
...
---
_id: '13399'
abstract:
- lang: eng
text: Nature has long inspired scientists with its seemingly unlimited ability to
harness solar energy and to utilize it to drive various physiological processes.
With the help of man-made molecular photoswitches, we now have the potential to
outperform natural systems in many ways, with the ultimate goal of fabricating
multifunctional materials that operate at different light wavelengths. An important
challenge in developing light-controlled artificial molecular machines lies in
attaining a detailed understanding of the photoisomerization-coupled conformational
changes that occur in macromolecules and molecular assemblies. In this issue of
ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting
insights into the behavior of individual photoresponsive molecules and to identify
contraction, extension, and crawling events accompanying light-induced isomerization.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Klajn R. Watching single molecules move in response to light. ACS
Nano. 2014;8(12):11913-11916. doi:10.1021/nn506656r
apa: Kundu, P. K., & Klajn, R. (2014). Watching single molecules move in response
to light. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn506656r
chicago: Kundu, Pintu K., and Rafal Klajn. “Watching Single Molecules Move in Response
to Light.” ACS Nano. American Chemical Society, 2014. https://doi.org/10.1021/nn506656r.
ieee: P. K. Kundu and R. Klajn, “Watching single molecules move in response to light,”
ACS Nano, vol. 8, no. 12. American Chemical Society, pp. 11913–11916, 2014.
ista: Kundu PK, Klajn R. 2014. Watching single molecules move in response to light.
ACS Nano. 8(12), 11913–11916.
mla: Kundu, Pintu K., and Rafal Klajn. “Watching Single Molecules Move in Response
to Light.” ACS Nano, vol. 8, no. 12, American Chemical Society, 2014, pp.
11913–16, doi:10.1021/nn506656r.
short: P.K. Kundu, R. Klajn, ACS Nano 8 (2014) 11913–11916.
date_created: 2023-08-01T09:45:42Z
date_published: 2014-12-23T00:00:00Z
date_updated: 2023-08-08T07:18:58Z
day: '23'
doi: 10.1021/nn506656r
extern: '1'
external_id:
pmid:
- '25474733'
intvolume: ' 8'
issue: '12'
keyword:
- General Physics and Astronomy
- General Engineering
- General Materials Science
language:
- iso: eng
month: '12'
oa_version: None
page: 11913-11916
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Watching single molecules move in response to light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2014'
...
---
_id: '13402'
abstract:
- lang: eng
text: Nanoporous frameworks are polymeric materials built from rigid molecules,
which give rise to their nanoporous structures with applications in gas sorption
and storage, catalysis and others. Conceptually new applications could emerge,
should these beneficial properties be manipulated by external stimuli in a reversible
manner. One approach to render nanoporous frameworks responsive to external signals
would be to immobilize molecular switches within their nanopores. Although the
majority of molecular switches require conformational freedom to isomerize, and
switching in the solid state is prohibited, the nanopores may provide enough room
for the switches to efficiently isomerize. Here we describe two families of nanoporous
materials incorporating the spiropyran molecular switch. These materials exhibit
a variety of interesting properties, including reversible photochromism and acidochromism
under solvent-free conditions, light-controlled capture and release of metal ions,
as well reversible chromism induced by solvation/desolvation.
article_number: '3588'
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Gregory L.
full_name: Olsen, Gregory L.
last_name: Olsen
- first_name: Vladimir
full_name: Kiss, Vladimir
last_name: Kiss
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Olsen GL, Kiss V, Klajn R. Nanoporous frameworks exhibiting multiple
stimuli responsiveness. Nature Communications. 2014;5. doi:10.1038/ncomms4588
apa: Kundu, P. K., Olsen, G. L., Kiss, V., & Klajn, R. (2014). Nanoporous frameworks
exhibiting multiple stimuli responsiveness. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms4588
chicago: Kundu, Pintu K., Gregory L. Olsen, Vladimir Kiss, and Rafal Klajn. “Nanoporous
Frameworks Exhibiting Multiple Stimuli Responsiveness.” Nature Communications.
Springer Nature, 2014. https://doi.org/10.1038/ncomms4588.
ieee: P. K. Kundu, G. L. Olsen, V. Kiss, and R. Klajn, “Nanoporous frameworks exhibiting
multiple stimuli responsiveness,” Nature Communications, vol. 5. Springer
Nature, 2014.
ista: Kundu PK, Olsen GL, Kiss V, Klajn R. 2014. Nanoporous frameworks exhibiting
multiple stimuli responsiveness. Nature Communications. 5, 3588.
mla: Kundu, Pintu K., et al. “Nanoporous Frameworks Exhibiting Multiple Stimuli
Responsiveness.” Nature Communications, vol. 5, 3588, Springer Nature,
2014, doi:10.1038/ncomms4588.
short: P.K. Kundu, G.L. Olsen, V. Kiss, R. Klajn, Nature Communications 5 (2014).
date_created: 2023-08-01T09:46:27Z
date_published: 2014-04-07T00:00:00Z
date_updated: 2023-08-08T07:28:10Z
day: '07'
doi: 10.1038/ncomms4588
extern: '1'
external_id:
pmid:
- '24709950'
intvolume: ' 5'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms4588
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoporous frameworks exhibiting multiple stimuli responsiveness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '13400'
abstract:
- lang: eng
text: Organizing inorganic nanocrystals into complex architectures is challenging
and typically relies on preexisting templates, such as properly folded DNA or
polypeptide chains. We found that under carefully controlled conditions, cubic
nanocrystals of magnetite self-assemble into arrays of helical superstructures
in a template-free manner with >99% yield. Computer simulations revealed that
the formation of helices is determined by the interplay of van der Waals and magnetic
dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed
to spontaneous formation of chiral nanocube clusters. Neighboring helices within
their densely packed ensembles tended to adopt the same handedness in order to
maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality
amplification.
article_processing_charge: No
article_type: original
author:
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Henry
full_name: Chan, Henry
last_name: Chan
- first_name: Artem
full_name: Baskin, Artem
last_name: Baskin
- first_name: Elijah
full_name: Gelman, Elijah
last_name: Gelman
- first_name: Nikita
full_name: Repnin, Nikita
last_name: Repnin
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Singh G, Chan H, Baskin A, et al. Self-assembly of magnetite nanocubes into
helical superstructures. Science. 2014;345(6201):1149-1153. doi:10.1126/science.1254132
apa: Singh, G., Chan, H., Baskin, A., Gelman, E., Repnin, N., Král, P., & Klajn,
R. (2014). Self-assembly of magnetite nanocubes into helical superstructures.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254132
chicago: Singh, Gurvinder, Henry Chan, Artem Baskin, Elijah Gelman, Nikita Repnin,
Petr Král, and Rafal Klajn. “Self-Assembly of Magnetite Nanocubes into Helical
Superstructures.” Science. American Association for the Advancement of
Science, 2014. https://doi.org/10.1126/science.1254132.
ieee: G. Singh et al., “Self-assembly of magnetite nanocubes into helical
superstructures,” Science, vol. 345, no. 6201. American Association for
the Advancement of Science, pp. 1149–1153, 2014.
ista: Singh G, Chan H, Baskin A, Gelman E, Repnin N, Král P, Klajn R. 2014. Self-assembly
of magnetite nanocubes into helical superstructures. Science. 345(6201), 1149–1153.
mla: Singh, Gurvinder, et al. “Self-Assembly of Magnetite Nanocubes into Helical
Superstructures.” Science, vol. 345, no. 6201, American Association for
the Advancement of Science, 2014, pp. 1149–53, doi:10.1126/science.1254132.
short: G. Singh, H. Chan, A. Baskin, E. Gelman, N. Repnin, P. Král, R. Klajn, Science
345 (2014) 1149–1153.
date_created: 2023-08-01T09:45:56Z
date_published: 2014-07-24T00:00:00Z
date_updated: 2023-08-08T07:23:05Z
day: '24'
doi: 10.1126/science.1254132
extern: '1'
external_id:
pmid:
- '25061133'
intvolume: ' 345'
issue: '6201'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 1149-1153
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of magnetite nanocubes into helical superstructures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 345
year: '2014'
...
---
_id: '13404'
abstract:
- lang: eng
text: In the past few years, spiropyran has emerged as the molecule-of-choice for
the construction of novel dynamic materials. This unique molecular switch undergoes
structural isomerisation in response to a variety of orthogonal stimuli, e.g.
light, temperature, metal ions, redox potential, and mechanical stress. Incorporation
of this switch onto macromolecular supports or inorganic scaffolds allows for
the creation of robust dynamic materials. This review discusses the synthesis,
switching conditions, and use of dynamic materials in which spiropyran has been
attached to the surfaces of polymers, biomacromolecules, inorganic nanoparticles,
as well as solid surfaces. The resulting materials show fascinating properties
whereby the state of the switch intimately affects a multitude of useful properties
of the support. The utility of the spiropyran switch will undoubtedly endow these
materials with far-reaching applications in the near future.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Klajn R. Spiropyran-based dynamic materials. Chemical Society Reviews.
2014;43(1):148-184. doi:10.1039/c3cs60181a
apa: Klajn, R. (2014). Spiropyran-based dynamic materials. Chemical Society Reviews.
Royal Society of Chemistry. https://doi.org/10.1039/c3cs60181a
chicago: Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society
Reviews. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c3cs60181a.
ieee: R. Klajn, “Spiropyran-based dynamic materials,” Chemical Society Reviews,
vol. 43, no. 1. Royal Society of Chemistry, pp. 148–184, 2014.
ista: Klajn R. 2014. Spiropyran-based dynamic materials. Chemical Society Reviews.
43(1), 148–184.
mla: Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society Reviews,
vol. 43, no. 1, Royal Society of Chemistry, 2014, pp. 148–84, doi:10.1039/c3cs60181a.
short: R. Klajn, Chemical Society Reviews 43 (2014) 148–184.
date_created: 2023-08-01T09:47:03Z
date_published: 2014-01-27T00:00:00Z
date_updated: 2023-08-08T07:41:38Z
day: '27'
doi: 10.1039/c3cs60181a
extern: '1'
external_id:
pmid:
- '23979515'
intvolume: ' 43'
issue: '1'
keyword:
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C3CS60181A
month: '01'
oa: 1
oa_version: Published Version
page: 148-184
pmid: 1
publication: Chemical Society Reviews
publication_identifier:
eissn:
- 1460-4744
issn:
- 0306-0012
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spiropyran-based dynamic materials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2014'
...
---
_id: '13401'
abstract:
- lang: eng
text: A compound combining the features of a molecular rotor and a photoswitch was
synthesized and was shown to exist as three diastereomers, which interconvert
via a reversible cyclic reaction scheme. Each of the three diastereomers was isolated,
and by following the equilibration kinetics, activation barriers for all reactions
were calculated. The results indicate that the properties of molecular switches
depend heavily on their immediate chemical environment. The conclusions are important
in the context of designing new switchable molecules and materials.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Avishai
full_name: Lerner, Avishai
last_name: Lerner
- first_name: Kristina
full_name: Kučanda, Kristina
last_name: Kučanda
- first_name: Gregory
full_name: Leitus, Gregory
last_name: Leitus
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Lerner A, Kučanda K, Leitus G, Klajn R. Cyclic kinetics during thermal
equilibration of an axially chiral bis-spiropyran. Journal of the American
Chemical Society. 2014;136(32):11276-11279. doi:10.1021/ja505948q
apa: Kundu, P. K., Lerner, A., Kučanda, K., Leitus, G., & Klajn, R. (2014).
Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja505948q
chicago: Kundu, Pintu K., Avishai Lerner, Kristina Kučanda, Gregory Leitus, and
Rafal Klajn. “Cyclic Kinetics during Thermal Equilibration of an Axially Chiral
Bis-Spiropyran.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja505948q.
ieee: P. K. Kundu, A. Lerner, K. Kučanda, G. Leitus, and R. Klajn, “Cyclic kinetics
during thermal equilibration of an axially chiral bis-spiropyran,” Journal
of the American Chemical Society, vol. 136, no. 32. American Chemical Society,
pp. 11276–11279, 2014.
ista: Kundu PK, Lerner A, Kučanda K, Leitus G, Klajn R. 2014. Cyclic kinetics during
thermal equilibration of an axially chiral bis-spiropyran. Journal of the American
Chemical Society. 136(32), 11276–11279.
mla: Kundu, Pintu K., et al. “Cyclic Kinetics during Thermal Equilibration of an
Axially Chiral Bis-Spiropyran.” Journal of the American Chemical Society,
vol. 136, no. 32, American Chemical Society, 2014, pp. 11276–79, doi:10.1021/ja505948q.
short: P.K. Kundu, A. Lerner, K. Kučanda, G. Leitus, R. Klajn, Journal of the American
Chemical Society 136 (2014) 11276–11279.
date_created: 2023-08-01T09:46:12Z
date_published: 2014-08-13T00:00:00Z
date_updated: 2023-08-08T07:25:37Z
day: '13'
doi: 10.1021/ja505948q
extern: '1'
external_id:
pmid:
- '25072292'
intvolume: ' 136'
issue: '32'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '08'
oa_version: None
page: 11276-11279
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '13403'
abstract:
- lang: eng
text: We show that bimolecular reactions between species confined to the surfaces
of nanoparticles can be manipulated by the nature of the linker, as well as by
the curvature of the underlying particles.
article_processing_charge: No
article_type: original
author:
- first_name: Tino
full_name: Zdobinsky, Tino
last_name: Zdobinsky
- first_name: Pradipta
full_name: Sankar Maiti, Pradipta
last_name: Sankar Maiti
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Zdobinsky T, Sankar Maiti P, Klajn R. Support curvature and conformational
freedom control chemical reactivity of immobilized species. Journal of the
American Chemical Society. 2014;136(7):2711-2714. doi:10.1021/ja411573a
apa: Zdobinsky, T., Sankar Maiti, P., & Klajn, R. (2014). Support curvature
and conformational freedom control chemical reactivity of immobilized species.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja411573a
chicago: Zdobinsky, Tino, Pradipta Sankar Maiti, and Rafal Klajn. “Support Curvature
and Conformational Freedom Control Chemical Reactivity of Immobilized Species.”
Journal of the American Chemical Society. American Chemical Society, 2014.
https://doi.org/10.1021/ja411573a.
ieee: T. Zdobinsky, P. Sankar Maiti, and R. Klajn, “Support curvature and conformational
freedom control chemical reactivity of immobilized species,” Journal of the
American Chemical Society, vol. 136, no. 7. American Chemical Society, pp.
2711–2714, 2014.
ista: Zdobinsky T, Sankar Maiti P, Klajn R. 2014. Support curvature and conformational
freedom control chemical reactivity of immobilized species. Journal of the American
Chemical Society. 136(7), 2711–2714.
mla: Zdobinsky, Tino, et al. “Support Curvature and Conformational Freedom Control
Chemical Reactivity of Immobilized Species.” Journal of the American Chemical
Society, vol. 136, no. 7, American Chemical Society, 2014, pp. 2711–14, doi:10.1021/ja411573a.
short: T. Zdobinsky, P. Sankar Maiti, R. Klajn, Journal of the American Chemical
Society 136 (2014) 2711–2714.
date_created: 2023-08-01T09:46:44Z
date_published: 2014-02-19T00:00:00Z
date_updated: 2023-08-08T07:32:11Z
day: '19'
doi: 10.1021/ja411573a
extern: '1'
external_id:
pmid:
- '24320557'
intvolume: ' 136'
issue: '7'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '02'
oa_version: None
page: 2711-2714
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Support curvature and conformational freedom control chemical reactivity of
immobilized species
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '14018'
abstract:
- lang: eng
text: The sensitivities of high-harmonic generation (HHG) and strong-field ionization
(SFI) to coupled electronic and nuclear dynamics are studied, using the nitric
oxide (NO) molecule as an example. A coherent superposition of electronic and
rotational states of NO is prepared by impulsive stimulated Raman scattering and
probed by simultaneous detection of HHG and SFI yields. We observe a fourfold
higher sensitivity of high-harmonic generation to electronic dynamics and attribute
it to the presence of inelastic quantum paths connecting coherently related electronic
states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic
orders display very different sensitivities to rotational or electronic dynamics,
strong-field ionization is found to be most sensitive to electronic motion. We
introduce a general theoretical formalism for high-harmonic generation from coupled
nuclear-electronic wave packets. We show that the unequal sensitivities of different
harmonic orders to electronic or rotational dynamics result from the angle dependence
of the photorecombination matrix elements which encode several autoionizing and
shape resonances in the photoionization continuum of NO. We further study the
dependence of rotational and electronic coherences on the intensity of the excitation
pulse and support the observations with calculations.
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Peter M.
full_name: Kraus, Peter M.
last_name: Kraus
- first_name: Song Bin
full_name: Zhang, Song Bin
last_name: Zhang
- first_name: Nina
full_name: Rohringer, Nina
last_name: Rohringer
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. The sensitivities
of high-harmonic generation and strong-field ionization to coupled electronic
and nuclear dynamics. Faraday Discussions. 2014;171:113-132. doi:10.1039/c4fd00018h
apa: Baykusheva, D. R., Kraus, P. M., Zhang, S. B., Rohringer, N., & Wörner,
H. J. (2014). The sensitivities of high-harmonic generation and strong-field ionization
to coupled electronic and nuclear dynamics. Faraday Discussions. Royal
Society of Chemistry. https://doi.org/10.1039/c4fd00018h
chicago: Baykusheva, Denitsa Rangelova, Peter M. Kraus, Song Bin Zhang, Nina Rohringer,
and Hans Jakob Wörner. “The Sensitivities of High-Harmonic Generation and Strong-Field
Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions.
Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4fd00018h.
ieee: D. R. Baykusheva, P. M. Kraus, S. B. Zhang, N. Rohringer, and H. J. Wörner,
“The sensitivities of high-harmonic generation and strong-field ionization to
coupled electronic and nuclear dynamics,” Faraday Discussions, vol. 171.
Royal Society of Chemistry, pp. 113–132, 2014.
ista: Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. 2014. The sensitivities
of high-harmonic generation and strong-field ionization to coupled electronic
and nuclear dynamics. Faraday Discussions. 171, 113–132.
mla: Baykusheva, Denitsa Rangelova, et al. “The Sensitivities of High-Harmonic Generation
and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday
Discussions, vol. 171, Royal Society of Chemistry, 2014, pp. 113–32, doi:10.1039/c4fd00018h.
short: D.R. Baykusheva, P.M. Kraus, S.B. Zhang, N. Rohringer, H.J. Wörner, Faraday
Discussions 171 (2014) 113–132.
date_created: 2023-08-10T06:38:19Z
date_published: 2014-04-14T00:00:00Z
date_updated: 2023-08-22T08:58:12Z
day: '14'
doi: 10.1039/c4fd00018h
extern: '1'
external_id:
pmid:
- '25415558'
intvolume: ' 171'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '04'
oa_version: None
page: 113-132
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sensitivities of high-harmonic generation and strong-field ionization to
coupled electronic and nuclear dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2014'
...
---
_id: '14019'
abstract:
- lang: eng
text: The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized
three-membered-ring hydrocarbon. We report on a measurement of the high-resolution
photoelectron and photoionization spectra of cyclopropene and several deuterated
isotopomers, from which we have determined the rovibrational energy level structure
of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first
time. The synthesis of the partially deuterated isotopomers always resulted in
mixtures of several isotopomers, differing in their number of D atoms and in the
location of these atoms, so that the photoelectron spectra of deuterated samples
are superpositions of the spectra of several isotopomers. The rotationally resolved
spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state
of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave
numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon.
The analysis of the isotopic shifts of the vibrational levels enabled the assignment
of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺)
to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency
mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2
rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional
coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.
article_number: '064317'
article_processing_charge: No
article_type: original
author:
- first_name: K.
full_name: Vasilatou, K.
last_name: Vasilatou
- first_name: J. M.
full_name: Michaud, J. M.
last_name: Michaud
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: G.
full_name: Grassi, G.
last_name: Grassi
- first_name: F.
full_name: Merkt, F.
last_name: Merkt
citation:
ama: 'Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene
radical cation: Rovibrational level structure at low energies from high-resolution
photoelectron spectra. The Journal of Chemical Physics. 2014;141(6). doi:10.1063/1.4890744'
apa: 'Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., & Merkt,
F. (2014). The cyclopropene radical cation: Rovibrational level structure at low
energies from high-resolution photoelectron spectra. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.4890744'
chicago: 'Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi,
and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure
at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of
Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4890744.'
ieee: 'K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The
cyclopropene radical cation: Rovibrational level structure at low energies from
high-resolution photoelectron spectra,” The Journal of Chemical Physics,
vol. 141, no. 6. AIP Publishing, 2014.'
ista: 'Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene
radical cation: Rovibrational level structure at low energies from high-resolution
photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.'
mla: 'Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level
Structure at Low Energies from High-Resolution Photoelectron Spectra.” The
Journal of Chemical Physics, vol. 141, no. 6, 064317, AIP Publishing, 2014,
doi:10.1063/1.4890744.'
short: K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal
of Chemical Physics 141 (2014).
date_created: 2023-08-10T06:38:30Z
date_published: 2014-08-14T00:00:00Z
date_updated: 2023-08-22T09:01:31Z
day: '14'
doi: 10.1063/1.4890744
extern: '1'
external_id:
pmid:
- '25134581'
intvolume: ' 141'
issue: '6'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The cyclopropene radical cation: Rovibrational level structure at low energies
from high-resolution photoelectron spectra'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2014'
...
---
_id: '14021'
abstract:
- lang: eng
text: We present the detailed analysis of a new two-pulse orientation scheme that
achieves macroscopic field-free orientation at the high particle densities required
for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923).
Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour
non-resonant femtosecond laser pulses. High-harmonic generation is used to probe
the oriented wave-packet dynamics and reveals that a very high degree of orientation
(Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting
carbonyl sulphide molecules. We show that the present two-pulse scheme selectively
enhances orientation created by the hyperpolarizability interaction whereas the
ionization-depletion mechanism plays no role. We further control and optimize
orientation through the delay between the one- and two-colour pump pulses. Finally,
we demonstrate a complementary encoding of electronic-structure features, such
as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress
makes two-pulse field-free orientation an attractive tool for a broad class of
time-resolved measurements.
article_number: '124030'
article_processing_charge: No
article_type: original
author:
- first_name: P M
full_name: Kraus, P M
last_name: Kraus
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H J
full_name: Wörner, H J
last_name: Wörner
citation:
ama: 'Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse orientation dynamics and high-harmonic
spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic,
Molecular and Optical Physics. 2014;47(12). doi:10.1088/0953-4075/47/12/124030'
apa: 'Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse orientation
dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal
of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/0953-4075/47/12/124030'
chicago: 'Kraus, P M, Denitsa Rangelova Baykusheva, and H J Wörner. “Two-Pulse Orientation
Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal
of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2014.
https://doi.org/10.1088/0953-4075/47/12/124030.'
ieee: 'P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse orientation dynamics
and high-harmonic spectroscopy of strongly-oriented molecules,” Journal of
Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12. IOP Publishing,
2014.'
ista: 'Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse orientation dynamics
and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics
B: Atomic, Molecular and Optical Physics. 47(12), 124030.'
mla: 'Kraus, P. M., et al. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy
of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and
Optical Physics, vol. 47, no. 12, 124030, IOP Publishing, 2014, doi:10.1088/0953-4075/47/12/124030.'
short: 'P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic,
Molecular and Optical Physics 47 (2014).'
date_created: 2023-08-10T06:38:48Z
date_published: 2014-06-10T00:00:00Z
date_updated: 2023-08-22T09:04:30Z
day: '10'
doi: 10.1088/0953-4075/47/12/124030
extern: '1'
external_id:
arxiv:
- '1311.3923'
intvolume: ' 47'
issue: '12'
keyword:
- Condensed Matter Physics
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3923
month: '06'
oa: 1
oa_version: Preprint
publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics'
publication_identifier:
eissn:
- 1361-6455
issn:
- 0953-4075
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented
molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2014'
...
---
_id: '14020'
abstract:
- lang: eng
text: We report the observation of macroscopic field-free orientation, i.e., more
than 73% of CO molecules pointing in the same direction. This is achieved through
an all-optical scheme operating at high particle densities (>10(17) cm(-3)) that
combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses.
We show that the achieved orientation solely relies on the hyperpolarizability
interaction as opposed to an ionization-depletion mechanism, thus, opening a wide
range of applications. The achieved strong orientation enables us to reveal the
molecular-frame anisotropies of the photorecombination amplitudes and phases caused
by a shape resonance. The resonance appears as a local maximum in the even-harmonic
emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in
this spectral region through the combined effects of an asymmetric photorecombination
phase and a subcycle Stark effect, generic for polar molecules, that we experimentally
identify.
article_number: '023001'
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse field-free orientation reveals
anisotropy of molecular shape resonance. Physical Review Letters. 2014;113(2).
doi:10.1103/physrevlett.113.023001
apa: Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse field-free
orientation reveals anisotropy of molecular shape resonance. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.113.023001
chicago: Kraus, P. M., Denitsa Rangelova Baykusheva, and H. J. Wörner. “Two-Pulse
Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical
Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.113.023001.
ieee: P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse field-free orientation
reveals anisotropy of molecular shape resonance,” Physical Review Letters,
vol. 113, no. 2. American Physical Society, 2014.
ista: Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse field-free orientation
reveals anisotropy of molecular shape resonance. Physical Review Letters. 113(2),
023001.
mla: Kraus, P. M., et al. “Two-Pulse Field-Free Orientation Reveals Anisotropy of
Molecular Shape Resonance.” Physical Review Letters, vol. 113, no. 2, 023001,
American Physical Society, 2014, doi:10.1103/physrevlett.113.023001.
short: P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014).
date_created: 2023-08-10T06:38:38Z
date_published: 2014-07-11T00:00:00Z
date_updated: 2023-08-22T09:02:56Z
day: '11'
doi: 10.1103/physrevlett.113.023001
extern: '1'
external_id:
arxiv:
- '1311.3923'
pmid:
- '25062172'
intvolume: ' 113'
issue: '2'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3923
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-pulse field-free orientation reveals anisotropy of molecular shape resonance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2014'
...
---
_id: '535'
abstract:
- lang: eng
text: Energy games belong to a class of turn-based two-player infinite-duration
games played on a weighted directed graph. It is one of the rare and intriguing
combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The
existence of polynomial-time algorithms has been a major open problem for decades
and apart from pseudopolynomial algorithms there is no algorithm that solves any
non-trivial subclass in polynomial time. In this paper, we give several results
based on the weight structures of the graph. First, we identify a notion of penalty
and present a polynomial-time algorithm when the penalty is large. Our algorithm
is the first polynomial-time algorithm on a large class of weighted graphs. It
includes several worst-case instances on which previous algorithms, such as value
iteration and random facet algorithms, require at least sub-exponential time.
Our main technique is developing the first non-trivial approximation algorithm
and showing how to convert it to an exact algorithm. Moreover, we show that in
a practical case in verification where weights are clustered around a constant
number of values, the energy game problem can be solved in polynomial time. We
also show that the problem is still as hard as in general when the clique-width
is bounded or the graph is strongly ergodic, suggesting that restricting the graph
structure does not necessarily help.
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms
for energy games with special weight structures. Algorithmica. 2014;70(3):457-492.
doi:10.1007/s00453-013-9843-7
apa: Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014).
Polynomial-time algorithms for energy games with special weight structures. Algorithmica.
Springer. https://doi.org/10.1007/s00453-013-9843-7
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon
Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.”
Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.
ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time
algorithms for energy games with special weight structures,” Algorithmica,
vol. 70, no. 3. Springer, pp. 457–492, 2014.
ista: Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time
algorithms for energy games with special weight structures. Algorithmica. 70(3),
457–492.
mla: Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games
with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer,
2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.
short: K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica
70 (2014) 457–492.
date_created: 2018-12-11T11:47:01Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2023-09-05T14:09:29Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s00453-013-9843-7
ec_funded: 1
external_id:
arxiv:
- '1604.08234'
intvolume: ' 70'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.08234
month: '11'
oa: 1
oa_version: Preprint
page: 457 - 492
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '7282'
quality_controlled: '1'
related_material:
record:
- id: '10905'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Polynomial-time algorithms for energy games with special weight structures
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 70
year: '2014'
...
---
_id: '10886'
abstract:
- lang: eng
text: We propose a method for visualizing two-dimensional symmetric positive definite
tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the
heat kernel and was originally introduced as an isometry invariant shape signature.
Each positive definite tensor field defines a Riemannian manifold by considering
the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply
the definition of the HKS. The resulting scalar quantity is used for the visualization
of tensor fields. The HKS is closely related to the Gaussian curvature of the
Riemannian manifold and the time parameter of the heat kernel allows a multiscale
analysis in a natural way. In this way, the HKS represents field related scale
space properties, enabling a level of detail analysis of tensor fields. This makes
the HKS an interesting new scalar quantity for tensor fields, which differs significantly
from usual tensor invariants like the trace or the determinant. A method for visualization
and a numerical realization of the HKS for tensor fields is proposed in this chapter.
To validate the approach we apply it to some illustrating simple examples as isolated
critical points and to a medical diffusion tensor data set.
acknowledgement: This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.
alternative_title:
- Mathematics and Visualization
article_processing_charge: No
author:
- first_name: Valentin
full_name: Zobel, Valentin
last_name: Zobel
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
citation:
ama: 'Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature. In: Topological
Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16'
apa: Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional
symmetric positive definite tensor fields using the heat kernel signature. In
Topological Methods in Data Analysis and Visualization III (pp. 249–262).
Springer. https://doi.org/10.1007/978-3-319-04099-8_16
chicago: Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional
Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In
Topological Methods in Data Analysis and Visualization III , 249–62. Springer,
2014. https://doi.org/10.1007/978-3-319-04099-8_16.
ieee: V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature,” in Topological
Methods in Data Analysis and Visualization III , 2014, pp. 249–262.
ista: Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric
positive definite tensor fields using the heat kernel signature. Topological Methods
in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.
mla: Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive
Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods
in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.
short: V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis
and Visualization III , Springer, 2014, pp. 249–262.
date_created: 2022-03-18T13:05:39Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2023-09-05T14:13:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_16
language:
- iso: eng
month: '03'
oa_version: None
page: 249-262
publication: 'Topological Methods in Data Analysis and Visualization III '
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualization of two-dimensional symmetric positive definite tensor fields
using the heat kernel signature
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '6178'
abstract:
- lang: eng
text: Mechanically coupled cells can generate forces driving cell and tissue morphogenesis
during development. Visualization and measuring of these forces is of major importance
to better understand the complexity of the biomechanic processes that shape cells
and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively
assess mechanical tension in different tissues of the developing zebrafish and
in cultures of primary germ layer progenitor cells ex vivo.
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- 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
citation:
ama: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation
to measure cell and tissue-generated forces in the zebrafish embryo in vivo and
ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. Methods in Molecular
Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15'
apa: 'Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P.
J. (2014). UV laser ablation to measure cell and tissue-generated forces in the
zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis
(Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15'
chicago: 'Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and
Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis,
edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York,
NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.'
ieee: 'M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg,
“UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson,
Ed. New York, NY: Springer, 2014, pp. 219–235.'
ista: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser
ablation to measure cell and tissue-generated forces in the zebrafish embryo in
vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.'
mla: Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis,
edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.
short: M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:,
C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.
date_created: 2019-03-26T08:55:59Z
date_published: 2014-08-22T00:00:00Z
date_updated: 2023-09-05T14:12:00Z
day: '22'
department:
- _id: CaHe
doi: 10.1007/978-1-4939-1164-6_15
editor:
- first_name: Celeste
full_name: Nelson, Celeste
last_name: Nelson
external_id:
pmid:
- '25245697'
intvolume: ' 1189'
language:
- iso: eng
month: '08'
oa_version: None
page: 219-235
place: New York, NY
pmid: 1
publication: Tissue Morphogenesis
publication_identifier:
eissn:
- 1940-6029
isbn:
- '9781493911639'
- '9781493911646'
issn:
- 1064-3745
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: Methods in Molecular Biology
status: public
title: UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1189
year: '2014'
...
---
_id: '10814'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the excitation
spectrum of bosonic quantum many-body systems. In particular, we explain how one
can rigorously establish the predictions resulting from the Bogoliubov approximation
in the mean field limit. The latter predicts that the spectrum is made up of elementary
excitations, whose energy behaves linearly in the momentum for small momentum.
This property is crucial for the superfluid behavior of the system. We also discuss
a list of open problems in this field.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht der Deutschen Mathematiker-Vereinigung. 2014;116:21-41. doi:10.1365/s13291-014-0083-9
apa: Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature.
https://doi.org/10.1365/s13291-014-0083-9
chicago: Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.”
Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature,
2014. https://doi.org/10.1365/s13291-014-0083-9.
ieee: R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,”
Jahresbericht der Deutschen Mathematiker-Vereinigung, vol. 116. Springer
Nature, pp. 21–41, 2014.
ista: Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions.
Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.
mla: Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.”
Jahresbericht Der Deutschen Mathematiker-Vereinigung, vol. 116, Springer
Nature, 2014, pp. 21–41, doi:10.1365/s13291-014-0083-9.
short: R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014)
21–41.
date_created: 2022-03-04T07:54:39Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-09-05T14:19:47Z
day: '01'
department:
- _id: RoSe
doi: 10.1365/s13291-014-0083-9
intvolume: ' 116'
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 21-41
publication: Jahresbericht der Deutschen Mathematiker-Vereinigung
publication_identifier:
eissn:
- 1869-7135
issn:
- 0012-0456
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitation spectrum for Bose fluids with weak interactions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2014'
...
---
_id: '10817'
abstract:
- lang: eng
text: The Morse-Smale complex can be either explicitly or implicitly represented.
Depending on the type of representation, the simplification of the Morse-Smale
complex works differently. In the explicit representation, the Morse-Smale complex
is directly simplified by explicitly reconnecting the critical points during the
simplification. In the implicit representation, on the other hand, the Morse-Smale
complex is given by a combinatorial gradient field. In this setting, the simplification
changes the combinatorial flow, which yields an indirect simplification of the
Morse-Smale complex. The topological complexity of the Morse-Smale complex is
reduced in both representations. However, the simplifications generally yield
different results. In this chapter, we emphasize properties of the two representations
that cause these differences. We also provide a complexity analysis of the two
schemes with respect to running time and memory consumption.
acknowledgement: This research is supported and funded by the Digiteo unTopoVis project,
the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.
article_processing_charge: No
author:
- first_name: David
full_name: Günther, David
last_name: Günther
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Tino
full_name: Weinkauf, Tino
last_name: Weinkauf
citation:
ama: 'Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification
of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds.
Topological Methods in Data Analysis and Visualization III. Mathematics
and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9'
apa: 'Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes
on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V.
Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and
Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9'
chicago: 'Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf.
“Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods
in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid
Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization.
Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.'
ieee: 'D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the
simplification of the Morse-Smale complex,” in Topological Methods in Data
Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R.
Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.'
ista: 'Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification
of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization
III. , 135–150.'
mla: Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.”
Topological Methods in Data Analysis and Visualization III., edited by
Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.
short: D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer,
I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis
and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.
date_created: 2022-03-04T08:33:57Z
date_published: 2014-03-19T00:00:00Z
date_updated: 2023-09-05T15:33:45Z
day: '19'
department:
- _id: HeEd
doi: 10.1007/978-3-319-04099-8_9
ec_funded: 1
editor:
- first_name: Peer-Timo
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
language:
- iso: eng
month: '03'
oa_version: None
page: 135-150
place: Cham
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Topological Methods in Data Analysis and Visualization III.
publication_identifier:
eisbn:
- '9783319040998'
eissn:
- 2197-666X
isbn:
- '9783319040981'
issn:
- 1612-3786
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: Mathematics and Visualization
status: public
title: Notes on the simplification of the Morse-Smale complex
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '1395'
abstract:
- lang: eng
text: In this thesis I studied various individual and social immune defences employed
by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The
first two chapters of this thesis address the phenomenon of 'social immunisation'.
Social immunisation, that is the immunological protection of group members due
to social contact to a pathogen-exposed nestmate, has been described in various
social insect species against different types of pathogens. However, in the case
of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation
exists at all. Its underlying mechanisms r any other properties were, however,
unknown. In the first chapter of this thesis I identified the mechanistic basis
of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium.
I could show that nestmates of a pathogen-exposed individual contract low-level
infections due to social interactions. These low-level infections are, however,
non-lethal and cause an active stimulation of the immune system, which protects
the nestmates upon subsequent pathogen encounters. In the second chapter of this
thesis I investigated the specificity and colony level effects of social immunisation.
I demonstrated that the protection conferred by social immunisation is highly
specific, protecting ants only against the same pathogen strain. In addition,
depending on the respective context, social immunisation may even cause fitness
costs. I further showed that social immunisation crucially affects sanitary behaviour
and disease dynamics within ant groups. In the third chapter of this thesis I
studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its
host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic
fungi, research concerning host fitness consequence is sparse. I showed that highly
Laboulbenia-infected ants sustain fitness costs under resource limitation, however,
gain fitness benefits when exposed to an entomopathogenus fungus. These effects
are probably cause by a prophylactic upregulation of behavioural as well as physiological
immune defences in highly infected ants.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
citation:
ama: 'Konrad M. Immune defences in ants: Effects of social immunisation and a fungal
ectosymbiont in the ant Lasius neglectus. 2014.'
apa: 'Konrad, M. (2014). Immune defences in ants: Effects of social immunisation
and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science
and Technology Austria.'
chicago: 'Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation
and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and
Technology Austria, 2014.'
ieee: 'M. Konrad, “Immune defences in ants: Effects of social immunisation and a
fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology
Austria, 2014.'
ista: 'Konrad M. 2014. Immune defences in ants: Effects of social immunisation and
a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology
Austria.'
mla: 'Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation
and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science
and Technology Austria, 2014.'
short: 'M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a
Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology
Austria, 2014.'
date_created: 2018-12-11T11:51:46Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2023-09-07T11:38:56Z
day: '01'
degree_awarded: PhD
department:
- _id: SyCr
language:
- iso: eng
month: '02'
oa_version: None
page: '131'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5814'
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: 'Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont
in the ant Lasius neglectus'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '1402'
abstract:
- lang: eng
text: Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated
into various lipid signaling molecules, designated polyphosphoinositides (PPIs).
The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol
is performed by a set of organelle-specific kinases and phosphatases, and the
characteristic head groups make these molecules ideal for regulating biological
processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2
play crucial roles in trafficking toward the lytic compartments, whereas the role
in plants is not yet fully understood. Here we identified the role of a land plant-specific
subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during
vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize
to the tonoplast along with Ptdlns3P, the presumable product of their activity.
in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates
and bisphosphates were changed, with opposite effects on the morphology of storage
and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover,
multiple sac knockout mutants had an increased number of smaller storage and lytic
vacuoles, whereas extralarge vacuoles were observed in the overexpression lines,
correlating with various growth and developmental defects. The fragmented vacuolar
phenotype of sac mutants could be mimicked by treating wild-type seedlings with
Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology.
Taken together, these results provide evidence that PPIs, together with their
metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar
morphology and function in plants.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
citation:
ama: Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in
Arabidopsis thaliana. 2014.
apa: Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria.
chicago: Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.
ieee: P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.
ista: Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014.
short: P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2023-09-07T11:39:38Z
day: '01'
degree_awarded: PhD
department:
- _id: JiFr
language:
- iso: eng
month: '12'
oa_version: None
page: '90'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5805'
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis
thaliana
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2014'
...
---
_id: '2255'
abstract:
- lang: eng
text: Motivated by applications in biology, we present an algorithm for estimating
the length of tube-like shapes in 3-dimensional Euclidean space. In a first step,
we combine the tube formula of Weyl with integral geometric methods to obtain
an integral representation of the length, which we approximate using a variant
of the Koksma-Hlawka Theorem. In a second step, we use tools from computational
topology to decrease the dependence on small perturbations of the shape. We present
computational experiments that shed light on the stability and the convergence
rate of our algorithm.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal
of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x
apa: Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like
shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates
of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer,
2014. https://doi.org/10.1007/s10851-013-0468-x.
ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,”
Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp.
164–177, 2014.
ista: Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes.
Journal of Mathematical Imaging and Vision. 50(1), 164–177.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like
Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer,
2014, pp. 164–77, doi:10.1007/s10851-013-0468-x.
short: H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision
50 (2014) 164–177.
date_created: 2018-12-11T11:56:36Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s10851-013-0468-x
ec_funded: 1
file:
- access_level: open_access
checksum: 2f93f3e63a38a85cd4404d7953913b14
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:18Z
date_updated: 2020-07-14T12:45:35Z
file_id: '5204'
file_name: IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf
file_size: 3941391
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 164 - 177
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer
publist_id: '4691'
pubrep_id: '549'
quality_controlled: '1'
related_material:
record:
- id: '2843'
relation: earlier_version
status: public
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Stable length estimates of tube-like shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '2159'
abstract:
- lang: eng
text: 'Motivated by topological Tverberg-type problems, we consider multiple (double,
triple, and higher multiplicity) selfintersection points of maps from finite simplicial
complexes (compact polyhedra) into ℝd and study conditions under which such multiple
points can be eliminated. The most classical case is that of embeddings (i.e.,
maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem,
the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary
condition for embeddability (namely, vanishing of the van Kampen ob-struction).
For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm
for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which
generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes
then one can successively remove these double points by local modifications of
the map f. One of the main tools is the famous Whitney trick that permits eliminating
pairs of double points of opposite intersection sign. We are interested in generalizing
this approach to intersection points of higher multiplicity. We call a point y
2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection
f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue
of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional
complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e.,
does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that
for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time
algorithm for deciding this (based on the vanishing of a cohomological obstruction,
as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney
trick: Given r pairwise disjoint simplices of K such that the intersection of
their images contains two r-fold Tverberg points y+ and y- of opposite intersection
sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper,
we plan to develop this further and present a generalization of the classical
Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability
of κ-complexes into ℝd for a wider range of dimensions) to intersection points
of higher multiplicity.'
acknowledgement: Swiss National Science Foundation (Project SNSF-PP00P2-138948)
author:
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Mabillard I, Wagner U. Eliminating Tverberg points, I. An analogue of the
Whitney trick. In: Proceedings of the Annual Symposium on Computational Geometry.
ACM; 2014:171-180. doi:10.1145/2582112.2582134'
apa: 'Mabillard, I., & Wagner, U. (2014). Eliminating Tverberg points, I. An
analogue of the Whitney trick. In Proceedings of the Annual Symposium on Computational
Geometry (pp. 171–180). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582134'
chicago: Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue
of the Whitney Trick.” In Proceedings of the Annual Symposium on Computational
Geometry, 171–80. ACM, 2014. https://doi.org/10.1145/2582112.2582134.
ieee: I. Mabillard and U. Wagner, “Eliminating Tverberg points, I. An analogue of
the Whitney trick,” in Proceedings of the Annual Symposium on Computational
Geometry, Kyoto, Japan, 2014, pp. 171–180.
ista: 'Mabillard I, Wagner U. 2014. Eliminating Tverberg points, I. An analogue
of the Whitney trick. Proceedings of the Annual Symposium on Computational Geometry.
SoCG: Symposium on Computational Geometry, 171–180.'
mla: Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue
of the Whitney Trick.” Proceedings of the Annual Symposium on Computational
Geometry, ACM, 2014, pp. 171–80, doi:10.1145/2582112.2582134.
short: I. Mabillard, U. Wagner, in:, Proceedings of the Annual Symposium on Computational
Geometry, ACM, 2014, pp. 171–180.
conference:
end_date: 2014-06-11
location: Kyoto, Japan
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2014-06-08
date_created: 2018-12-11T11:56:03Z
date_published: 2014-06-08T00:00:00Z
date_updated: 2023-09-07T11:56:27Z
day: '08'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1145/2582112.2582134
file:
- access_level: open_access
checksum: 2aae223fee8ffeaf57bbabd8d92b6a2c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:12Z
date_updated: 2020-07-14T12:45:30Z
file_id: '4735'
file_name: IST-2016-534-v1+1_Eliminating_Tverberg_points_I._An_analogue_of_the_Whitney_trick.pdf
file_size: 914396
relation: main_file
file_date_updated: 2020-07-14T12:45:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 171 - 180
publication: Proceedings of the Annual Symposium on Computational Geometry
publication_status: published
publisher: ACM
publist_id: '4847'
pubrep_id: '534'
quality_controlled: '1'
related_material:
record:
- id: '1123'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Eliminating Tverberg points, I. An analogue of the Whitney trick
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2023'
abstract:
- lang: eng
text: 'Understanding the evolution of dispersal is essential for understanding and
predicting the dynamics of natural populations. Two main factors are known to
influence dispersal evolution: spatio-temporal variation in the environment and
relatedness between individuals. However, the relation between these factors is
still poorly understood, and they are usually treated separately. In this article,
I present a theoretical framework that contains and connects effects of both environmental
variation and relatedness, and reproduces and extends their known features. Spatial
habitat variation selects for balanced dispersal strategies, whereby the population
is kept at an ideal free distribution. Within this class of dispersal strategies,
I explain how increased dispersal is promoted by perturbations to the dispersal
type frequencies. An explicit formula shows the magnitude of the selective advantage
of increased dispersal in terms of the spatial variability in the frequencies
of the different dispersal strategies present. These variances are capable of
capturing various sources of stochasticity and hence establish a common scale
for their effects on the evolution of dispersal. The results furthermore indicate
an alternative approach to identifying effects of relatedness on dispersal evolution.'
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Habitat heterogeneities versus spatial type frequency variances as
driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597.
doi:10.1002/ece3.1289
apa: Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell.
https://doi.org/10.1002/ece3.1289
chicago: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency
Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution.
Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.
ieee: S. Novak, “Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution,” Ecology and Evolution, vol.
4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.
ista: Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.
mla: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances
as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol.
4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.
short: S. Novak, Ecology and Evolution 4 (2014) 4589–4597.
date_created: 2018-12-11T11:55:16Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/ece3.1289
ec_funded: 1
file:
- access_level: open_access
checksum: 9ab43db1b0fede7bfe560ed77e177b76
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:28Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4946'
file_name: IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf
file_size: 118813
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '24'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 4589 - 4597
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5049'
pubrep_id: '462'
quality_controlled: '1'
related_material:
record:
- id: '1125'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Habitat heterogeneities versus spatial type frequency variances as driving
forces of dispersal evolution
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '2218'
abstract:
- lang: eng
text: While fixing concurrency bugs, program repair algorithms may introduce new
concurrency bugs. We present an algorithm that avoids such regressions. The solution
space is given by a set of program transformations we consider in the repair process.
These include reordering of instructions within a thread and inserting atomic
sections. The new algorithm learns a constraint on the space of candidate solutions,
from both positive examples (error-free traces) and counterexamples (error traces).
From each counterexample, the algorithm learns a constraint necessary to remove
the errors. From each positive examples, it learns a constraint that is necessary
in order to prevent the repair from turning the trace into an error trace. We
implemented the algorithm and evaluated it on simplified Linux device drivers
with known bugs.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
last_name: Cerny
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free
synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38'
apa: 'Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach,
T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584).
Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer.
https://doi.org/10.1007/978-3-319-08867-9_38'
chicago: Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and
Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer,
2014. https://doi.org/10.1007/978-3-319-08867-9_38.
ieee: 'P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free
synthesis for concurrency,” presented at the CAV: Computer Aided Verification,
Vienna, Austria, 2014, vol. 8559, pp. 568–584.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free
synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559,
568–584.'
mla: Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol.
8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer,
2014, pp. 568–584.
conference:
end_date: 2014-07-22
location: Vienna, Austria
name: 'CAV: Computer Aided Verification'
start_date: 2014-07-18
date_created: 2018-12-11T11:56:23Z
date_published: 2014-07-22T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-08867-9_38
ec_funded: 1
file:
- access_level: open_access
checksum: a631d3105509f239724644e77a1212e2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:14Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4995'
file_name: IST-2014-297-v1+1_cav14-final.pdf
file_size: 416732
relation: main_file
- access_level: open_access
checksum: f8b0f748cc9fa697ca992cc56c87bc4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:15Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4996'
file_name: IST-2014-297-v2+1_cav14-final2.pdf
file_size: 616293
relation: main_file
file_date_updated: 2020-07-14T12:45:33Z
has_accepted_license: '1'
intvolume: ' 8559'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38
month: '07'
oa: 1
oa_version: Submitted Version
page: 568 - 584
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
isbn:
- 978-331908866-2
publication_status: published
publisher: Springer
publist_id: '4749'
pubrep_id: '297'
quality_controlled: '1'
related_material:
record:
- id: '1130'
relation: dissertation_contains
status: public
status: public
title: Regression-free synthesis for concurrency
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2167'
abstract:
- lang: eng
text: Model-based testing is a promising technology for black-box software and hardware
testing, in which test cases are generated automatically from high-level specifications.
Nowadays, systems typically consist of multiple interacting components and, due
to their complexity, testing presents a considerable portion of the effort and
cost in the design process. Exploiting the compositional structure of system specifications
can considerably reduce the effort in model-based testing. Moreover, inferring
properties about the system from testing its individual components allows the
designer to reduce the amount of integration testing. In this paper, we study
compositional properties of the ioco-testing theory. We propose a new approach
to composition and hiding operations, inspired by contract-based design and interface
theories. These operations preserve behaviors that are compatible under composition
and hiding, and prune away incompatible ones. The resulting specification characterizes
the input sequences for which the unit testing of components is sufficient to
infer the correctness of component integration without the need for further tests.
We provide a methodology that uses these results to minimize integration testing
effort, but also to detect potential weaknesses in specifications. While we focus
on asynchronous models and the ioco conformance relation, the resulting methodology
can be applied to a broader class of systems.
article_number: '6823899'
article_processing_charge: No
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: Willibald
full_name: Krenn, Willibald
last_name: Krenn
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
citation:
ama: 'Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional specifications for
IOCO testing. In: IEEE 7th International Conference on Software Testing, Verification
and Validation. IEEE; 2014. doi:10.1109/ICST.2014.50'
apa: 'Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional
specifications for IOCO testing. In IEEE 7th International Conference on Software
Testing, Verification and Validation. Cleveland, USA: IEEE. https://doi.org/10.1109/ICST.2014.50'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic.
“Compositional Specifications for IOCO Testing.” In IEEE 7th International
Conference on Software Testing, Verification and Validation. IEEE, 2014. https://doi.org/10.1109/ICST.2014.50.
ieee: P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, “Compositional specifications
for IOCO testing,” in IEEE 7th International Conference on Software Testing,
Verification and Validation, Cleveland, USA, 2014.
ista: 'Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications
for IOCO testing. IEEE 7th International Conference on Software Testing, Verification
and Validation. ICST: International Conference on Software Testing, Verification
and Validation, 6823899.'
mla: Daca, Przemyslaw, et al. “Compositional Specifications for IOCO Testing.” IEEE
7th International Conference on Software Testing, Verification and Validation,
6823899, IEEE, 2014, doi:10.1109/ICST.2014.50.
short: P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, in:, IEEE 7th International
Conference on Software Testing, Verification and Validation, IEEE, 2014.
conference:
end_date: 2014-04-04
location: Cleveland, USA
name: 'ICST: International Conference on Software Testing, Verification and Validation'
start_date: 2014-03-31
date_created: 2018-12-11T11:56:06Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
doi: 10.1109/ICST.2014.50
ec_funded: 1
external_id:
arxiv:
- '1904.07083'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1904.07083
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: IEEE 7th International Conference on Software Testing, Verification and
Validation
publication_identifier:
isbn:
- 978-1-4799-2255-0
issn:
- 2159-4848
publication_status: published
publisher: IEEE
publist_id: '4817'
quality_controlled: '1'
related_material:
record:
- id: '5411'
relation: earlier_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Compositional specifications for IOCO testing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2063'
abstract:
- lang: eng
text: We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems.We focus on qualitative properties forMDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability. We introduce a new simulation relation to capture
the refinement relation ofMDPs with respect to qualitative properties, and present
discrete graph theoretic algorithms with quadratic complexity to compute the simulation
relation.We present an automated technique for assume-guarantee style reasoning
for compositional analysis ofMDPs with qualitative properties by giving a counterexample
guided abstraction-refinement approach to compute our new simulation relation.
We have implemented our algorithms and show that the compositional analysis leads
to significant improvements.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
citation:
ama: 'Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic
systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31'
apa: 'Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative
analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV:
Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31'
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for
Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31.
ieee: 'K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of
probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna,
Austria, 2014, vol. 8559, pp. 473–490.'
ista: 'Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of
probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.'
mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic
Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.
short: K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.
conference:
end_date: 2014-07-22
location: Vienna, Austria
name: 'CAV: Computer Aided Verification'
start_date: 2014-07-18
date_created: 2018-12-11T11:55:30Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-08867-9_31
ec_funded: 1
intvolume: ' 8559'
language:
- iso: eng
month: '07'
oa_version: None
page: 473 - 490
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '4978'
quality_controlled: '1'
related_material:
record:
- id: '5412'
relation: earlier_version
status: public
- id: '5413'
relation: earlier_version
status: public
- id: '5414'
relation: earlier_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
status: public
title: CEGAR for qualitative analysis of probabilistic systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2001'
abstract:
- lang: eng
text: Antibiotics affect bacterial cell physiology at many levels. Rather than just
compensating for the direct cellular defects caused by the drug, bacteria respond
to antibiotics by changing their morphology, macromolecular composition, metabolism,
gene expression and possibly even their mutation rate. Inevitably, these processes
affect each other, resulting in a complex response with changes in the expression
of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive
understanding of bacterial responses to antibiotics. In addition, a combination
of experimental and theoretical approaches is needed for identifying general principles
that underlie these responses. Here, we review recent progress in our understanding
of bacterial responses to antibiotics and their combinations, focusing on effects
at the levels of growth rate and gene expression. We concentrate on studies performed
in controlled laboratory conditions, which combine promising experimental techniques
with quantitative data analysis and mathematical modeling. While these basic research
approaches are not immediately applicable in the clinic, uncovering the principles
and mechanisms underlying bacterial responses to antibiotics may, in the long
term, contribute to the development of new treatment strategies to cope with and
prevent the rise of resistant pathogenic bacteria.
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations.
Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190
apa: Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics
and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190
chicago: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014.
https://doi.org/10.1111/1758-2229.12190.
ieee: K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their
combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley,
pp. 545–557, 2014.
ista: Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their
combinations. Environmental Microbiology Reports. 6(6), 545–557.
mla: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports, vol. 6, no.
6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190.
short: K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014)
545–557.
date_created: 2018-12-11T11:55:08Z
date_published: 2014-06-22T00:00:00Z
date_updated: 2023-09-07T12:00:25Z
day: '22'
department:
- _id: ToBo
doi: 10.1111/1758-2229.12190
ec_funded: 1
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 545 - 557
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Environmental Microbiology Reports
publication_status: published
publisher: Wiley
publist_id: '5076'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Bacterial responses to antibiotics and their combinations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2014'
...
---
_id: '2082'
abstract:
- lang: eng
text: 'NMAC is a mode of operation which turns a fixed input-length keyed hash function
f into a variable input-length function. A practical single-key variant of NMAC
called HMAC is a very popular and widely deployed message authentication code
(MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC
was introduced by Bellare, Canetti and Krawczyk [Crypto''96], who proved it to
be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1)
f is a PRF and (2) the function we get when cascading f is weakly collision-resistant.
Unfortunately, HMAC is typically instantiated with cryptographic hash functions
like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable
guarantees for NMAC, Bellare [Crypto''06] showed its security based solely on
the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first
contribution is a simpler and uniform proof for this fact: If f is an ε-secure
PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries),
then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks
each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting
case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with
advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of
NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security
of a modification of NMAC called NI [An and Bellare, Crypto''99] that differs
mainly by using a compression function with an additional keying input. This avoids
the constant rekeying on multi-block messages in NMAC and allows for a security
proof starting by the standard switch from a PRF to a random function, followed
by an information-theoretic analysis. We carry out such an analysis, obtaining
a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c.
The proof borrows combinatorial techniques originally developed for proving the
security of CBC-MAC [Bellare et al., Crypto''05].'
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: 'Gazi P, Pietrzak KZ, Rybar M. The exact PRF-security of NMAC and HMAC. In:
Garay J, Gennaro R, eds. Vol 8616. Springer; 2014:113-130. doi:10.1007/978-3-662-44371-2_7'
apa: 'Gazi, P., Pietrzak, K. Z., & Rybar, M. (2014). The exact PRF-security
of NMAC and HMAC. In J. Garay & R. Gennaro (Eds.) (Vol. 8616, pp. 113–130).
Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA:
Springer. https://doi.org/10.1007/978-3-662-44371-2_7'
chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact PRF-Security
of NMAC and HMAC.” edited by Juan Garay and Rosario Gennaro, 8616:113–30. Springer,
2014. https://doi.org/10.1007/978-3-662-44371-2_7.
ieee: 'P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact PRF-security of NMAC and
HMAC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara,
USA, 2014, vol. 8616, no. 1, pp. 113–130.'
ista: 'Gazi P, Pietrzak KZ, Rybar M. 2014. The exact PRF-security of NMAC and HMAC.
CRYPTO: International Cryptology Conference, LNCS, vol. 8616, 113–130.'
mla: Gazi, Peter, et al. The Exact PRF-Security of NMAC and HMAC. Edited
by Juan Garay and Rosario Gennaro, vol. 8616, no. 1, Springer, 2014, pp. 113–30,
doi:10.1007/978-3-662-44371-2_7.
short: P. Gazi, K.Z. Pietrzak, M. Rybar, in:, J. Garay, R. Gennaro (Eds.), Springer,
2014, pp. 113–130.
conference:
end_date: 2014-08-21
location: Santa Barbara, USA
name: 'CRYPTO: International Cryptology Conference'
start_date: 2014-08-17
date_created: 2018-12-11T11:55:36Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-09-07T12:02:27Z
day: '01'
ddc:
- '000'
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-662-44371-2_7
ec_funded: 1
editor:
- first_name: Juan
full_name: Garay, Juan
last_name: Garay
- first_name: Rosario
full_name: Gennaro, Rosario
last_name: Gennaro
file:
- access_level: open_access
checksum: dab6ab36a5f6af94f2b597e6404ed11d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2020-07-14T12:45:28Z
file_id: '4999'
file_name: IST-2016-682-v1+1_578.pdf
file_size: 492310
relation: main_file
file_date_updated: 2020-07-14T12:45:28Z
has_accepted_license: '1'
intvolume: ' 8616'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 113 - 130
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: '4955'
pubrep_id: '682'
quality_controlled: '1'
related_material:
record:
- id: '838'
relation: dissertation_contains
status: public
status: public
title: The exact PRF-security of NMAC and HMAC
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8616
year: '2014'
...
---
_id: '1912'
abstract:
- lang: eng
text: Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the
embryo along its left-right (LR) axis. Regional differences in cell shape within
the lumen-lining KV epithelium are essential for its LR patterning function. However,
the processes by which KV cells acquire their characteristic shapes are largely
unknown. Here, we show that the notochord induces regional differences in cell
shape within KV by triggering extracellular matrix (ECM) accumulation adjacent
to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts
apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen
growth. Our study provides mechanistic insight into the processes by which KV
translates global embryonic patterning into regional cell shape differences required
for its LR symmetry-breaking function.
acknowledgement: We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus,
and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing
reagents. This work was supported by the Institute of Science and Technology Austria
and an Alexander von Humboldt Foundation fellowship to J.C.
article_processing_charge: No
author:
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Srivarsha
full_name: Rajshekar, Srivarsha
last_name: Rajshekar
- first_name: Rita
full_name: Kottmeier, Rita
last_name: Kottmeier
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- 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
citation:
ama: Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry
by controlling cell shapes in the Zebrafish laterality organ. Developmental
Cell. 2014;31(6):774-783. doi:10.1016/j.devcel.2014.11.003
apa: Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K.,
Behrndt, M., & Heisenberg, C.-P. J. (2014). The notochord breaks bilateral
symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental
Cell. Cell Press. https://doi.org/10.1016/j.devcel.2014.11.003
chicago: Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier,
Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The
Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish
Laterality Organ.” Developmental Cell. Cell Press, 2014. https://doi.org/10.1016/j.devcel.2014.11.003.
ieee: J. Compagnon et al., “The notochord breaks bilateral symmetry by controlling
cell shapes in the Zebrafish laterality organ,” Developmental Cell, vol.
31, no. 6. Cell Press, pp. 774–783, 2014.
ista: Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt
M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling
cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.
mla: Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling
Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell, vol.
31, no. 6, Cell Press, 2014, pp. 774–83, doi:10.1016/j.devcel.2014.11.003.
short: J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha,
M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-12-22T00:00:00Z
date_updated: 2023-09-07T12:05:08Z
day: '22'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2014.11.003
external_id:
pmid:
- '25535919'
intvolume: ' 31'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/25535919
month: '12'
oa: 1
oa_version: Published Version
page: 774 - 783
pmid: 1
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '5182'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish
laterality organ
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2014'
...
---
_id: '2084'
abstract:
- lang: eng
text: Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors
that sense growth factors and hormones and regulate a variety of cell behaviours
in health and disease. Contactless activation of RTKs with spatial and temporal
precision is currently not feasible. Here, we generated RTKs that are insensitive
to endogenous ligands but can be selectively activated by low-intensity blue light.
We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate
RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome
photoreceptors of stramenopiles resulted in robust activation of the fibroblast
growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and
rearranged during transfection (RET). In human cancer and endothelial cells, light
induced cellular signalling with spatial and temporal precision. Furthermore,
light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced
by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic
approach to actuate cellular signals and manipulate cell behaviour.
acknowledgement: European Union Seventh Framework Programme; Human Frontier Science
Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research
Promotion Agency; FemTech
author:
- first_name: Michael
full_name: Grusch, Michael
last_name: Grusch
- first_name: Karin
full_name: Schelch, Karin
last_name: Schelch
- first_name: Robert
full_name: Riedler, Robert
last_name: Riedler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Christopher
full_name: Differ, Christopher
last_name: Differ
- first_name: Walter
full_name: Berger, Walter
last_name: Berger
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Grusch M, Schelch K, Riedler R, et al. Spatio-temporally precise activation
of engineered receptor tyrosine kinases by light. EMBO Journal. 2014;33(15):1713-1726.
doi:10.15252/embj.201387695
apa: Grusch, M., Schelch, K., Riedler, R., Gschaider-Reichhart, E., Differ, C.,
Berger, W., … Janovjak, H. L. (2014). Spatio-temporally precise activation of
engineered receptor tyrosine kinases by light. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.15252/embj.201387695
chicago: Grusch, Michael, Karin Schelch, Robert Riedler, Eva Gschaider-Reichhart,
Christopher Differ, Walter Berger, Álvaro Inglés Prieto, and Harald L Janovjak.
“Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases
by Light.” EMBO Journal. Wiley-Blackwell, 2014. https://doi.org/10.15252/embj.201387695.
ieee: M. Grusch et al., “Spatio-temporally precise activation of engineered
receptor tyrosine kinases by light,” EMBO Journal, vol. 33, no. 15. Wiley-Blackwell,
pp. 1713–1726, 2014.
ista: Grusch M, Schelch K, Riedler R, Gschaider-Reichhart E, Differ C, Berger W,
Inglés Prieto Á, Janovjak HL. 2014. Spatio-temporally precise activation of engineered
receptor tyrosine kinases by light. EMBO Journal. 33(15), 1713–1726.
mla: Grusch, Michael, et al. “Spatio-Temporally Precise Activation of Engineered
Receptor Tyrosine Kinases by Light.” EMBO Journal, vol. 33, no. 15, Wiley-Blackwell,
2014, pp. 1713–26, doi:10.15252/embj.201387695.
short: M. Grusch, K. Schelch, R. Riedler, E. Gschaider-Reichhart, C. Differ, W.
Berger, Á. Inglés Prieto, H.L. Janovjak, EMBO Journal 33 (2014) 1713–1726.
date_created: 2018-12-11T11:55:37Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-09-07T12:49:09Z
day: '01'
department:
- _id: HaJa
doi: 10.15252/embj.201387695
intvolume: ' 33'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/
month: '07'
oa: 1
oa_version: Submitted Version
page: 1713 - 1726
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4953'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Spatio-temporally precise activation of engineered receptor tyrosine kinases
by light
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2014'
...
---
_id: '2157'
abstract:
- lang: eng
text: 'We show that the following algorithmic problem is decidable: given a 2-dimensional
simplicial complex, can it be embedded (topologically, or equivalently, piecewise
linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability
of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which
allows us to simplify X and recurse, is in proving that if X can be embedded in
S3, then there is also an embedding in which X has a short meridian, i.e., an
essential curve in the boundary of X bounding a disk in S3 nX with length bounded
by a computable function of the number of tetrahedra of X.'
acknowledgement: ERC Advanced Grant No. 267165; Grant GRADR Eurogiga GIG/11/E023 (SNSF-PP00P2-138948);
Swiss National Science Foundation (SNSF-200020-138230).
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3 sphere
is decidable. In: Proceedings of the Annual Symposium on Computational Geometry.
ACM; 2014:78-84. doi:10.1145/2582112.2582137'
apa: 'Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2014). Embeddability
in the 3 sphere is decidable. In Proceedings of the Annual Symposium on Computational
Geometry (pp. 78–84). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582137'
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability
in the 3 Sphere Is Decidable.” In Proceedings of the Annual Symposium on Computational
Geometry, 78–84. ACM, 2014. https://doi.org/10.1145/2582112.2582137.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the
3 sphere is decidable,” in Proceedings of the Annual Symposium on Computational
Geometry, Kyoto, Japan, 2014, pp. 78–84.
ista: 'Matoušek J, Sedgwick E, Tancer M, Wagner U. 2014. Embeddability in the 3
sphere is decidable. Proceedings of the Annual Symposium on Computational Geometry.
SoCG: Symposium on Computational Geometry, 78–84.'
mla: Matoušek, Jiří, et al. “Embeddability in the 3 Sphere Is Decidable.” Proceedings
of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84, doi:10.1145/2582112.2582137.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, in:, Proceedings of the Annual
Symposium on Computational Geometry, ACM, 2014, pp. 78–84.
conference:
end_date: 2014-06-11
location: Kyoto, Japan
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2014-06-08
date_created: 2018-12-11T11:56:02Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2023-09-11T13:38:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/2582112.2582137
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0815
month: '06'
oa: 1
oa_version: Submitted Version
page: 78 - 84
publication: Proceedings of the Annual Symposium on Computational Geometry
publication_status: published
publisher: ACM
publist_id: '4849'
quality_controlled: '1'
related_material:
record:
- id: '425'
relation: later_version
status: public
scopus_import: 1
status: public
title: Embeddability in the 3 sphere is decidable
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '10894'
abstract:
- lang: eng
text: PHAT is a C++ library for the computation of persistent homology by matrix
reduction. We aim for a simple generic design that decouples algorithms from data
structures without sacrificing efficiency or user-friendliness. This makes PHAT
a versatile platform for experimenting with algorithmic ideas and comparing them
to state of the art implementations.
article_processing_charge: No
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Hubert
full_name: Wagner, Hubert
last_name: Wagner
citation:
ama: 'Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms
Toolbox. In: ICMS 2014: International Congress on Mathematical Software.
Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143.
doi:10.1007/978-3-662-44199-2_24'
apa: 'Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent
Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical
Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg.
https://doi.org/10.1007/978-3-662-44199-2_24'
chicago: 'Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT
– Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress
on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer
Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24.'
ieee: 'U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology
Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software,
Seoul, South Korea, 2014, vol. 8592, pp. 137–143.'
ista: 'Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology
Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software.
ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.'
mla: 'Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS
2014: International Congress on Mathematical Software, vol. 8592, Springer
Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24.'
short: 'U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International
Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg,
2014, pp. 137–143.'
conference:
end_date: 2014-08-09
location: Seoul, South Korea
name: 'ICMS: International Congress on Mathematical Software'
start_date: 2014-08-05
date_created: 2022-03-21T07:12:16Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-09-20T09:42:40Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-662-44199-2_24
intvolume: ' 8592'
language:
- iso: eng
month: '09'
oa_version: None
page: 137-143
place: Berlin, Heidelberg
publication: 'ICMS 2014: International Congress on Mathematical Software'
publication_identifier:
eisbn:
- '9783662441992'
eissn:
- 1611-3349
isbn:
- '9783662441985'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
quality_controlled: '1'
related_material:
record:
- id: '1433'
relation: later_version
status: public
scopus_import: '1'
series_title: LNCS
status: public
title: PHAT – Persistent Homology Algorithms Toolbox
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8592
year: '2014'
...
---
_id: '5428'
abstract:
- lang: eng
text: "Simulation is an attractive alternative for language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. For non-deterministic automata, while language inclusion is PSPACE-complete,
simulation can be computed in polynomial time. Simulation has also been extended
in two orthogonal directions, namely, (1) fair simulation, for simulation over
specified set of infinite runs; and (2) quantitative simulation, for simulation
between weighted automata. Again, while fair trace inclusion is PSPACE-complete,
fair simulation can be computed in polynomial time. For weighted automata, the
(quantitative) language inclusion problem is undecidable for mean-payoff automata
and the decidability is open for discounted-sum automata, whereas the (quantitative)
simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial
time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted
automata with Büchi acceptance conditions, i.e., we generalize fair simulation
from non-weighted automata to weighted automata. We show that imposing Büchi acceptance
conditions on weighted automata changes many fundamental properties of the simulation
games. For example, whereas for mean-payoff and discounted-sum games, the players
do not need memory to play optimally; we show in contrast that for simulation
games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal
strategies for both players require infinite memory in general, and (ii) for discounted-sum
objectives, optimal strategies need not exist for both players. While the simulation
games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory
requirements for mean-payoff objectives) as compared to their counterpart without
Büchi acceptance conditions, we still present pseudo-polynomial time algorithms
to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff
and weighted discounted-sum automata."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: 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: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation
Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative
fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair
simulation games. IST Austria, 2014.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation
games, IST Austria, 26p.
mla: Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST
Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation
Games, IST Austria, 2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2023-09-20T12:07:48Z
day: '05'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.15479/AT:IST-2014-315-v1-1
file:
- access_level: open_access
checksum: b1d573bc04365625ff9974880c0aa807
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:59Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5521'
file_name: IST-2014-315-v1+1_report.pdf
file_size: 531046
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '315'
related_material:
record:
- id: '1066'
relation: later_version
status: public
status: public
title: Quantitative fair simulation games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1887'
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.
2014:23-30.
apa: Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.
Deutsche Zoologische Gesellschaft.
chicago: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.”
Zoologie. Deutsche Zoologische Gesellschaft, 2014.
ieee: S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” Zoologie.
Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.
ista: Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie.,
23–30.
mla: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie,
Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.
short: S. Cremer, Zoologie (2014) 23–30.
date_created: 2018-12-11T11:54:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-17T07:54:57Z
day: '01'
department:
- _id: SyCr
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf
month: '01'
oa: 1
oa_version: Published Version
page: 23 - 30
publication: Zoologie
publication_status: published
publisher: Deutsche Zoologische Gesellschaft
publist_id: '5208'
quality_controlled: '1'
status: public
title: Gemeinsame Krankheitsabwehr in Ameisengesellschaften
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2175'
abstract:
- lang: eng
text: The cerebral cortex, the seat of our cognitive abilities, is composed of an
intricate network of billions of excitatory projection and inhibitory interneurons.
Postmitotic cortical neurons are generated by a diverse set of neural stem cell
progenitors within dedicated zones and defined periods of neurogenesis during
embryonic development. Disruptions in neurogenesis can lead to alterations in
the neuronal cytoarchitecture, which is thought to represent a major underlying
cause for several neurological disorders, including microcephaly, autism and epilepsy.
Although a number of signaling pathways regulating neurogenesis have been described,
the precise cellular and molecular mechanisms regulating the functional neural
stem cell properties in cortical neurogenesis remain unclear. Here, we discuss
the most up-to-date strategies to monitor the fundamental mechanistic parameters
of neuronal progenitor proliferation, and recent advances deciphering the logic
and dynamics of neurogenesis.
article_processing_charge: No
author:
- first_name: Maria P
full_name: Postiglione, Maria P
id: 2C67902A-F248-11E8-B48F-1D18A9856A87
last_name: Postiglione
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Postiglione MP, Hippenmeyer S. Monitoring neurogenesis in the cerebral cortex:
an update. Future Neurology. 2014;9(3):323-340. doi:10.2217/fnl.14.18'
apa: 'Postiglione, M. P., & Hippenmeyer, S. (2014). Monitoring neurogenesis
in the cerebral cortex: an update. Future Neurology. Future Science Group.
https://doi.org/10.2217/fnl.14.18'
chicago: 'Postiglione, Maria P, and Simon Hippenmeyer. “Monitoring Neurogenesis
in the Cerebral Cortex: An Update.” Future Neurology. Future Science Group,
2014. https://doi.org/10.2217/fnl.14.18.'
ieee: 'M. P. Postiglione and S. Hippenmeyer, “Monitoring neurogenesis in the cerebral
cortex: an update,” Future Neurology, vol. 9, no. 3. Future Science Group,
pp. 323–340, 2014.'
ista: 'Postiglione MP, Hippenmeyer S. 2014. Monitoring neurogenesis in the cerebral
cortex: an update. Future Neurology. 9(3), 323–340.'
mla: 'Postiglione, Maria P., and Simon Hippenmeyer. “Monitoring Neurogenesis in
the Cerebral Cortex: An Update.” Future Neurology, vol. 9, no. 3, Future
Science Group, 2014, pp. 323–40, doi:10.2217/fnl.14.18.'
short: M.P. Postiglione, S. Hippenmeyer, Future Neurology 9 (2014) 323–340.
date_created: 2018-12-11T11:56:09Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2023-10-17T08:34:27Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.2217/fnl.14.18
ec_funded: 1
file:
- access_level: open_access
checksum: ba06659ecadabceec9a37dd8c4586dce
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:25Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4812'
file_name: IST-2016-528-v1+1_fnl.14.18.pdf
file_size: 3848424
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 323 - 340
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
publication: Future Neurology
publication_identifier:
eissn:
- 1748-6971
issn:
- 1479-6708
publication_status: published
publisher: Future Science Group
publist_id: '4806'
pubrep_id: '528'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Monitoring neurogenesis in the cerebral cortex: an update'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '1913'
abstract:
- lang: eng
text: 'Deposits of phosphorylated tau protein and convergence of pathology in the
hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed
to evaluate whether regional and cellular vulnerability patterns in the hippocampus
distinguish tauopathies or are influenced by their concomitant presence. Methods:
We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal
subregions/layers in individuals with Alzheimer''s disease (AD)-related neurofibrillary
degeneration (n = 40), Pick''s disease (n = 8), progressive supranuclear palsy
(n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n
= 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly
(n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis.
Results: Our study reveals disease-specific hot spots and regional selective vulnerability
for these disorders. The pattern of hippocampal AD-related tau pathology is strongly
influenced by concomitant AGD. Mathematical analysis reveals that hippocampal
involvement in primary tauopathies is distinguishable from early-stage AD-related
neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific
AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies,
which primarily do not affect the hippocampus. These hot spots can be shifted
to other regions by the co-occurrence of tauopathies like AGD. Our observations
support the notion that globular glial tauopathies and tau-astrogliopathy of the
elderly are distinct entities.'
acknowledgement: This study was supported by the European Commission’s 7th Framework
Programme under GA No. 278486, ‘DEVELAGE’.
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Milenković, Ivan
last_name: Milenković
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Gábor
full_name: Kovács, Gábor
last_name: Kovács
citation:
ama: Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate
neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders.
2014;38(5-6):375-388. doi:10.1159/000365548
apa: Milenković, I., Petrov, T., & Kovács, G. (2014). Patterns of hippocampal
tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric
Cognitive Disorders. Karger Publishers. https://doi.org/10.1159/000365548
chicago: Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal
Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric
Cognitive Disorders. Karger Publishers, 2014. https://doi.org/10.1159/000365548.
ieee: I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology
differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive
Disorders, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.
ista: Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology
differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders.
38(5–6), 375–388.
mla: Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate
Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders,
vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:10.1159/000365548.
short: I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders
38 (2014) 375–388.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-10-17T10:21:17Z
day: '07'
department:
- _id: CaGu
doi: 10.1159/000365548
external_id:
pmid:
- '25195847'
intvolume: ' 38'
issue: 5-6
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 375 - 388
pmid: 1
publication: Dementia and Geriatric Cognitive Disorders
publication_identifier:
issn:
- 1420-8008
publication_status: published
publisher: Karger Publishers
publist_id: '5181'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Patterns of hippocampal tau pathology differentiate neurodegenerative dementias
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2014'
...
---
_id: '1507'
abstract:
- lang: eng
text: The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue
statistics of large real and complex Hermitian matrices with independent, identically
distributed entries are universal in a sense that they depend only on the symmetry
class of the matrix and otherwise are independent of the details of the distribution.
We present the recent solution to this half-century old conjecture. We explain
how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as
De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also
show related results for log-gases that represent a universal model for strongly
correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss
the extensions of these universality results to more realistic physical systems
such as random band matrices.
acknowledgement: The author is partially supported by SFB-TR 12 Grant of the German
Research Council.
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: 'Erdös L. Random matrices, log-gases and Hölder regularity. In: Proceedings
of the International Congress of Mathematicians. Vol 3. International Congress
of Mathematicians; 2014:214-236.'
apa: 'Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In Proceedings
of the International Congress of Mathematicians (Vol. 3, pp. 214–236). Seoul,
Korea: International Congress of Mathematicians.'
chicago: Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In Proceedings
of the International Congress of Mathematicians, 3:214–36. International Congress
of Mathematicians, 2014.
ieee: L. Erdös, “Random matrices, log-gases and Hölder regularity,” in Proceedings
of the International Congress of Mathematicians, Seoul, Korea, 2014, vol.
3, pp. 214–236.
ista: 'Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings
of the International Congress of Mathematicians. ICM: International Congress of
Mathematicians vol. 3, 214–236.'
mla: Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” Proceedings
of the International Congress of Mathematicians, vol. 3, International Congress
of Mathematicians, 2014, pp. 214–36.
short: L. Erdös, in:, Proceedings of the International Congress of Mathematicians,
International Congress of Mathematicians, 2014, pp. 214–236.
conference:
end_date: 2014-08-21
location: Seoul, Korea
name: 'ICM: International Congress of Mathematicians'
start_date: 2014-08-13
date_created: 2018-12-11T11:52:25Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:55Z
day: '01'
department:
- _id: LaEr
ec_funded: 1
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.5752
month: '08'
oa: 1
oa_version: Submitted Version
page: 214 - 236
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Proceedings of the International Congress of Mathematicians
publication_status: published
publisher: International Congress of Mathematicians
publist_id: '5670'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Random matrices, log-gases and Hölder regularity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '8044'
abstract:
- lang: eng
text: Many questions concerning models in quantum mechanics require a detailed analysis
of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable
Hilbert space. Of particular relevance for an understanding of the low-temperature
properties of a system is the structure of the excitation spectrum, which is the
part of the spectrum close to the spectral bottom. We present recent progress
on this question for bosonic many-body quantum systems with weak two-body interactions.
Such system are currently of great interest, due to their experimental realization
in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations,
which predicts that the low-energy spectrum is made up of sums of elementary excitations,
with linear dispersion law at low momentum. The latter property is crucial for
the superfluid behavior the system.
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Seiringer R. Structure of the excitation spectrum for many-body quantum systems.
In: Proceeding of the International Congress of Mathematicans. Vol 3. International
Congress of Mathematicians; 2014:1175-1194.'
apa: 'Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum
systems. In Proceeding of the International Congress of Mathematicans (Vol.
3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.'
chicago: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body
Quantum Systems.” In Proceeding of the International Congress of Mathematicans,
3:1175–94. International Congress of Mathematicians, 2014.
ieee: R. Seiringer, “Structure of the excitation spectrum for many-body quantum
systems,” in Proceeding of the International Congress of Mathematicans,
Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.
ista: 'Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum
systems. Proceeding of the International Congress of Mathematicans. ICM: International
Congress of Mathematicans vol. 3, 1175–1194.'
mla: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum
Systems.” Proceeding of the International Congress of Mathematicans, vol.
3, International Congress of Mathematicians, 2014, pp. 1175–94.
short: R. Seiringer, in:, Proceeding of the International Congress of Mathematicans,
International Congress of Mathematicians, 2014, pp. 1175–1194.
conference:
end_date: 2014-08-21
location: Seoul, South Korea
name: 'ICM: International Congress of Mathematicans'
start_date: 2014-08-13
date_created: 2020-06-29T07:59:35Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:33Z
day: '01'
department:
- _id: RoSe
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.icm2014.org/en/vod/proceedings.html
month: '08'
oa: 1
oa_version: Published Version
page: 1175-1194
publication: Proceeding of the International Congress of Mathematicans
publication_identifier:
isbn:
- '9788961058063'
publication_status: published
publisher: International Congress of Mathematicians
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the excitation spectrum for many-body quantum systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '2160'
abstract:
- lang: eng
text: Transfer learning has received a lot of attention in the machine learning
community over the last years, and several effective algorithms have been developed.
However, relatively little is known about their theoretical properties, especially
in the setting of lifelong learning, where the goal is to transfer information
to tasks for which no data have been observed so far. In this work we study lifelong
learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization
bound that offers a unified view on existing paradigms for transfer learning,
such as the transfer of parameters or the transfer of low-dimensional representations.
We also use the bound to derive two principled lifelong learning algorithms, and
we show that these yield results comparable with existing methods.
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. A PAC-Bayesian bound for Lifelong Learning. In: Vol
32. ML Research Press; 2014:991-999.'
apa: 'Pentina, A., & Lampert, C. (2014). A PAC-Bayesian bound for Lifelong Learning
(Vol. 32, pp. 991–999). Presented at the ICML: International Conference on Machine
Learning, Beijing, China: ML Research Press.'
chicago: Pentina, Anastasia, and Christoph Lampert. “A PAC-Bayesian Bound for Lifelong
Learning,” 32:991–99. ML Research Press, 2014.
ieee: 'A. Pentina and C. Lampert, “A PAC-Bayesian bound for Lifelong Learning,”
presented at the ICML: International Conference on Machine Learning, Beijing,
China, 2014, vol. 32, pp. 991–999.'
ista: 'Pentina A, Lampert C. 2014. A PAC-Bayesian bound for Lifelong Learning. ICML:
International Conference on Machine Learning vol. 32, 991–999.'
mla: Pentina, Anastasia, and Christoph Lampert. A PAC-Bayesian Bound for Lifelong
Learning. Vol. 32, ML Research Press, 2014, pp. 991–99.
short: A. Pentina, C. Lampert, in:, ML Research Press, 2014, pp. 991–999.
conference:
end_date: 2014-06-26
location: Beijing, China
name: 'ICML: International Conference on Machine Learning'
start_date: 2014-06-21
date_created: 2018-12-11T11:56:03Z
date_published: 2014-05-10T00:00:00Z
date_updated: 2023-10-17T11:54:24Z
day: '10'
department:
- _id: ChLa
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/citation.cfm?id=3045003
month: '05'
oa: 1
oa_version: Submitted Version
page: 991 - 999
publication_status: published
publisher: ML Research Press
publist_id: '4844'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A PAC-Bayesian bound for Lifelong Learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2014'
...
---
_id: '1403'
abstract:
- lang: eng
text: A variety of developmental and disease related processes depend on epithelial
cell sheet spreading. In order to gain insight into the biophysical mechanism(s)
underlying the tissue morphogenesis we studied the spreading of an epithelium
during the early development of the zebrafish embryo. In zebrafish epiboly the
enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk
cell to completely engulf it at the end of gastrulation. Previous studies have
proposed that an actomyosin ring forming within the yolk syncytial layer (YSL)
acts as purse string that through constriction along its circumference pulls on
the margin of the EVL. Direct biophysical evidence for this hypothesis has however
been missing. The aim of the thesis was to understand how the actomyosin ring
may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate
the spreading of the epithelium. Using laser ablation to measure cortical tension
within the actomyosin ring we found an anisotropic tension distribution, which
was highest along the circumference of the ring. However the low degree of anisotropy
was incompatible with the actomyosin ring functioning as a purse string only.
Additionally, we observed retrograde cortical flow from vegetal parts of the ring
into the EVL margin. Interpreting the experimental data using a theoretical distribution
that models the tissues as active viscous gels led us to proposen that the actomyosin
ring has a twofold contribution to EVL epiboly. It not only acts as a purse string
through constriction along its circumference, but in addition constriction along
the width of the ring generates pulling forces through friction-resisted cortical
flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly
proceeded normally indicating that the flow-friction mechanism is sufficient to
drive the process. Aiming to understand what cellular mechanism(s) may facilitate
the spreading of the epithelium we found that tension-oriented EVL cell divisions
limit tissue anisotropy by releasing tension along the division axis and promote
epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions
in which oriented-cell division is impaired or the epithelium is mechanically
challenged. Taken together our study of EVL epiboly suggests a novel mechanism
of force generation for actomyosin rings through friction-resisted cortical flow
and highlights the importance of tension-oriented cell divisions in epithelial
morphogenesis.
acknowledged_ssus:
- _id: SSU
alternative_title:
- IST Austria Thesis
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
citation:
ama: Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.
apa: Behrndt, M. (2014). Forces driving epithelial spreading in zebrafish epiboly.
IST Austria.
chicago: Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.”
IST Austria, 2014.
ieee: M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST
Austria, 2014.
ista: Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly.
IST Austria.
mla: Behrndt, Martin. Forces Driving Epithelial Spreading in Zebrafish Epiboly.
IST Austria, 2014.
short: M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST
Austria, 2014.
date_created: 2018-12-11T11:51:49Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T12:16:58Z
day: '01'
department:
- _id: CaHe
language:
- iso: eng
month: '08'
oa_version: None
page: '91'
publication_status: published
publisher: IST Austria
publist_id: '5804'
related_material:
record:
- id: '2282'
relation: part_of_dissertation
status: public
- id: '2950'
relation: part_of_dissertation
status: public
- id: '3373'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Forces driving epithelial spreading in zebrafish epiboly
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1888'
abstract:
- lang: ger
text: 'Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften
interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten
wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig?
Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen
Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits
haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere
zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der
engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits
kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen
ergänzt werden.'
alternative_title:
- Rundgespräche der Kommission für Ökologie
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische
Akademie der Wissenschaften. In: Soziale Insekten in Einer Sich Wandelnden
Welt. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.'
apa: 'Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften. In Soziale Insekten in einer sich wandelnden
Welt (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.'
chicago: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene
Wehrt Bayerische Akademie Der Wissenschaften.” In Soziale Insekten in Einer
Sich Wandelnden Welt, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014.'
ieee: 'S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften,” in Soziale Insekten in einer sich
wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.'
ista: 'Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt
Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden
Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.'
mla: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt
Bayerische Akademie Der Wissenschaften.” Soziale Insekten in Einer Sich Wandelnden
Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.'
short: S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr.
Friedrich Pfeil, 2014, pp. 65–72.
date_created: 2018-12-11T11:54:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-17T12:28:45Z
day: '01'
department:
- _id: SyCr
intvolume: ' 43'
language:
- iso: eng
month: '01'
oa_version: None
page: 65 - 72
publication: Soziale Insekten in einer sich wandelnden Welt
publication_identifier:
issn:
- 2366-2875
publication_status: published
publisher: Verlag Dr. Friedrich Pfeil
publist_id: '5207'
quality_controlled: '1'
status: public
title: 'Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie
der Wissenschaften'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2014'
...
---
_id: '2012'
abstract:
- lang: eng
text: The classical sphere packing problem asks for the best (infinite) arrangement
of non-overlapping unit balls which cover as much space as possible. We define
a generalized version of the problem, where we allow each ball a limited amount
of overlap with other balls. We study two natural choices of overlap measures
and obtain the optimal lattice packings in a parameterized family of lattices
which contains the FCC, BCC, and integer lattice.
acknowledgement: We thank Herbert Edelsbrunner for his valuable discussions and ideas
on the topic of this paper. The second author has been supported by the Max Planck
Center for Visual Computing and Communication
article_number: '1401.0468'
article_processing_charge: No
author:
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv.
doi:10.48550/arXiv.1401.0468
apa: Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited
overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468
chicago: Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing
with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468.
ieee: M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,”
arXiv. .
ista: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv,
1401.0468.
mla: Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv,
1401.0468, doi:10.48550/arXiv.1401.0468.
short: M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.).
date_created: 2018-12-11T11:55:12Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-18T08:06:45Z
day: '01'
department:
- _id: HeEd
- _id: CaUh
doi: 10.48550/arXiv.1401.0468
external_id:
arxiv:
- '1401.0468'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://cccg.ca/proceedings/2014/papers/paper23.pdf
month: '01'
oa: 1
oa_version: Submitted Version
publication: arXiv
publication_status: submitted
publist_id: '5064'
status: public
title: Sphere packing with limited overlap
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '14301'
abstract:
- lang: eng
text: DNA has become a prime material for assembling complex three-dimensional objects
that promise utility in various areas of application. However, achieving user-defined
goals with DNA objects has been hampered by the difficulty to prepare them at
arbitrary concentrations and in user-defined solution conditions. Here, we describe
a method that solves this problem. The method is based on poly(ethylene glycol)-induced
depletion of species with high molecular weight. We demonstrate that our method
is applicable to a wide spectrum of DNA shapes and that it achieves excellent
recovery yields of target objects up to 97 %, while providing efficient separation
from non-integrated DNA strands. DNA objects may be prepared at concentrations
up to the limit of solubility, including the possibility for bringing DNA objects
into a solid phase. Due to the fidelity and simplicity of our method we anticipate
that it will help to catalyze the development of new types of applications that
use self-assembled DNA objects.
article_processing_charge: No
article_type: original
author:
- first_name: Evi
full_name: Stahl, Evi
last_name: Stahl
- first_name: Thomas
full_name: Martin, Thomas
last_name: Martin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation
of pure and dense DNA origami solutions. Angewandte Chemie International Edition.
2014;126(47):12949-12954. doi:10.1002/ange.201405991
apa: Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and
scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/ange.201405991
chicago: Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile
and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte
Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991.
ieee: E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable
preparation of pure and dense DNA origami solutions,” Angewandte Chemie International
Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.
ista: Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation
of pure and dense DNA origami solutions. Angewandte Chemie International Edition.
126(47), 12949–12954.
mla: Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami
Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47,
Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991.
short: E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International
Edition 126 (2014) 12949–12954.
date_created: 2023-09-06T12:51:14Z
date_published: 2014-11-17T00:00:00Z
date_updated: 2023-11-07T12:14:30Z
day: '17'
doi: 10.1002/ange.201405991
extern: '1'
external_id:
pmid:
- '25346175'
intvolume: ' 126'
issue: '47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/ange.201405991
month: '11'
oa: 1
oa_version: Published Version
page: 12949-12954
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Facile and scalable preparation of pure and dense DNA origami solutions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2014'
...
---
_id: '7699'
article_processing_charge: No
article_type: original
author:
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Darcy B
full_name: Kelley, Darcy B
last_name: Kelley
citation:
ama: Sweeney LB, Kelley DB. Harnessing vocal patterns for social communication.
Current Opinion in Neurobiology. 2014;28(10):34-41. doi:10.1016/j.conb.2014.06.006
apa: Sweeney, L. B., & Kelley, D. B. (2014). Harnessing vocal patterns for social
communication. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2014.06.006
chicago: Sweeney, Lora B., and Darcy B Kelley. “Harnessing Vocal Patterns for Social
Communication.” Current Opinion in Neurobiology. Elsevier, 2014. https://doi.org/10.1016/j.conb.2014.06.006.
ieee: L. B. Sweeney and D. B. Kelley, “Harnessing vocal patterns for social communication,”
Current Opinion in Neurobiology, vol. 28, no. 10. Elsevier, pp. 34–41,
2014.
ista: Sweeney LB, Kelley DB. 2014. Harnessing vocal patterns for social communication.
Current Opinion in Neurobiology. 28(10), 34–41.
mla: Sweeney, Lora B., and Darcy B. Kelley. “Harnessing Vocal Patterns for Social
Communication.” Current Opinion in Neurobiology, vol. 28, no. 10, Elsevier,
2014, pp. 34–41, doi:10.1016/j.conb.2014.06.006.
short: L.B. Sweeney, D.B. Kelley, Current Opinion in Neurobiology 28 (2014) 34–41.
date_created: 2020-04-30T10:35:39Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2024-01-31T10:14:08Z
day: '01'
doi: 10.1016/j.conb.2014.06.006
extern: '1'
intvolume: ' 28'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 34-41
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Harnessing vocal patterns for social communication
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2014'
...
---
_id: '2281'
abstract:
- lang: eng
text: We consider two-dimensional Bose-Einstein condensates with attractive interaction,
described by the Gross-Pitaevskii functional. Minimizers of this functional exist
only if the interaction strength a satisfies {Mathematical expression}, where
Q is the unique positive radial solution of {Mathematical expression} in {Mathematical
expression}. We present a detailed analysis of the behavior of minimizers as a
approaches a*, where all the mass concentrates at a global minimum of the trapping
potential.
article_processing_charge: No
article_type: original
author:
- first_name: Yujin
full_name: Guo, Yujin
last_name: Guo
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Guo Y, Seiringer R. On the mass concentration for Bose-Einstein condensates
with attractive interactions. Letters in Mathematical Physics. 2014;104(2):141-156.
doi:10.1007/s11005-013-0667-9
apa: Guo, Y., & Seiringer, R. (2014). On the mass concentration for Bose-Einstein
condensates with attractive interactions. Letters in Mathematical Physics.
Springer. https://doi.org/10.1007/s11005-013-0667-9
chicago: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein
Condensates with Attractive Interactions.” Letters in Mathematical Physics.
Springer, 2014. https://doi.org/10.1007/s11005-013-0667-9.
ieee: Y. Guo and R. Seiringer, “On the mass concentration for Bose-Einstein condensates
with attractive interactions,” Letters in Mathematical Physics, vol. 104,
no. 2. Springer, pp. 141–156, 2014.
ista: Guo Y, Seiringer R. 2014. On the mass concentration for Bose-Einstein condensates
with attractive interactions. Letters in Mathematical Physics. 104(2), 141–156.
mla: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein
Condensates with Attractive Interactions.” Letters in Mathematical Physics,
vol. 104, no. 2, Springer, 2014, pp. 141–56, doi:10.1007/s11005-013-0667-9.
short: Y. Guo, R. Seiringer, Letters in Mathematical Physics 104 (2014) 141–156.
date_created: 2018-12-11T11:56:44Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2024-02-14T12:19:42Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s11005-013-0667-9
external_id:
arxiv:
- '1301.5682'
intvolume: ' 104'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1301.5682
month: '02'
oa: 1
oa_version: Preprint
page: 141 - 156
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4653'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mass concentration for Bose-Einstein condensates with attractive interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2014'
...
---
_id: '2257'
abstract:
- lang: eng
text: 'Maximum entropy models are the least structured probability distributions
that exactly reproduce a chosen set of statistics measured in an interacting network.
Here we use this principle to construct probabilistic models which describe the
correlated spiking activity of populations of up to 120 neurons in the salamander
retina as it responds to natural movies. Already in groups as small as 10 neurons,
interactions between spikes can no longer be regarded as small perturbations in
an otherwise independent system; for 40 or more neurons pairwise interactions
need to be supplemented by a global interaction that controls the distribution
of synchrony in the population. Here we show that such “K-pairwise” models—being
systematic extensions of the previously used pairwise Ising models—provide an
excellent account of the data. We explore the properties of the neural vocabulary
by: 1) estimating its entropy, which constrains the population''s capacity to
represent visual information; 2) classifying activity patterns into a small set
of metastable collective modes; 3) showing that the neural codeword ensembles
are extremely inhomogenous; 4) demonstrating that the state of individual neurons
is highly predictable from the rest of the population, allowing the capacity for
error correction.'
acknowledgement: "\r\n\r\n\r\n\r\nThis work was funded by NSF grant IIS-0613435, NSF
grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508,
the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation,
ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES:
ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651."
article_number: e1003408
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for
collective behavior in a large network of sensory neurons. PLoS Computational
Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408
apa: Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry,
M. (2014). Searching for collective behavior in a large network of sensory neurons.
PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003408
chicago: Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek,
and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory
Neurons.” PLoS Computational Biology. Public Library of Science, 2014.
https://doi.org/10.1371/journal.pcbi.1003408.
ieee: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching
for collective behavior in a large network of sensory neurons,” PLoS Computational
Biology, vol. 10, no. 1. Public Library of Science, 2014.
ista: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching
for collective behavior in a large network of sensory neurons. PLoS Computational
Biology. 10(1), e1003408.
mla: Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network
of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408,
Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
short: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS
Computational Biology 10 (2014).
date_created: 2018-12-11T11:56:36Z
date_published: 2014-01-02T00:00:00Z
date_updated: 2024-02-21T13:46:14Z
day: '02'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1003408
file:
- access_level: open_access
checksum: c720222c5e924a4acb17f23b9381a6ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:46Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4965'
file_name: IST-2016-436-v1+1_journal.pcbi.1003408.pdf
file_size: 2194790
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/436
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '4689'
pubrep_id: '436'
quality_controlled: '1'
related_material:
record:
- id: '5562'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Searching for collective behavior in a large network of sensory neurons
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '15161'
abstract:
- lang: eng
text: The copper-catalyzed diboration of ketones followed by an acid-catalyzed elimination
leads to the formation of 1,1-disubstituted and trisubstituted vinyl boronate
esters with moderate to good yields and selectivity. Addition of tosic acid to
the crude diboration products provides the corresponding vinyl boronate esters
upon elimination. The trisubstituted vinyl boronate esters are formed as the (Z)-olefin
isomer, which was established by subjecting the products to a Suzuki–Miyaura coupling
reaction to obtain alkenes of known geometry.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Weiye
full_name: Guan, Weiye
last_name: Guan
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Melissa L.
full_name: McIntosh, Melissa L.
last_name: McIntosh
- first_name: Liza
full_name: Koren-Selfridge, Liza
last_name: Koren-Selfridge
- first_name: John P.
full_name: Scott, John P.
last_name: Scott
- first_name: Timothy B.
full_name: Clark, Timothy B.
last_name: Clark
citation:
ama: Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. Stereoselective
formation of trisubstituted vinyl boronate esters by the acid-mediated elimination
of α-hydroxyboronate esters. The Journal of Organic Chemistry. 2014;79(15):7199-7204.
doi:10.1021/jo500773t
apa: Guan, W., Michael, A. K., McIntosh, M. L., Koren-Selfridge, L., Scott, J. P.,
& Clark, T. B. (2014). Stereoselective formation of trisubstituted vinyl boronate
esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal
of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/jo500773t
chicago: Guan, Weiye, Alicia K. Michael, Melissa L. McIntosh, Liza Koren-Selfridge,
John P. Scott, and Timothy B. Clark. “Stereoselective Formation of Trisubstituted
Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.”
The Journal of Organic Chemistry. American Chemical Society, 2014. https://doi.org/10.1021/jo500773t.
ieee: W. Guan, A. K. Michael, M. L. McIntosh, L. Koren-Selfridge, J. P. Scott, and
T. B. Clark, “Stereoselective formation of trisubstituted vinyl boronate esters
by the acid-mediated elimination of α-hydroxyboronate esters,” The Journal
of Organic Chemistry, vol. 79, no. 15. American Chemical Society, pp. 7199–7204,
2014.
ista: Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. 2014.
Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated
elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. 79(15),
7199–7204.
mla: Guan, Weiye, et al. “Stereoselective Formation of Trisubstituted Vinyl Boronate
Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” The Journal
of Organic Chemistry, vol. 79, no. 15, American Chemical Society, 2014, pp.
7199–204, doi:10.1021/jo500773t.
short: W. Guan, A.K. Michael, M.L. McIntosh, L. Koren-Selfridge, J.P. Scott, T.B.
Clark, The Journal of Organic Chemistry 79 (2014) 7199–7204.
date_created: 2024-03-21T07:58:31Z
date_published: 2014-06-10T00:00:00Z
date_updated: 2024-03-25T11:50:01Z
day: '10'
doi: 10.1021/jo500773t
extern: '1'
intvolume: ' 79'
issue: '15'
keyword:
- Organic Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/jo500773t
month: '06'
oa: 1
oa_version: Published Version
page: 7199-7204
publication: The Journal of Organic Chemistry
publication_identifier:
eissn:
- 1520-6904
issn:
- 0022-3263
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated
elimination of α-hydroxyboronate esters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2014'
...
---
_id: '1999'
abstract:
- lang: eng
text: Selection for disease control is believed to have contributed to shape the
organisation of insect societies — leading to interaction patterns that mitigate
disease transmission risk within colonies, conferring them ‘organisational immunity’.
Recent studies combining epidemiological models with social network analysis have
identified general properties of interaction networks that may hinder propagation
of infection within groups. These can be prophylactic and/or induced upon pathogen
exposure. Here we review empirical evidence for these two types of organisational
immunity in social insects and describe the individual-level behaviours that underlie
it. We highlight areas requiring further investigation, and emphasise the need
for tighter links between theory and empirical research and between individual-level
and collective-level analyses.
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social
insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001
apa: Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational
immunity in social insects. Current Opinion in Insect Science. Elsevier.
https://doi.org/10.1016/j.cois.2014.09.001
chicago: Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational
Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier,
2014. https://doi.org/10.1016/j.cois.2014.09.001.
ieee: N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity
in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier,
pp. 1–15, 2014.
ista: Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in
social insects. Current Opinion in Insect Science. 5(1), 1–15.
mla: Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current
Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001.
short: N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect
Science 5 (2014) 1–15.
date_created: 2018-12-11T11:55:08Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2024-03-28T23:30:05Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2014.09.001
ec_funded: 1
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 1 - 15
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Current Opinion in Insect Science
publication_status: published
publisher: Elsevier
publist_id: '5080'
quality_controlled: '1'
related_material:
record:
- id: '6383'
relation: dissertation_contains
- id: '6435'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Organisational immunity in social insects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '10384'
abstract:
- lang: eng
text: 'Recent studies aimed at investigating artificial analogs of bacterial colonies
have shown that low-density suspensions of self-propelled particles confined in
two dimensions can assemble into finite aggregates that merge and split, but have
a typical size that remains constant (living clusters). In this Letter, we address
the problem of the formation of living clusters and crystals of active particles
in three dimensions. We study two systems: self-propelled particles interacting
via a generic attractive potential and colloids that can move toward each other
as a result of active agents (e.g., by molecular motors). In both cases, fluidlike
“living” clusters form. We explain this general feature in terms of the balance
between active forces and regression to thermodynamic equilibrium. This balance
can be quantified in terms of a dimensionless number that allows us to collapse
the observed clustering behavior onto a universal curve. We also discuss how active
motion affects the kinetics of crystal formation.'
acknowledgement: This work was supported by the ERC Advanced Grant 227758, the National
Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3
of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge
T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support
from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941
ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support
from the Alexander von Humboldt Foundation.
article_number: '245702'
article_processing_charge: No
article_type: original
author:
- first_name: B. M.
full_name: Mognetti, B. M.
last_name: Mognetti
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: S.
full_name: Angioletti-Uberti, S.
last_name: Angioletti-Uberti
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel
D. Living clusters and crystals from low-density suspensions of active colloids.
Physical Review Letters. 2013;111(24). doi:10.1103/physrevlett.111.245702
apa: Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani,
C., & Frenkel, D. (2013). Living clusters and crystals from low-density suspensions
of active colloids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/physrevlett.111.245702
chicago: Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of
Active Colloids.” Physical Review Letters. American Physical Society, 2013.
https://doi.org/10.1103/physrevlett.111.245702.
ieee: B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
and D. Frenkel, “Living clusters and crystals from low-density suspensions of
active colloids,” Physical Review Letters, vol. 111, no. 24. American Physical
Society, 2013.
ista: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel
D. 2013. Living clusters and crystals from low-density suspensions of active colloids.
Physical Review Letters. 111(24), 245702.
mla: Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions
of Active Colloids.” Physical Review Letters, vol. 111, no. 24, 245702,
American Physical Society, 2013, doi:10.1103/physrevlett.111.245702.
short: B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani,
D. Frenkel, Physical Review Letters 111 (2013).
date_created: 2021-11-29T13:29:31Z
date_published: 2013-12-11T00:00:00Z
date_updated: 2021-11-29T14:05:19Z
day: '11'
doi: 10.1103/physrevlett.111.245702
extern: '1'
external_id:
arxiv:
- '1311.4681'
pmid:
- '24483677'
intvolume: ' 111'
issue: '24'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.4681
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Living clusters and crystals from low-density suspensions of active colloids
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2013'
...
---
_id: '10386'
abstract:
- lang: eng
text: In this paper we review recent numerical and theoretical developments of particle
self-assembly on fluid and elastic membranes and compare them to available experimental
realizations. We discuss the problem and its applications in biology and materials
science, and give an overview of numerical models and strategies to study these
systems across all length-scales. As this is a very broad field, this review focuses
exclusively on surface-driven aggregation of nanoparticles that are at least one
order of magnitude larger than the surface thickness and are adsorbed onto it.
In this regime, all chemical details of the surface can be ignored in favor of
a coarse-grained representation, and the collective behavior of many particles
can be monitored and analyzed. We review the existing literature on how the mechanical
properties and the geometry of the surface affect the structure of the particle
aggregates and how these can drive shape deformation on the surface.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions
on the subject.
article_number: '6677'
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic
membranes. Soft Matter. 2013;9(29). doi:10.1039/c3sm50188d
apa: Šarić, A., & Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed
on fluid and elastic membranes. Soft Matter. Royal Society of Chemistry.
https://doi.org/10.1039/c3sm50188d
chicago: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed
on Fluid and Elastic Membranes.” Soft Matter. Royal Society of Chemistry,
2013. https://doi.org/10.1039/c3sm50188d.
ieee: A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid
and elastic membranes,” Soft Matter, vol. 9, no. 29. Royal Society of Chemistry,
2013.
ista: Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid
and elastic membranes. Soft Matter. 9(29), 6677.
mla: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed
on Fluid and Elastic Membranes.” Soft Matter, vol. 9, no. 29, 6677, Royal
Society of Chemistry, 2013, doi:10.1039/c3sm50188d.
short: A. Šarić, A. Cacciuto, Soft Matter 9 (2013).
date_created: 2021-11-29T14:06:32Z
date_published: 2013-05-03T00:00:00Z
date_updated: 2021-11-29T14:29:31Z
day: '03'
doi: 10.1039/c3sm50188d
extern: '1'
intvolume: ' 9'
issue: '29'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- url: https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d
month: '05'
oa_version: None
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of nanoparticles adsorbed on fluid and elastic membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9
year: '2013'
...
---
_id: '10385'
abstract:
- lang: eng
text: We show how self-assembly of sticky nanoparticles can drive radial collapse
of thin-walled nanotubes. Using numerical simulations, we study the transition
as a function of the geometric and elastic parameters of the nanotube and the
binding strength of the nanoparticles. We find that it is possible to derive a
simple scaling law relating all these parameters, and estimate bounds for the
onset conditions leading to the collapse of the nanotube. We also study the reverse
process – the nanoparticle release from the folded state – and find that the stability
of the collapsed state can be greatly improved by increasing the bending rigidity
of the nanotubes. Our results suggest ways to strengthen the mechanical properties
of nanotubes, but also indicate that the control of nanoparticle self-assembly
on these nanotubes can lead to nanoparticle-laden responsive materials.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant no. DMR-0846426.
article_processing_charge: No
article_type: original
author:
- first_name: Joseph A.
full_name: Napoli, Joseph A.
last_name: Napoli
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. Soft
Matter. 2013;9(37):8881-8886. doi:10.1039/c3sm51495a
apa: Napoli, J. A., Šarić, A., & Cacciuto, A. (2013). Collapsing nanoparticle-laden
nanotubes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51495a
chicago: Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden
Nanotubes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51495a.
ieee: J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,”
Soft Matter, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886,
2013.
ista: Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes.
Soft Matter. 9(37), 8881–8886.
mla: Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” Soft
Matter, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:10.1039/c3sm51495a.
short: J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.
date_created: 2021-11-29T13:31:24Z
date_published: 2013-08-08T00:00:00Z
date_updated: 2021-11-29T14:05:23Z
day: '08'
doi: 10.1039/c3sm51495a
extern: '1'
intvolume: ' 9'
issue: '37'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
month: '08'
oa_version: None
page: 8881-8886
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Collapsing nanoparticle-laden nanotubes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9
year: '2013'
...
---
_id: '10396'
abstract:
- lang: eng
text: Stimfit is a free cross-platform software package for viewing and analyzing
electrophysiological data. It supports most standard file types for cellular neurophysiology
and other biomedical formats. Its analysis algorithms have been used and validated
in several experimental laboratories. Its embedded Python scripting interface
makes Stimfit highly extensible and customizable.
article_number: '000010151520134181'
article_processing_charge: No
article_type: original
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: C.
full_name: Schmidt-Hieber, C.
last_name: Schmidt-Hieber
- first_name: S. J.
full_name: Guzman, S. J.
last_name: Guzman
citation:
ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181'
apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013).
Stimfit: A fast visualization and analysis environment for cellular neurophysiology.
Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter.
https://doi.org/10.1515/bmt-2013-4181'
chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit:
A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical
Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.'
ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A
fast visualization and analysis environment for cellular neurophysiology,” Biomedical
Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter,
2013.'
ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.'
mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment
for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik,
vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.'
short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering
/ Biomedizinische Technik 58 (2013).
conference:
end_date: 2013-09-21
location: Graz, Austria
name: 'BMT: Biomedizinische Technik '
start_date: 2013-09-19
date_created: 2021-12-01T14:35:35Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-12-02T12:51:12Z
day: '01'
ddc:
- '005'
- '610'
department:
- _id: PeJo
doi: 10.1515/bmt-2013-4181
external_id:
pmid:
- '24042795'
file:
- access_level: open_access
checksum: cdfc5339b530a25d6079f7223f0b1f16
content_type: application/pdf
creator: schloegl
date_created: 2021-12-01T14:38:08Z
date_updated: 2021-12-01T14:38:08Z
file_id: '10397'
file_name: Schloegl_Abstract-BMT2013.pdf
file_size: 149825
relation: main_file
success: 1
file_date_updated: 2021-12-01T14:38:08Z
has_accepted_license: '1'
intvolume: ' 58'
issue: SI-1-Track-G
keyword:
- biomedical engineering
- data analysis
- free software
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Biomedical Engineering / Biomedizinische Technik
publication_identifier:
eissn:
- 1862-278X
issn:
- 0013-5585
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
status: public
title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2013'
...
---
_id: '10749'
abstract:
- lang: eng
text: Fluxoid quantization provides a direct means to study phase coherence. In
cuprate superconductors, there have been observations which suggest that phase
coherent superconducting fluctuations may persist at temperatures significantly
above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate
superconducting samples to directly probe phase coherence over a wide range of
temperatures. We present cantilever torque susceptometry measurements of micron
and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique
allowed observation of transitions between different fluxoid states of a single
ring, and the discrete vortex states of micron size disks. The dependence of magnetic
susceptibility on diameter and wall thickness of the ring was investigated. Measurements
were made at different values of the in-plane magnetic field, and over a wide
range of temperatures.
acknowledgement: This work was supported by the Center for Emergent Superconductivity,
an Energy Frontier Research Center funded by the US DOE, Office of Science.
alternative_title:
- Bulletin of the American Physical Society
article_number: N36.00001
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
- first_name: Genda
full_name: Gu, Genda
last_name: Gu
citation:
ama: 'Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. In: APS March Meeting 2013. Vol 58. American Physical Society;
2013.'
apa: 'Polshyn, H., Budakian, R., & Gu, G. (2013). Cantilever micro-susceptometry
of mesoscopic Bi2212 samples. In APS March Meeting 2013 (Vol. 58). Baltimore,
MD, United States: American Physical Society.'
chicago: Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry
of Mesoscopic Bi2212 Samples.” In APS March Meeting 2013, Vol. 58. American
Physical Society, 2013.
ieee: H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic
Bi2212 samples,” in APS March Meeting 2013, Baltimore, MD, United States,
2013, vol. 58, no. 1.
ista: 'Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin
of the American Physical Society, vol. 58, N36.00001.'
mla: Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212
Samples.” APS March Meeting 2013, vol. 58, no. 1, N36.00001, American Physical
Society, 2013.
short: H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical
Society, 2013.
conference:
end_date: 2013-03-22
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2013-03-18
date_created: 2022-02-08T10:34:29Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-02-08T10:48:06Z
day: '01'
extern: '1'
intvolume: ' 58'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR13/Event/186873
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2013
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Cantilever micro-susceptometry of mesoscopic Bi2212 samples
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2013'
...
---
_id: '10895'
abstract:
- lang: eng
text: 'Due to their sessile lifestyles, plants need to deal with the limitations
and stresses imposed by the changing environment. Plants cope with these by a
remarkable developmental flexibility, which is embedded in their strategy to survive.
Plants can adjust their size, shape and number of organs, bend according to gravity
and light, and regenerate tissues that were damaged, utilizing a coordinating,
intercellular signal, the plant hormone, auxin. Another versatile signal is the
cation, Ca2+, which is a crucial second messenger for many rapid cellular processes
during responses to a wide range of endogenous and environmental signals, such
as hormones, light, drought stress and others. Auxin is a good candidate for one
of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling
is poorly understood. Here, we will provide an overview of possible developmental
and physiological roles, as well as mechanisms underlying the interconnection
of Ca2+ and auxin signaling. '
article_processing_charge: No
article_type: original
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants.
2013;2(4):650-675. doi:10.3390/plants2040650'
apa: 'Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action.
Plants. MDPI. https://doi.org/10.3390/plants2040650'
chicago: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin
Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.'
ieee: 'S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants,
vol. 2, no. 4. MDPI, pp. 650–675, 2013.'
ista: 'Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants.
2(4), 650–675.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.”
Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.'
short: S. Vanneste, J. Friml, Plants 2 (2013) 650–675.
date_created: 2022-03-21T07:13:49Z
date_published: 2013-10-21T00:00:00Z
date_updated: 2022-03-21T12:15:29Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants2040650
external_id:
pmid:
- '27137397'
file:
- access_level: open_access
checksum: fb4ff2e820e344e253c9197544610be6
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T12:12:56Z
date_updated: 2022-03-21T12:12:56Z
file_id: '10916'
file_name: 2013_Plants_Vanneste.pdf
file_size: 670188
relation: main_file
success: 1
file_date_updated: 2022-03-21T12:12:56Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
keyword:
- Plant Science
- Ecology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 650-675
pmid: 1
publication: Plants
publication_identifier:
issn:
- 2223-7747
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calcium: The missing link in auxin action'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2013'
...
---
_id: '10898'
abstract:
- lang: eng
text: A prominent remedy to multicore scalability issues in concurrent data structure
implementations is to relax the sequential specification of the data structure.
We present distributed queues (DQ), a new family of relaxed concurrent queue implementations.
DQs implement relaxed queues with linearizable emptiness check and either configurable
or bounded out-of-order behavior or pool behavior. Our experiments show that DQs
outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue
as well as pool implementations that we considered.
article_number: '17'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Haas, Andreas
last_name: Haas
- first_name: Michael
full_name: Lippautz, Michael
last_name: Lippautz
- 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: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
- first_name: Christoph M.
full_name: Kirsch, Christoph M.
last_name: Kirsch
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory:
Multicore performance and scalability through quantitative relaxation. In: Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. ACM Press;
2013. doi:10.1145/2482767.2482789'
apa: 'Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch,
C. M., & Sezgin, A. (2013). Distributed queues in shared memory: Multicore
performance and scalability through quantitative relaxation. In Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. Ischia,
Italy: ACM Press. https://doi.org/10.1145/2482767.2482789'
chicago: 'Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana
Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory:
Multicore Performance and Scalability through Quantitative Relaxation.” In Proceedings
of the ACM International Conference on Computing Frontiers - CF ’13. ACM Press,
2013. https://doi.org/10.1145/2482767.2482789.'
ieee: 'A. Haas et al., “Distributed queues in shared memory: Multicore performance
and scalability through quantitative relaxation,” in Proceedings of the ACM
International Conference on Computing Frontiers - CF ’13, Ischia, Italy, 2013,
no. 5.'
ista: 'Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin
A. 2013. Distributed queues in shared memory: Multicore performance and scalability
through quantitative relaxation. Proceedings of the ACM International Conference
on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.'
mla: 'Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance
and Scalability through Quantitative Relaxation.” Proceedings of the ACM International
Conference on Computing Frontiers - CF ’13, no. 5, 17, ACM Press, 2013, doi:10.1145/2482767.2482789.'
short: A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch,
A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers
- CF ’13, ACM Press, 2013.
conference:
end_date: 2013-05-16
location: Ischia, Italy
name: 'CF: Conference on Computing Frontiers'
start_date: 2013-05-14
date_created: 2022-03-21T07:33:22Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2022-06-21T08:01:19Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2482767.2482789
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
publication: Proceedings of the ACM International Conference on Computing Frontiers
- CF '13
publication_identifier:
isbn:
- 978-145032053-5
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Distributed queues in shared memory: Multicore performance and scalability
through quantitative relaxation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '10899'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed.
Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9'
apa: Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity
(2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9
chicago: Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity,
2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9.
ieee: N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd
ed., Elsevier, 2013, pp. 508–515.
ista: 'Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.'
mla: Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity,
2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.
short: N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013,
pp. 508–515.
date_created: 2022-03-21T07:46:22Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2022-06-20T09:18:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/b978-0-12-384719-5.00031-9
edition: '2'
keyword:
- Adaptive landscape
- Cline
- Coalescent process
- Gene flow
- Hybrid zone
- Local adaptation
- Natural selection
- Neutral theory
- Population structure
- Speciation
language:
- iso: eng
month: '01'
oa_version: None
page: 508-515
publication: Encyclopedia of Biodiversity
publication_identifier:
isbn:
- 978-0-12-384720-1
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differentiation
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '11086'
abstract:
- lang: eng
text: Faithful execution of developmental gene expression programs occurs at multiple
levels and involves many different components such as transcription factors, histone-modification
enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins,
well known components that control nucleo-cytoplasmic trafficking, have wide-ranging
functions in developmental gene regulation that potentially extend beyond their
role in nuclear transport. Whether the unexpected role of nuclear pore proteins
in transcription regulation, which initially has been described in fungi and flies,
also applies to human cells is unknown. Here we show at a genome-wide level that
the nuclear pore protein NUP98 associates with developmentally regulated genes
active during human embryonic stem cell differentiation. Overexpression of a dominant
negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes.
In addition, we identify two modes of developmental gene regulation by NUP98 that
are differentiated by the spatial localization of NUP98 target genes. Genes in
the initial stage of developmental induction can associate with NUP98 that is
embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that
are highly induced can interact with NUP98 in the nuclear interior, away from
the nuclear pores. This work demonstrates for the first time that NUP98 dynamically
associates with the human genome during differentiation, revealing a role of a
nuclear pore protein in regulating developmental gene expression programs.
article_number: e1003308
article_processing_charge: No
article_type: original
author:
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Maria C.
full_name: Marchetto, Maria C.
last_name: Marchetto
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of
NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308
apa: Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013).
Dynamic association of NUP98 with the human genome. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1003308
chicago: Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin
Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308.
ieee: Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic
association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no.
2. Public Library of Science, 2013.
ista: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association
of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308.
mla: Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS
Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308.
short: Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics
9 (2013).
date_created: 2022-04-07T07:50:59Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2022-07-18T08:45:58Z
day: '28'
doi: 10.1371/journal.pgen.1003308
extern: '1'
external_id:
pmid:
- '23468646'
intvolume: ' 9'
issue: '2'
keyword:
- Cancer Research
- Genetics (clinical)
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1003308
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic association of NUP98 with the human genome
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 9
year: '2013'
...
---
_id: '11087'
abstract:
- lang: eng
text: Intracellular proteins with long lifespans have recently been linked to age-dependent
defects, ranging from decreased fertility to the functional decline of neurons.
Why long-lived proteins exist in metabolically active cellular environments and
how they are maintained over time remains poorly understood. Here, we provide
a system-wide identification of proteins with exceptional lifespans in the rat
brain. These proteins are inefficiently replenished despite being translated robustly
throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence,
we found that nuclear pore complexes (NPCs) are maintained over a cell’s life
through slow but finite exchange of even its most stable subcomplexes. This maintenance
is limited, however, as some nucleoporin levels decrease during aging, providing
a rationale for the previously observed age-dependent deterioration of NPC function.
Our identification of a long-lived proteome reveals cellular components that are
at increased risk for damage accumulation, linking long-term protein persistence
to the cellular aging process.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Jeffrey N.
full_name: Savas, Jeffrey N.
last_name: Savas
- first_name: Sung Kyu
full_name: Park, Sung Kyu
last_name: Park
- first_name: Michael S.
full_name: Harris, Michael S.
last_name: Harris
- first_name: Nicholas T.
full_name: Ingolia, Nicholas T.
last_name: Ingolia
- first_name: John R.
full_name: Yates, John R.
last_name: Yates
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins
reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982.
doi:10.1016/j.cell.2013.07.037
apa: Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates,
J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals
exceptional stability of essential cellular structures. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.07.037
chicago: Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris,
Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived
Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.
ieee: B. H. Toyama et al., “Identification of long-lived proteins reveals
exceptional stability of essential cellular structures,” Cell, vol. 154,
no. 5. Elsevier, pp. 971–982, 2013.
ista: Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013.
Identification of long-lived proteins reveals exceptional stability of essential
cellular structures. Cell. 154(5), 971–982.
mla: Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional
Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier,
2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037.
short: B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates,
M. Hetzer, Cell 154 (2013) 971–982.
date_created: 2022-04-07T07:51:08Z
date_published: 2013-08-29T00:00:00Z
date_updated: 2022-07-18T08:50:47Z
day: '29'
doi: 10.1016/j.cell.2013.07.037
extern: '1'
external_id:
pmid:
- '23993091'
intvolume: ' 154'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.07.037
month: '08'
oa: 1
oa_version: Published Version
page: 971-982
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins reveals exceptional stability of essential
cellular structures
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11085'
abstract:
- lang: eng
text: During mitotic exit, missegregated chromosomes can recruit their own nuclear
envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to
primary nuclei in the same cell, although the two compartments appear to be structurally
comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization
during interphase due to NE collapse. This disruption of the MN, which is induced
by defects in nuclear lamina assembly, drastically reduces nuclear functions and
can trigger massive DNA damage. MN disruption is associated with chromatin compaction
and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified
disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting
that disrupted MN could be a useful objective biomarker for genomic instability
in solid tumors. Our study shows that NE collapse is a key event underlying MN
dysfunction and establishes a link between aberrant NE organization and aneuploidy.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Andrew H.
full_name: Fischer, Andrew H.
last_name: Fischer
- first_name: Thomas J.
full_name: Deerinck, Thomas J.
last_name: Deerinck
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007
apa: Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic
nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007
chicago: Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer.
“Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.
ieee: E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear
envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier,
pp. 47–60, 2013.
ista: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 154(1), 47–60.
mla: Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell
Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.
short: E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.
date_created: 2022-04-07T07:50:51Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2022-07-18T08:45:47Z
day: '03'
doi: 10.1016/j.cell.2013.06.007
extern: '1'
external_id:
pmid:
- '23827674'
intvolume: ' 154'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.06.007
month: '07'
oa: 1
oa_version: Published Version
page: 47-60
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catastrophic nuclear envelope collapse in cancer cell micronuclei
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11088'
abstract:
- lang: eng
text: 'The crowded intracellular environment poses a formidable challenge to experimental
and theoretical analyses of intracellular transport mechanisms. Our measurements
of single-particle trajectories in cytoplasm and their random-walk interpretations
elucidate two of these mechanisms: molecular diffusion in crowded environments
and cytoskeletal transport along microtubules. We employed acousto-optic deflector
microscopy to map out the three-dimensional trajectories of microspheres migrating
in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM),
continuous time random walk, and fractional BM were alternatively used to represent
these trajectories. The comparison of the experimental and numerical data demonstrates
that cytoskeletal transport along microtubules and diffusion in the cytosolic
fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct
signatures. Among the three random-walk models used, continuous time random walk
provides the best representation of diffusion, whereas microtubular transport
is accurately modeled with fractional BM.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin M.
full_name: Regner, Benjamin M.
last_name: Regner
- first_name: Dejan
full_name: Vučinić, Dejan
last_name: Vučinić
- first_name: Cristina
full_name: Domnisoru, Cristina
last_name: Domnisoru
- first_name: Thomas M.
full_name: Bartol, Thomas M.
last_name: Bartol
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Daniel M.
full_name: Tartakovsky, Daniel M.
last_name: Tartakovsky
- first_name: Terrence J.
full_name: Sejnowski, Terrence J.
last_name: Sejnowski
citation:
ama: Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles
in cytoplasm. Biophysical Journal. 2013;104(8):1652-1660. doi:10.1016/j.bpj.2013.01.049
apa: Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky,
D. M., & Sejnowski, T. J. (2013). Anomalous diffusion of single particles
in cytoplasm. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2013.01.049
chicago: Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol,
Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion
of Single Particles in Cytoplasm.” Biophysical Journal. Elsevier, 2013.
https://doi.org/10.1016/j.bpj.2013.01.049.
ieee: B. M. Regner et al., “Anomalous diffusion of single particles in cytoplasm,”
Biophysical Journal, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013.
ista: Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski
TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal.
104(8), 1652–1660.
mla: Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.”
Biophysical Journal, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:10.1016/j.bpj.2013.01.049.
short: B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky,
T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660.
date_created: 2022-04-07T07:51:26Z
date_published: 2013-04-16T00:00:00Z
date_updated: 2022-07-18T08:51:01Z
day: '16'
doi: 10.1016/j.bpj.2013.01.049
extern: '1'
external_id:
pmid:
- '23601312'
intvolume: ' 104'
issue: '8'
keyword:
- Biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.bpj.2013.01.049
month: '04'
oa: 1
oa_version: Published Version
page: 1652-1660
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous diffusion of single particles in cytoplasm
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 104
year: '2013'
...
---
_id: '11083'
abstract:
- lang: eng
text: Nuclear pore complex (NPC) proteins are known for their critical roles in
regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope.
However, recent findings suggest that some nucleoporins (Nups), including Nup98,
have additional functions in developmental gene regulation. Nup98, which exhibits
transcription-dependent mobility at the NPC but can also bind chromatin away from
the nuclear envelope, is frequently involved in chromosomal translocations in
a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm
suggests that Nup98 translocations cause aberrant transcription when they are
recuited to aberrant genomic loci. Importantly, this model fails to account for
the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation
mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein
levels to control transcription in healthy cells. In addition, we discuss the
possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional
activity of WT Nup98 in the nucleoplasm to drive AML.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Franks TM, Hetzer M. The role of Nup98 in transcription regulation in healthy
and diseased cells. Trends in Cell Biology. 2013;23(3):112-117. doi:10.1016/j.tcb.2012.10.013
apa: Franks, T. M., & Hetzer, M. (2013). The role of Nup98 in transcription
regulation in healthy and diseased cells. Trends in Cell Biology. Elsevier.
https://doi.org/10.1016/j.tcb.2012.10.013
chicago: Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription
Regulation in Healthy and Diseased Cells.” Trends in Cell Biology. Elsevier,
2013. https://doi.org/10.1016/j.tcb.2012.10.013.
ieee: T. M. Franks and M. Hetzer, “The role of Nup98 in transcription regulation
in healthy and diseased cells,” Trends in Cell Biology, vol. 23, no. 3.
Elsevier, pp. 112–117, 2013.
ista: Franks TM, Hetzer M. 2013. The role of Nup98 in transcription regulation in
healthy and diseased cells. Trends in Cell Biology. 23(3), 112–117.
mla: Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation
in Healthy and Diseased Cells.” Trends in Cell Biology, vol. 23, no. 3,
Elsevier, 2013, pp. 112–17, doi:10.1016/j.tcb.2012.10.013.
short: T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117.
date_created: 2022-04-07T07:50:33Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-07-18T08:45:34Z
day: '01'
doi: 10.1016/j.tcb.2012.10.013
extern: '1'
external_id:
pmid:
- '23246429'
intvolume: ' 23'
issue: '3'
keyword:
- Cell Biology
language:
- iso: eng
month: '03'
oa_version: None
page: 112-117
pmid: 1
publication: Trends in Cell Biology
publication_identifier:
issn:
- 0962-8924
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of Nup98 in transcription regulation in healthy and diseased cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 23
year: '2013'
...
---
_id: '11084'
abstract:
- lang: eng
text: Protein turnover is an effective way of maintaining a functional proteome,
as old and potentially damaged polypeptides are destroyed and replaced by newly
synthesized copies. An increasing number of intracellular proteins, however, have
been identified that evade this turnover process and instead are maintained over
a cell's lifetime. This diverse group of long-lived proteins might be particularly
prone to accumulation of damage and thus have a crucial role in the functional
deterioration of key regulatory processes during ageing.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: 'Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. Nature
Reviews Molecular Cell Biology. 2013;14:55-61. doi:10.1038/nrm3496'
apa: 'Toyama, B. H., & Hetzer, M. (2013). Protein homeostasis: Live long, won’t
prosper. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/nrm3496'
chicago: 'Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long,
Won’t Prosper.” Nature Reviews Molecular Cell Biology. Springer Nature,
2013. https://doi.org/10.1038/nrm3496.'
ieee: 'B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,”
Nature Reviews Molecular Cell Biology, vol. 14. Springer Nature, pp. 55–61,
2013.'
ista: 'Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper.
Nature Reviews Molecular Cell Biology. 14, 55–61.'
mla: 'Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t
Prosper.” Nature Reviews Molecular Cell Biology, vol. 14, Springer Nature,
2013, pp. 55–61, doi:10.1038/nrm3496.'
short: B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61.
date_created: 2022-04-07T07:50:43Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2022-07-18T08:37:53Z
day: '01'
doi: 10.1038/nrm3496
extern: '1'
external_id:
pmid:
- '23258296'
intvolume: ' 14'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
month: '01'
oa_version: None
page: 55-61
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
issn:
- 1471-0072
- 1471-0080
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Protein homeostasis: Live long, won''t prosper'
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 14
year: '2013'
...
---
_id: '115'
abstract:
- lang: eng
text: We present the design and performance characterization of a new experimental
technique for measuring individual particle charges in large ensembles of macroscopic
grains. The measurement principle is qualitatively similar to that used in determining
the elementary charge by Millikan in that it follows individual particle trajectories.
However, by taking advantage of new technology we are able to work with macroscopic
grains and achieve several orders of magnitude better resolution in charge to
mass ratios. By observing freely falling grains accelerated in a horizontal electric
field with a co-falling, high-speed video camera, we dramatically increase particle
tracking time and measurement precision. Keeping the granular medium under vacuum,
we eliminate air drag, leaving the electrostatic force as the primary source of
particle accelerations in the co-moving frame. Because the technique is based
on direct imaging, we can distinguish between different particle types during
the experiment, opening up the possibility of studying charge transfer processes
between different particle species. For the ∼300 μm diameter grains reported here,
we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution
of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain
(corresponding to surface charge densities ∼1 elementary charges per μm2). The
primary source of error is indeterminacy in the grain mass, but with higher resolution
cameras and better optics this can be further improved. The high degree of resolution
and the ability to visually identify particles of different species or sizes with
direct imaging make this a powerful new tool to characterize charging processes
in granular media.
acknowledgement: This work was supported financially by the National Science Foundation
(NSF) through its Materials Research Science and Engineering Center (MRSEC) program
(DMR-0820054) and by the US Army Research Office through Grant No. W911NF-12-1-0182.
S.R.W. acknowledges support from a University of Chicago Millikan Fellowship.
article_number: '025104'
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
citation:
ama: Waitukaitis SR, Jaeger H. In situ granular charge measurement by free-fall
videography. Review of Scientific Instruments. 2013;84(2). doi:10.1063/1.4789496
apa: Waitukaitis, S. R., & Jaeger, H. (2013). In situ granular charge measurement
by free-fall videography. Review of Scientific Instruments. AIP. https://doi.org/10.1063/1.4789496
chicago: Waitukaitis, Scott R, and Heinrich Jaeger. “In Situ Granular Charge Measurement
by Free-Fall Videography.” Review of Scientific Instruments. AIP, 2013.
https://doi.org/10.1063/1.4789496.
ieee: S. R. Waitukaitis and H. Jaeger, “In situ granular charge measurement by free-fall
videography,” Review of Scientific Instruments, vol. 84, no. 2. AIP, 2013.
ista: Waitukaitis SR, Jaeger H. 2013. In situ granular charge measurement by free-fall
videography. Review of Scientific Instruments. 84(2), 025104.
mla: Waitukaitis, Scott R., and Heinrich Jaeger. “In Situ Granular Charge Measurement
by Free-Fall Videography.” Review of Scientific Instruments, vol. 84, no.
2, 025104, AIP, 2013, doi:10.1063/1.4789496.
short: S.R. Waitukaitis, H. Jaeger, Review of Scientific Instruments 84 (2013).
date_created: 2018-12-11T11:44:42Z
date_published: 2013-02-07T00:00:00Z
date_updated: 2021-01-12T06:48:39Z
day: '07'
doi: 10.1063/1.4789496
extern: '1'
intvolume: ' 84'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Review of Scientific Instruments
publication_status: published
publisher: AIP
publist_id: '7939'
quality_controlled: '1'
status: public
title: In situ granular charge measurement by free-fall videography
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2013'
...
---
_id: '11520'
abstract:
- lang: eng
text: We present the spatially resolved Hα dynamics of 16 star-forming galaxies
at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the
ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging
from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc
overdensity of Hα emitters and likely reside in a group/intermediate environment,
but not a cluster. We confirm and identify a rich group of star-forming galaxies
at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven
within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies
at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star
formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close
to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα
dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can
be described by rotating disks and use the data to derive inclination corrected
rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75%
± 8%, consistent with previous results based on Hubble Space Telescope morphologies
of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density
at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation,
confirming the evolution seen in the zero point. Apart from having, on average,
higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present
the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all
disk galaxies.
acknowledgement: 'We thank the referee for many helpful comments and suggestions which
greatly improved the clarity and quality of this work. D.S. acknowledges financial
support from the Netherlands Organisation for Scientific research (NWO) through
a Veni fellowship and also funding from the European Community Seventh Framework
Programme (FP7/2007-2013) under grant agreement number RG226604 (OPTICON) which
allowed access to CFHT time (proposals: 11BO29 & 12AO19). A.M.S. gratefully acknowledges
an STFC Advanced Fellowship through grant number ST/H005234/1. I.R.S., J.P.S., and
R.G.B. acknowledge support from the UK Science and Technology Facilities Council
(STFC) under ST/I001573/1. I.R.S. acknowledges STFC (ST/J001422/1), the ERC Advanced
Investigator program DUSTYGAL and a Royal Society/Wolfson Merit Award. P.N.B. acknowledges
support from STFC. R.M.S. acknowledges support from the grant ST/1001573/1. The
data presented here are based on observations with the KMOS spectrograph on the
ESO/VLT under program 60.A-9460 and can be accessed through the ESO data archive.
The authors also wish to acknowledge the help from Michael Hilker in preparing the
KMOS observations.'
article_number: '139'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Sobral, D.
last_name: Sobral
- first_name: A. M.
full_name: Swinbank, A. M.
last_name: Swinbank
- first_name: J. P.
full_name: Stott, J. P.
last_name: Stott
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: R. G.
full_name: Bower, R. G.
last_name: Bower
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: P.
full_name: Best, P.
last_name: Best
- first_name: J. E.
full_name: Geach, J. E.
last_name: Geach
- first_name: R. M.
full_name: Sharples, R. M.
last_name: Sharples
citation:
ama: Sobral D, Swinbank AM, Stott JP, et al. The dynamics of z=0.8 H-alpha-selected
star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. 2013;779(2).
doi:10.1088/0004-637x/779/2/139
apa: Sobral, D., Swinbank, A. M., Stott, J. P., Matthee, J. J., Bower, R. G., Smail,
I., … Sharples, R. M. (2013). The dynamics of z=0.8 H-alpha-selected star-forming
galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. IOP Publishing.
https://doi.org/10.1088/0004-637x/779/2/139
chicago: Sobral, D., A. M. Swinbank, J. P. Stott, Jorryt J Matthee, R. G. Bower,
Ian Smail, P. Best, J. E. Geach, and R. M. Sharples. “The Dynamics of Z=0.8 H-Alpha-Selected
Star-Forming Galaxies from KMOS/CF-HiZELS.” The Astrophysical Journal.
IOP Publishing, 2013. https://doi.org/10.1088/0004-637x/779/2/139.
ieee: D. Sobral et al., “The dynamics of z=0.8 H-alpha-selected star-forming
galaxies from KMOS/CF-HiZELS,” The Astrophysical Journal, vol. 779, no.
2. IOP Publishing, 2013.
ista: Sobral D, Swinbank AM, Stott JP, Matthee JJ, Bower RG, Smail I, Best P, Geach
JE, Sharples RM. 2013. The dynamics of z=0.8 H-alpha-selected star-forming galaxies
from KMOS/CF-HiZELS. The Astrophysical Journal. 779(2), 139.
mla: Sobral, D., et al. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies
from KMOS/CF-HiZELS.” The Astrophysical Journal, vol. 779, no. 2, 139,
IOP Publishing, 2013, doi:10.1088/0004-637x/779/2/139.
short: D. Sobral, A.M. Swinbank, J.P. Stott, J.J. Matthee, R.G. Bower, I. Smail,
P. Best, J.E. Geach, R.M. Sharples, The Astrophysical Journal 779 (2013).
date_created: 2022-07-07T09:14:48Z
date_published: 2013-12-03T00:00:00Z
date_updated: 2022-08-18T10:43:07Z
day: '03'
doi: 10.1088/0004-637x/779/2/139
extern: '1'
external_id:
arxiv:
- '1310.3822'
intvolume: ' 779'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution – galaxies'
- high-redshift – galaxies
- starburst
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3822
month: '12'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 779
year: '2013'
...
---
_id: '116'
abstract:
- lang: eng
text: 'We describe a model experiment for dynamic jamming: a two-dimensional collection
of initially unjammed disks that are forced into the jammed state by uniaxial
compression via a rake. This leads to a stable densification front that travels
ahead of the rake, leaving regions behind it jammed. Using disk conservation in
conjunction with an upper limit to the packing fraction at jamming onset, we predict
the front speed as a function of packing fraction and rake speed. However, we
find that the jamming front has a finite width, a feature that cannot be explained
by disk conservation alone. This width appears to diverge on approach to jamming,
which suggests that it may be related to growing lengthscales encountered in other
jamming studies.'
acknowledgement: This work was supported by the National Science Foundation (NSF)
through its Materials Research Science and Engineering program (DMR-0820054). SRW
was supported by the U.S. Department of Energy, Office of Basic Energy Sciences,
Division of Materials Sciences and Engineering under Award DE-FG02-03ER46088. LKR
acknowledges support through the NSF Research Experience for Undergraduates program.
article_number: '44001'
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Leah
full_name: Roth, Leah
last_name: Roth
- first_name: Vincenzo
full_name: Vitelli, Vincenzo
last_name: Vitelli
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
citation:
ama: Waitukaitis SR, Roth L, Vitelli V, Jaeger H. Dynamic jamming fronts. EPL.
2013;102(4). doi:10.1209/0295-5075/102/44001
apa: Waitukaitis, S. R., Roth, L., Vitelli, V., & Jaeger, H. (2013). Dynamic
jamming fronts. EPL. Elsevier. https://doi.org/10.1209/0295-5075/102/44001
chicago: Waitukaitis, Scott R, Leah Roth, Vincenzo Vitelli, and Heinrich Jaeger.
“Dynamic Jamming Fronts.” EPL. Elsevier, 2013. https://doi.org/10.1209/0295-5075/102/44001.
ieee: S. R. Waitukaitis, L. Roth, V. Vitelli, and H. Jaeger, “Dynamic jamming fronts,”
EPL, vol. 102, no. 4. Elsevier, 2013.
ista: Waitukaitis SR, Roth L, Vitelli V, Jaeger H. 2013. Dynamic jamming fronts.
EPL. 102(4), 44001.
mla: Waitukaitis, Scott R., et al. “Dynamic Jamming Fronts.” EPL, vol. 102,
no. 4, 44001, Elsevier, 2013, doi:10.1209/0295-5075/102/44001.
short: S.R. Waitukaitis, L. Roth, V. Vitelli, H. Jaeger, EPL 102 (2013).
date_created: 2018-12-11T11:44:43Z
date_published: 2013-05-24T00:00:00Z
date_updated: 2021-01-12T06:48:44Z
day: '24'
doi: 10.1209/0295-5075/102/44001
extern: '1'
intvolume: ' 102'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
publication: EPL
publication_status: published
publisher: Elsevier
publist_id: '7938'
quality_controlled: '1'
status: public
title: Dynamic jamming fronts
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2013'
...
---
_id: '11671'
abstract:
- lang: eng
text: "Given only the URL of a Web page, can we identify its language? In this article
we examine this question. URL-based language classification is useful when the
content of the Web page is not available or downloading the content is a waste
of bandwidth and time.\r\nWe built URL-based language classifiers for English,
German, French, Spanish, and Italian by applying a variety of algorithms and features.
As algorithms we used machine learning algorithms which are widely applied for
text classification and state-of-art algorithms for language identification of
text. As features we used words, various sized n-grams, and custom-made features
(our novel feature set). We compared our approaches with two baseline methods,
namely classification by country code top-level domains and classification by
IP addresses of the hosting Web servers.\r\n\r\nWe trained and tested our classifiers
in a 10-fold cross-validation setup on a dataset obtained from the Open Directory
Project and from querying a commercial search engine. We obtained the lowest F1-measure
for English (94) and the highest F1-measure for German (98) with the best performing
classifiers.\r\n\r\nWe also evaluated the performance of our methods: (i) on a
set of Web pages written in Adobe Flash and (ii) as part of a language-focused
crawler. In the first case, the content of the Web page is hard to extract and
in the second page downloading pages of the “wrong” language constitutes a waste
of bandwidth. In both settings the best classifiers have a high accuracy with
an F1-measure between 95 (for English) and 98 (for Italian) for the Adobe Flash
pages and a precision between 90 (for Italian) and 97 (for French) for the language-focused
crawler."
article_number: '3'
article_processing_charge: No
article_type: original
author:
- first_name: Eda
full_name: Baykan, Eda
last_name: Baykan
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: Baykan E, Weber I, Henzinger MH. A comprehensive study of techniques for URL-based
web page language classification. ACM Transactions on the Web. 2013;7(1).
doi:10.1145/2435215.2435218
apa: Baykan, E., Weber, I., & Henzinger, M. H. (2013). A comprehensive study
of techniques for URL-based web page language classification. ACM Transactions
on the Web. Association for Computing Machinery. https://doi.org/10.1145/2435215.2435218
chicago: Baykan, Eda, Ingmar Weber, and Monika H Henzinger. “A Comprehensive Study
of Techniques for URL-Based Web Page Language Classification.” ACM Transactions
on the Web. Association for Computing Machinery, 2013. https://doi.org/10.1145/2435215.2435218.
ieee: E. Baykan, I. Weber, and M. H. Henzinger, “A comprehensive study of techniques
for URL-based web page language classification,” ACM Transactions on the Web,
vol. 7, no. 1. Association for Computing Machinery, 2013.
ista: Baykan E, Weber I, Henzinger MH. 2013. A comprehensive study of techniques
for URL-based web page language classification. ACM Transactions on the Web. 7(1),
3.
mla: Baykan, Eda, et al. “A Comprehensive Study of Techniques for URL-Based Web
Page Language Classification.” ACM Transactions on the Web, vol. 7, no.
1, 3, Association for Computing Machinery, 2013, doi:10.1145/2435215.2435218.
short: E. Baykan, I. Weber, M.H. Henzinger, ACM Transactions on the Web 7 (2013).
date_created: 2022-07-27T12:50:18Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-09-12T08:51:57Z
day: '01'
doi: 10.1145/2435215.2435218
extern: '1'
intvolume: ' 7'
issue: '1'
keyword:
- Computer Networks and Communications
language:
- iso: eng
month: '03'
oa_version: None
publication: ACM Transactions on the Web
publication_identifier:
eissn:
- 1559-114X
issn:
- 1559-1131
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comprehensive study of techniques for URL-based web page language classification
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '117'
abstract:
- lang: eng
text: The packing arrangement of individual particles inside a granular material
and the resulting response to applied stresses depend critically on particle-particle
interactions. One aspect that recently received attention are nanoscale surface
features of particles, which play an important role in determining the strength
of cohesive van der Waals and capillary interactions and also affect tribo-charging
of grains. We describe experiments on freely falling granular streams that can
detect the contributions from all three of these forces. We show that it is possible
to measure the charge of individual grains and build up distributions that are
detailed enough to provide stringent tests of tribo-charging models currently
available. A second aspect concerns particle shape. In this case steric interactions
become important and new types of aggregate behavior can be expected when non-convex
particle shapes are considered that can interlock or entangle. However, a general
connection between the mechanical response of a granular material and the constituents\'
shape remains unknown. This has made it infeasible to tackle the "inverse
packing problem", namely to start from a given, desired behavior for the
aggregate as a whole and then find the particle shape the produces it. We discuss
a new approach, using concepts rooted in artificial evolution that provides a
way to solve this inverse problem. This approach facilitates exploring the role
of arbitrary particle geometry in jammed systems and invites the discovery and
design of granular matter with optimized properties.
acknowledgement: This work was supported by the NSF MRSEC program under DMR-0820054.
Additional support came from the US Army Research Office through W911NF-12-1-0182.
author:
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
- first_name: Marc
full_name: Miskin, Marc
last_name: Miskin
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Jaeger H, Miskin M, Waitukaitis SR. From nanoscale cohesion to macroscale
entanglement: opportunities for designing granular aggregate behaviour by tailoring
grain shape and interactions. In: AIP Conference Proceedings. Vol 1542.
AIP; 2013:3-6. doi:10.1063/1.4811858'
apa: 'Jaeger, H., Miskin, M., & Waitukaitis, S. R. (2013). From nanoscale cohesion
to macroscale entanglement: opportunities for designing granular aggregate behaviour
by tailoring grain shape and interactions. In AIP Conference Proceedings
(Vol. 1542, pp. 3–6). Sydney, Australia: AIP. https://doi.org/10.1063/1.4811858'
chicago: 'Jaeger, Heinrich, Marc Miskin, and Scott R Waitukaitis. “From Nanoscale
Cohesion to Macroscale Entanglement: Opportunities for Designing Granular Aggregate
Behaviour by Tailoring Grain Shape and Interactions.” In AIP Conference Proceedings,
1542:3–6. AIP, 2013. https://doi.org/10.1063/1.4811858.'
ieee: 'H. Jaeger, M. Miskin, and S. R. Waitukaitis, “From nanoscale cohesion to
macroscale entanglement: opportunities for designing granular aggregate behaviour
by tailoring grain shape and interactions,” in AIP Conference Proceedings,
Sydney, Australia, 2013, vol. 1542, pp. 3–6.'
ista: 'Jaeger H, Miskin M, Waitukaitis SR. 2013. From nanoscale cohesion to macroscale
entanglement: opportunities for designing granular aggregate behaviour by tailoring
grain shape and interactions. AIP Conference Proceedings. Powders and Grains
vol. 1542, 3–6.'
mla: 'Jaeger, Heinrich, et al. “From Nanoscale Cohesion to Macroscale Entanglement:
Opportunities for Designing Granular Aggregate Behaviour by Tailoring Grain Shape
and Interactions.” AIP Conference Proceedings, vol. 1542, AIP, 2013, pp.
3–6, doi:10.1063/1.4811858.'
short: H. Jaeger, M. Miskin, S.R. Waitukaitis, in:, AIP Conference Proceedings,
AIP, 2013, pp. 3–6.
conference:
end_date: 2013-07-12
location: Sydney, Australia
name: Powders and Grains
start_date: 2013-07-08
date_created: 2018-12-11T11:44:43Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T06:48:49Z
day: '01'
doi: 10.1063/1.4811858
extern: '1'
intvolume: ' 1542'
language:
- iso: eng
month: '06'
oa_version: None
page: 3 - 6
publication: ' AIP Conference Proceedings'
publication_status: published
publisher: AIP
publist_id: '7937'
quality_controlled: '1'
status: public
title: 'From nanoscale cohesion to macroscale entanglement: opportunities for designing
granular aggregate behaviour by tailoring grain shape and interactions'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1542
year: '2013'
...
---
_id: '11759'
abstract:
- lang: eng
text: Matching markets play a prominent role in economic theory. A prime example
of such a market is the sponsored search market. Here, as in other markets of
that kind, market equilibria correspond to feasible, envy free, and bidder optimal
outcomes. For settings without budgets such an outcome always exists and can be
computed in polynomial-time by the so-called Hungarian Method. Moreover, every
mechanism that computes such an outcome is incentive compatible. We show that
the Hungarian Method can be modified so that it finds a feasible, envy free, and
bidder optimal outcome for settings with budgets. We also show that in settings
with budgets no mechanism that computes such an outcome can be incentive compatible
for all inputs. For inputs in general position, however, the presented mechanism—as
any other mechanism that computes such an outcome for settings with budgets—is
incentive compatible.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and
the Hungarian Method. Information Processing Letters. 2013;113(3):67-73.
doi:10.1016/j.ipl.2012.11.006
apa: Dütting, P., Henzinger, M. H., & Weber, I. (2013). Sponsored search, market
equilibria, and the Hungarian Method. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2012.11.006
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search,
Market Equilibria, and the Hungarian Method.” Information Processing Letters.
Elsevier, 2013. https://doi.org/10.1016/j.ipl.2012.11.006.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria,
and the Hungarian Method,” Information Processing Letters, vol. 113, no.
3. Elsevier, pp. 67–73, 2013.
ista: Dütting P, Henzinger MH, Weber I. 2013. Sponsored search, market equilibria,
and the Hungarian Method. Information Processing Letters. 113(3), 67–73.
mla: Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian
Method.” Information Processing Letters, vol. 113, no. 3, Elsevier, 2013,
pp. 67–73, doi:10.1016/j.ipl.2012.11.006.
short: P. Dütting, M.H. Henzinger, I. Weber, Information Processing Letters 113
(2013) 67–73.
date_created: 2022-08-08T11:29:08Z
date_published: 2013-02-15T00:00:00Z
date_updated: 2022-09-12T09:36:15Z
day: '15'
doi: 10.1016/j.ipl.2012.11.006
extern: '1'
external_id:
arxiv:
- '0912.1934'
intvolume: ' 113'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0912.1934
month: '02'
oa: 1
oa_version: Preprint
page: 67-73
publication: Information Processing Letters
publication_identifier:
issn:
- 0020-0190
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sponsored search, market equilibria, and the Hungarian Method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2013'
...
---
_id: '11793'
abstract:
- lang: eng
text: "We study the problem of maintaining a breadth-first spanning tree (BFS tree)
in partially dynamic distributed networks modeling a sequence of either failures
or additions of communication links (but not both). We show (1 + ε)-approximation
algorithms whose amortized time (over some number of link changes) is sublinear
in D, the maximum diameter of the network. This breaks the Θ(D) time bound of
recomputing “from scratch”.\r\n\r\nOur technique also leads to a (1 + ε)-approximate
incremental algorithm for single-source shortest paths (SSSP) in the sequential
(usual RAM) model. Prior to our work, the state of the art was the classic exact
algorithm of [9] that is optimal under some assumptions [27]. Our result is the
first to show that, in the incremental setting, this bound can be beaten in certain
cases if a small approximation is allowed."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time maintenance of breadth-first
spanning tree in partially dynamic networks. In: 40th International Colloquium
on Automata, Languages, and Programming. Vol 7966. Springer Nature; 2013:607–619.
doi:10.1007/978-3-642-39212-2_53'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Sublinear-time
maintenance of breadth-first spanning tree in partially dynamic networks. In 40th
International Colloquium on Automata, Languages, and Programming (Vol. 7966,
pp. 607–619). Riga, Latvia: Springer Nature. https://doi.org/10.1007/978-3-642-39212-2_53'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time
Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” In
40th International Colloquium on Automata, Languages, and Programming,
7966:607–619. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-39212-2_53.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance
of breadth-first spanning tree in partially dynamic networks,” in 40th International
Colloquium on Automata, Languages, and Programming, Riga, Latvia, 2013, vol.
7966, pp. 607–619.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2013. Sublinear-time maintenance
of breadth-first spanning tree in partially dynamic networks. 40th International
Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium
on Automata, Languages, and Programming, LNCS, vol. 7966, 607–619.'
mla: Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning
Tree in Partially Dynamic Networks.” 40th International Colloquium on Automata,
Languages, and Programming, vol. 7966, Springer Nature, 2013, pp. 607–619,
doi:10.1007/978-3-642-39212-2_53.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 40th International Colloquium
on Automata, Languages, and Programming, Springer Nature, 2013, pp. 607–619.
conference:
end_date: 2013-07-12
location: Riga, Latvia
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2013-07-08
date_created: 2022-08-11T11:25:13Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-21T16:28:26Z
day: '01'
doi: 10.1007/978-3-642-39212-2_53
extern: '1'
external_id:
arxiv:
- '1512.08147'
intvolume: ' 7966'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.08147
month: '07'
oa: 1
oa_version: Preprint
page: 607–619
publication: 40th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783642392115'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11793'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Sublinear-time maintenance of breadth-first spanning tree in partially dynamic
networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7966
year: '2013'
...
---
_id: '11791'
abstract:
- lang: eng
text: The focus of classic mechanism design has been on truthful direct-revelation
mechanisms. In the context of combinatorial auctions the truthful direct-revelation
mechanism that maximizes social welfare is the VCG mechanism. For many valuation
spaces computing the allocation and payments of the VCG mechanism, however, is
a computationally hard problem. We thus study the performance of the VCG mechanism
when bidders are forced to choose bids from a subspace of the valuation space
for which the VCG outcome can be computed efficiently. We prove improved upper
bounds on the welfare loss for restrictions to additive bids and upper and lower
bounds for restrictions to non-additive bids. These bounds show that the welfare
loss increases in expressiveness. All our bounds apply to equilibrium concepts
that can be computed in polynomial time as well as to learning outcomes.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Martin
full_name: Starnberger, Martin
last_name: Starnberger
citation:
ama: 'Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based
combinatorial auctions. In: 9th International Conference on Web and Internet
Economics. Vol 8289. Springer Nature; 2013:146–159. doi:10.1007/978-3-642-45046-4_13'
apa: 'Dütting, P., Henzinger, M. H., & Starnberger, M. (2013). Valuation compressions
in VCG-based combinatorial auctions. In 9th International Conference on Web
and Internet Economics (Vol. 8289, pp. 146–159). Cambridge, MA, USA: Springer
Nature. https://doi.org/10.1007/978-3-642-45046-4_13'
chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions
in VCG-Based Combinatorial Auctions.” In 9th International Conference on Web
and Internet Economics, 8289:146–159. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-45046-4_13.
ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in
VCG-based combinatorial auctions,” in 9th International Conference on Web and
Internet Economics, Cambridge, MA, USA, 2013, vol. 8289, pp. 146–159.
ista: 'Dütting P, Henzinger MH, Starnberger M. 2013. Valuation compressions in VCG-based
combinatorial auctions. 9th International Conference on Web and Internet Economics.
WINE: International Conference on Web and Internet Economics, LNCS, vol. 8289,
146–159.'
mla: Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.”
9th International Conference on Web and Internet Economics, vol. 8289,
Springer Nature, 2013, pp. 146–159, doi:10.1007/978-3-642-45046-4_13.
short: P. Dütting, M.H. Henzinger, M. Starnberger, in:, 9th International Conference
on Web and Internet Economics, Springer Nature, 2013, pp. 146–159.
conference:
end_date: 2013-12-14
location: Cambridge, MA, USA
name: 'WINE: International Conference on Web and Internet Economics'
start_date: 2013-12-01
date_created: 2022-08-11T11:05:14Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2023-02-13T11:20:42Z
day: '01'
doi: 10.1007/978-3-642-45046-4_13
extern: '1'
external_id:
arxiv:
- '1310.3153'
intvolume: ' 8289'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3153
month: '12'
oa: 1
oa_version: Preprint
page: 146–159
publication: 9th International Conference on Web and Internet Economics
publication_identifier:
isbn:
- '9783642450457'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Valuation compressions in VCG-based combinatorial auctions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8289
year: '2013'
...
---
_id: '11792'
abstract:
- lang: eng
text: "We study the problem of maximizing a monotone submodular function with viability
constraints. This problem originates from computational biology, where we are
given a phylogenetic tree over a set of species and a directed graph, the so-called
food web, encoding viability constraints between these species. These food webs
usually have constant depth. The goal is to select a subset of k species that
satisfies the viability constraints and has maximal phylogenetic diversity. As
this problem is known to be NP-hard, we investigate approximation algorithm. We
present the first constant factor approximation algorithm if the depth is constant.
Its approximation ratio is (1−1\U0001D452√). This algorithm not only applies to
phylogenetic trees with viability constraints but for arbitrary monotone submodular
set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation
algorithm for our problem setting (even for additive functions) and that there
is no approximation algorithm for a slight extension of this setting."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: David P.
full_name: Williamson, David P.
last_name: Williamson
citation:
ama: 'Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with
viability constraints. In: 21st Annual European Symposium on Algorithms.
Vol 8125. Springer Nature; 2013:409-420. doi:10.1007/978-3-642-40450-4_35'
apa: 'Dvořák, W., Henzinger, M. H., & Williamson, D. P. (2013). Maximizing a
submodular function with viability constraints. In 21st Annual European Symposium
on Algorithms (Vol. 8125, pp. 409–420). Sophia Antipolis, France: Springer
Nature. https://doi.org/10.1007/978-3-642-40450-4_35'
chicago: Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing
a Submodular Function with Viability Constraints.” In 21st Annual European
Symposium on Algorithms, 8125:409–20. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-40450-4_35.
ieee: W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular
function with viability constraints,” in 21st Annual European Symposium on
Algorithms, Sophia Antipolis, France, 2013, vol. 8125, pp. 409–420.
ista: 'Dvořák W, Henzinger MH, Williamson DP. 2013. Maximizing a submodular function
with viability constraints. 21st Annual European Symposium on Algorithms. ESA:
European Symposium on Algorithms, LNCS, vol. 8125, 409–420.'
mla: Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.”
21st Annual European Symposium on Algorithms, vol. 8125, Springer Nature,
2013, pp. 409–20, doi:10.1007/978-3-642-40450-4_35.
short: W. Dvořák, M.H. Henzinger, D.P. Williamson, in:, 21st Annual European Symposium
on Algorithms, Springer Nature, 2013, pp. 409–420.
conference:
end_date: 2013-09-04
location: Sophia Antipolis, France
name: 'ESA: European Symposium on Algorithms'
start_date: 2013-09-02
date_created: 2022-08-11T11:18:19Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2023-02-21T16:28:24Z
day: '01'
doi: 10.1007/978-3-642-40450-4_35
extern: '1'
external_id:
arxiv:
- '1611.05753'
intvolume: ' 8125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.05753
month: '09'
oa: 1
oa_version: Preprint
page: 409 - 420
publication: 21st Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783642404498'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11792'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Maximizing a submodular function with viability constraints
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8125
year: '2013'
...
---
_id: '11856'
abstract:
- lang: eng
text: 'We study dynamic (1 + ϵ)-approximation algorithms for the all-pairs shortest
paths problem in unweighted undirected n-node m-edge graphs under edge deletions.
The fastest algorithm for this problem is a randomized algorithm with a total
update time of Ȏ(mn) and constant query time by Roditty and Zwick (FOCS 2004).
The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach
(JACM 1981); it has a total update time of O(mn 2 ) and constant query time. We
improve these results as follows: (1) We present an algorithm with a total update
time of Ȏ(n 5/2 ) and constant query time that has an additive error of two in
addition to the 1 + ϵ multiplicative error. This beats the previous Ȏ(mn) time
when m = Ω(n 3/2 ). Note that the additive error is unavoidable since, even in
the static case, an O(n 3-δ )-time (a so-called truly sub cubic) combinatorial
algorithm with 1 + ϵ multiplicative error cannot have an additive error less than
2 - ϵ, unless we make a major breakthrough for Boolean matrix multiplication (Dor,
Halperin and Zwick FOCS 1996) and many other long-standing problems (Vassilevska
Williams and Williams FOCS 2010). The algorithm can also be turned into a (2 +
ϵ)-approximation algorithm (without an additive error) with the same time guarantees,
improving the recent (3 + ϵ)-approximation algorithm with Ȏ(n 5/2+O(1√(log n))
) running time of Bernstein and Roditty (SODA 2011) in terms of both approximation
and time guarantees. (2) We present a deterministic algorithm with a total update
time of Ȏ(mn) and a query time of O(log log n). The algorithm has a multiplicative
error of 1 + ϵ and gives the first improved deterministic algorithm since 1981.
It also answers an open question raised by Bernstein in his STOC 2013 paper. In
order to achieve our results, we introduce two new techniques: (1) A lazy Even-Shiloach
tree algorithm which maintains a bounded-distance shortest-paths tree on a certain
type of emulator called locally persevering emulator. (2) A derandomization technique
based on moving Even-Shiloach trees as a way to derandomize the standard random
set argument. These techniques might be of independent interest.'
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest
paths: Breaking the O(mn) barrier and derandomization. In: 54th Annual Symposium
on Foundations of Computer Science. Institute of Electrical and Electronics
Engineers; 2013:538-547. doi:10.1109/focs.2013.64'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Dynamic approximate
all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. In 54th
Annual Symposium on Foundations of Computer Science (pp. 538–547). Berkeley,
CA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2013.64'
chicago: 'Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic
Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.”
In 54th Annual Symposium on Foundations of Computer Science, 538–47. Institute
of Electrical and Electronics Engineers, 2013. https://doi.org/10.1109/focs.2013.64.'
ieee: 'M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization,” in 54th Annual
Symposium on Foundations of Computer Science, Berkeley, CA, United States,
2013, pp. 538–547.'
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2013. Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization. 54th Annual Symposium
on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer
Science, 538–547.'
mla: 'Henzinger, Monika H., et al. “Dynamic Approximate All-Pairs Shortest Paths:
Breaking the O(Mn) Barrier and Derandomization.” 54th Annual Symposium on Foundations
of Computer Science, Institute of Electrical and Electronics Engineers, 2013,
pp. 538–47, doi:10.1109/focs.2013.64.'
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 54th Annual Symposium on
Foundations of Computer Science, Institute of Electrical and Electronics Engineers,
2013, pp. 538–547.
conference:
end_date: 2013-10-29
location: Berkeley, CA, United States
name: 'FOCS: Symposium on Foundations of Computer Science'
start_date: 2013-10-26
date_created: 2022-08-16T08:22:37Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-02-17T09:56:04Z
day: '01'
doi: 10.1109/focs.2013.64
extern: '1'
external_id:
arxiv:
- '1308.0776'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1308.0776
month: '10'
oa: 1
oa_version: Preprint
page: 538-547
publication: 54th Annual Symposium on Foundations of Computer Science
publication_identifier:
eisbn:
- 978-0-7695-5135-7
issn:
- 0272-5428
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and
derandomization'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '11902'
abstract:
- lang: eng
text: "We study the problem of matching bidders to items where each bidder i has
general, strictly monotonic utility functions ui,j(pj) expressing his utility
of being matched to item j at price pj. For this setting we prove that a bidder
optimal outcome always exists, even when the utility functions are non-linear
and non-continuous. We give sufficient conditions under\r\nwhich every mechanism
that finds a bidder optimal outcome is incentive compatible. We also give a mechanism
that finds a bidder optimal outcome if the conditions for incentive compatibility
are satisfied. The running time of this mechanism is exponential in the number
of items, but polynomial in the number of bidders."
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: Dütting P, Henzinger MH, Weber I. Bidder optimal assignments for general utilities.
Theoretical Computer Science. 2013;478(3):22-32. doi:10.1016/j.tcs.2013.01.030
apa: Dütting, P., Henzinger, M. H., & Weber, I. (2013). Bidder optimal assignments
for general utilities. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2013.01.030
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Bidder Optimal Assignments
for General Utilities.” Theoretical Computer Science. Elsevier, 2013. https://doi.org/10.1016/j.tcs.2013.01.030.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Bidder optimal assignments for
general utilities,” Theoretical Computer Science, vol. 478, no. 3. Elsevier,
pp. 22–32, 2013.
ista: Dütting P, Henzinger MH, Weber I. 2013. Bidder optimal assignments for general
utilities. Theoretical Computer Science. 478(3), 22–32.
mla: Dütting, Paul, et al. “Bidder Optimal Assignments for General Utilities.” Theoretical
Computer Science, vol. 478, no. 3, Elsevier, 2013, pp. 22–32, doi:10.1016/j.tcs.2013.01.030.
short: P. Dütting, M.H. Henzinger, I. Weber, Theoretical Computer Science 478 (2013)
22–32.
date_created: 2022-08-17T11:11:04Z
date_published: 2013-03-25T00:00:00Z
date_updated: 2023-02-21T16:28:41Z
day: '25'
doi: 10.1016/j.tcs.2013.01.030
extern: '1'
intvolume: ' 478'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 22-32
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11799'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Bidder optimal assignments for general utilities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 478
year: '2013'
...
---
_id: '11959'
abstract:
- lang: eng
text: No catalyst required! A highly efficient, catalyst-free process to generate
diimide in situ from hydrazine monohydrate and molecular oxygen for the selective
reduction of alkenes has been developed. The use of a gas–liquid segmented flow
system allowed safe operating conditions and dramatically enhanced this atom-economical
reaction, resulting in short processing times.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Sabrina Teixeira
full_name: Martinez, Sabrina Teixeira
last_name: Martinez
- first_name: David
full_name: Cantillo, David
last_name: Cantillo
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: 'Pieber B, Martinez ST, Cantillo D, Kappe CO. In situ generation of diimide
from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins.
Angewandte Chemie International Edition. 2013;52(39):10241-10244. doi:10.1002/anie.201303528'
apa: 'Pieber, B., Martinez, S. T., Cantillo, D., & Kappe, C. O. (2013). In situ
generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation
of olefins. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201303528'
chicago: 'Pieber, Bartholomäus, Sabrina Teixeira Martinez, David Cantillo, and C.
Oliver Kappe. “In Situ Generation of Diimide from Hydrazine and Oxygen: Continuous-Flow
Transfer Hydrogenation of Olefins.” Angewandte Chemie International Edition.
Wiley, 2013. https://doi.org/10.1002/anie.201303528.'
ieee: 'B. Pieber, S. T. Martinez, D. Cantillo, and C. O. Kappe, “In situ generation
of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of
olefins,” Angewandte Chemie International Edition, vol. 52, no. 39. Wiley,
pp. 10241–10244, 2013.'
ista: 'Pieber B, Martinez ST, Cantillo D, Kappe CO. 2013. In situ generation of
diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins.
Angewandte Chemie International Edition. 52(39), 10241–10244.'
mla: 'Pieber, Bartholomäus, et al. “In Situ Generation of Diimide from Hydrazine
and Oxygen: Continuous-Flow Transfer Hydrogenation of Olefins.” Angewandte
Chemie International Edition, vol. 52, no. 39, Wiley, 2013, pp. 10241–44,
doi:10.1002/anie.201303528.'
short: B. Pieber, S.T. Martinez, D. Cantillo, C.O. Kappe, Angewandte Chemie International
Edition 52 (2013) 10241–10244.
date_created: 2022-08-24T11:01:47Z
date_published: 2013-09-23T00:00:00Z
date_updated: 2023-02-21T10:09:21Z
day: '23'
doi: 10.1002/anie.201303528
extern: '1'
intvolume: ' 52'
issue: '39'
language:
- iso: eng
month: '09'
oa_version: None
page: 10241-10244
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer
hydrogenation of olefins'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2013'
...
---
_id: '11960'
abstract:
- lang: eng
text: It's not magic! The effects observed in microwave-irradiated chemical transformations
can in most cases be rationalized by purely bulk thermal phenomena associated
with rapid heating to elevated temperatures. As discussed in this Essay, the existence
of so-called nonthermal or specific microwave effects is highly doubtful.
article_processing_charge: No
article_type: letter_note
author:
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Doris
full_name: Dallinger, Doris
last_name: Dallinger
citation:
ama: 'Kappe CO, Pieber B, Dallinger D. Microwave effects in organic synthesis: Myth
or reality? Angewandte Chemie International Edition. 2013;52(4):1088-1094.
doi:10.1002/anie.201204103'
apa: 'Kappe, C. O., Pieber, B., & Dallinger, D. (2013). Microwave effects in
organic synthesis: Myth or reality? Angewandte Chemie International Edition.
Wiley. https://doi.org/10.1002/anie.201204103'
chicago: 'Kappe, C. Oliver, Bartholomäus Pieber, and Doris Dallinger. “Microwave
Effects in Organic Synthesis: Myth or Reality?” Angewandte Chemie International
Edition. Wiley, 2013. https://doi.org/10.1002/anie.201204103.'
ieee: 'C. O. Kappe, B. Pieber, and D. Dallinger, “Microwave effects in organic synthesis:
Myth or reality?,” Angewandte Chemie International Edition, vol. 52, no.
4. Wiley, pp. 1088–1094, 2013.'
ista: 'Kappe CO, Pieber B, Dallinger D. 2013. Microwave effects in organic synthesis:
Myth or reality? Angewandte Chemie International Edition. 52(4), 1088–1094.'
mla: 'Kappe, C. Oliver, et al. “Microwave Effects in Organic Synthesis: Myth or
Reality?” Angewandte Chemie International Edition, vol. 52, no. 4, Wiley,
2013, pp. 1088–94, doi:10.1002/anie.201204103.'
short: C.O. Kappe, B. Pieber, D. Dallinger, Angewandte Chemie International Edition
52 (2013) 1088–1094.
date_created: 2022-08-24T11:05:04Z
date_published: 2013-01-21T00:00:00Z
date_updated: 2023-02-21T10:09:26Z
day: '21'
doi: 10.1002/anie.201204103
extern: '1'
intvolume: ' 52'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 1088-1094
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Microwave effects in organic synthesis: Myth or reality?'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2013'
...
---
_id: '11973'
abstract:
- lang: eng
text: The use of high-temperature/pressure gas–liquid continuous flow conditions
dramatically enhances the iron-catalyzed aerobic oxidation of 2-benzylpyridines
to their corresponding ketones. Pressurized air serves as a readily available
oxygen source and propylene carbonate as a green solvent in this radically intensified
preparation of synthetically valuable 2-aroylpyridines.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: Pieber B, Kappe CO. Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid
continuous-flow regime using propylene carbonate as a solvent. Green Chemistry.
2013;15(2):320-324. doi:10.1039/c2gc36896j
apa: Pieber, B., & Kappe, C. O. (2013). Direct aerobic oxidation of 2-benzylpyridines
in a gas-liquid continuous-flow regime using propylene carbonate as a solvent.
Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36896j
chicago: Pieber, Bartholomäus, and C. Oliver Kappe. “Direct Aerobic Oxidation of
2-Benzylpyridines in a Gas-Liquid Continuous-Flow Regime Using Propylene Carbonate
as a Solvent.” Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36896j.
ieee: B. Pieber and C. O. Kappe, “Direct aerobic oxidation of 2-benzylpyridines
in a gas-liquid continuous-flow regime using propylene carbonate as a solvent,”
Green Chemistry, vol. 15, no. 2. Royal Society of Chemistry, pp. 320–324,
2013.
ista: Pieber B, Kappe CO. 2013. Direct aerobic oxidation of 2-benzylpyridines in
a gas-liquid continuous-flow regime using propylene carbonate as a solvent. Green
Chemistry. 15(2), 320–324.
mla: Pieber, Bartholomäus, and C. Oliver Kappe. “Direct Aerobic Oxidation of 2-Benzylpyridines
in a Gas-Liquid Continuous-Flow Regime Using Propylene Carbonate as a Solvent.”
Green Chemistry, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp.
320–24, doi:10.1039/c2gc36896j.
short: B. Pieber, C.O. Kappe, Green Chemistry 15 (2013) 320–324.
date_created: 2022-08-25T10:29:21Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2023-02-21T10:09:54Z
day: '01'
doi: 10.1039/c2gc36896j
extern: '1'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 320-324
publication: Green Chemistry
publication_identifier:
eissn:
- 1463-9270
issn:
- 1463-9262
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow
regime using propylene carbonate as a solvent
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '12642'
abstract:
- lang: eng
text: Near-surface air temperature, typically measured at a height of 2 m, is the
most important control on the energy exchange and the melt rate at a snow or ice
surface. It is distributed in a simplistic manner in most glacier melt models
by using constant linear lapse rates, which poorly represent the actual spatial
and temporal variability of air temperature. In this paper, we test a simple thermodynamic
model proposed by Greuell and Böhm in 1998 as an alternative, using a new dataset
of air temperature measurements from along the flowline of Haut Glacier d’Arolla,
Switzerland. The unmodified model performs little better than assuming a constant
linear lapse rate. When modified to allow the ratio of the boundary layer height
to the bulk heat transfer coefficient to vary along the flowline, the model matches
measured air temperatures better, and a further reduction of the root-mean-square
error is obtained, although there is still considerable scope for improvement.
The modified model is shown to perform best under conditions favourable to the
development of katabatic winds – few clouds, positive ambient air temperature,
limited influence of synoptic or valley winds and a long fetch – but its performance
is poor under cloudy conditions.
article_processing_charge: No
article_type: original
author:
- first_name: Lene
full_name: Petersen, Lene
last_name: Petersen
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Inge
full_name: Juszak, Inge
last_name: Juszak
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
- first_name: Ben
full_name: Brock, Ben
last_name: Brock
citation:
ama: 'Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. Suitability of a
constant air temperature lapse rate over an Alpine glacier: Testing the Greuell
and Böhm model as an alternative. Annals of Glaciology. 2013;54(63):120-130.
doi:10.3189/2013aog63a477'
apa: 'Petersen, L., Pellicciotti, F., Juszak, I., Carenzo, M., & Brock, B. (2013).
Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing
the Greuell and Böhm model as an alternative. Annals of Glaciology. International
Glaciological Society. https://doi.org/10.3189/2013aog63a477'
chicago: 'Petersen, Lene, Francesca Pellicciotti, Inge Juszak, Marco Carenzo, and
Ben Brock. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine
Glacier: Testing the Greuell and Böhm Model as an Alternative.” Annals of Glaciology.
International Glaciological Society, 2013. https://doi.org/10.3189/2013aog63a477.'
ieee: 'L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, and B. Brock, “Suitability
of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell
and Böhm model as an alternative,” Annals of Glaciology, vol. 54, no. 63.
International Glaciological Society, pp. 120–130, 2013.'
ista: 'Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. 2013. Suitability
of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell
and Böhm model as an alternative. Annals of Glaciology. 54(63), 120–130.'
mla: 'Petersen, Lene, et al. “Suitability of a Constant Air Temperature Lapse Rate
over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.”
Annals of Glaciology, vol. 54, no. 63, International Glaciological Society,
2013, pp. 120–30, doi:10.3189/2013aog63a477.'
short: L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, B. Brock, Annals of
Glaciology 54 (2013) 120–130.
date_created: 2023-02-20T08:17:29Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-21T10:18:24Z
day: '01'
doi: 10.3189/2013aog63a477
extern: '1'
intvolume: ' 54'
issue: '63'
keyword:
- Earth-Surface Processes
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2013aog63a477
month: '08'
oa: 1
oa_version: Published Version
page: 120-130
publication: Annals of Glaciology
publication_identifier:
eissn:
- 1727-5644
issn:
- 0260-3055
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Suitability of a constant air temperature lapse rate over an Alpine glacier:
Testing the Greuell and Böhm model as an alternative'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2013'
...
---
_id: '12643'
abstract:
- lang: eng
text: Parameterizations of incoming longwave radiation are increasingly receiving
attention for both low and high elevation glacierized sites. In this paper, we
test 13 clear-sky parameterizations combined with seven cloud corrections for
all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also
analyze the four seasons separately and conduct a cross-validation to test the
parameters’ robustness. The best parameterization is the one by Dilley and O'Brien,
B for clear-sky conditions combined with Unsworth and Monteith cloud correction.
This model is also the most robust when tested in cross-validation. When validated
at different sites in the southern Alps of Switzerland and north-western Italian
Alps, all parameterizations show a substantial decrease in performance, except
for one site, thus suggesting that it is important to recalibrate parameterizations
of incoming longwave radiation for different locations. We argue that this is
due to differences in the structure of the atmosphere at the sites. We also quantify
the effect that the incoming longwave radiation parameterizations have on energy-balance
melt modeling, and show that recalibration of model parameters is needed. Using
parameters from other sites leads to a significant underestimation of melt and
to an error that is larger than that associated with using different parameterizations.
Once recalibrated, however, the parameters of most models seem to be stable over
seasons and years at the location on Haut Glacier d'Arolla.
article_processing_charge: No
article_type: original
author:
- first_name: I.
full_name: Juszak, I.
last_name: Juszak
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: 'Juszak I, Pellicciotti F. A comparison of parameterizations of incoming longwave
radiation over melting glaciers: Model robustness and seasonal variability. Journal
of Geophysical Research: Atmospheres. 2013;118(8):3066-3084. doi:10.1002/jgrd.50277'
apa: 'Juszak, I., & Pellicciotti, F. (2013). A comparison of parameterizations
of incoming longwave radiation over melting glaciers: Model robustness and seasonal
variability. Journal of Geophysical Research: Atmospheres. American Geophysical
Union. https://doi.org/10.1002/jgrd.50277'
chicago: 'Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations
of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal
Variability.” Journal of Geophysical Research: Atmospheres. American Geophysical
Union, 2013. https://doi.org/10.1002/jgrd.50277.'
ieee: 'I. Juszak and F. Pellicciotti, “A comparison of parameterizations of incoming
longwave radiation over melting glaciers: Model robustness and seasonal variability,”
Journal of Geophysical Research: Atmospheres, vol. 118, no. 8. American
Geophysical Union, pp. 3066–3084, 2013.'
ista: 'Juszak I, Pellicciotti F. 2013. A comparison of parameterizations of incoming
longwave radiation over melting glaciers: Model robustness and seasonal variability.
Journal of Geophysical Research: Atmospheres. 118(8), 3066–3084.'
mla: 'Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations
of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal
Variability.” Journal of Geophysical Research: Atmospheres, vol. 118, no.
8, American Geophysical Union, 2013, pp. 3066–84, doi:10.1002/jgrd.50277.'
short: 'I. Juszak, F. Pellicciotti, Journal of Geophysical Research: Atmospheres
118 (2013) 3066–3084.'
date_created: 2023-02-20T08:17:34Z
date_published: 2013-04-27T00:00:00Z
date_updated: 2023-02-21T10:10:46Z
day: '27'
doi: 10.1002/jgrd.50277
extern: '1'
intvolume: ' 118'
issue: '8'
keyword:
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/jgrd.50277
month: '04'
oa: 1
oa_version: Published Version
page: 3066-3084
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 2169-897X
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A comparison of parameterizations of incoming longwave radiation over melting
glaciers: Model robustness and seasonal variability'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2013'
...
---
_id: '12640'
abstract:
- lang: eng
text: Greater Himalayan glaciers are retreating and losing mass at rates comparable
to glaciers in other regions of the world1,2,3,4,5. Assessments of future changes
and their associated hydrological impacts are scarce, oversimplify glacier dynamics
or include a limited number of climate models6,7,8,9. Here, we use results from
the latest ensemble of climate models in combination with a high-resolution glacio-hydrological
model to assess the hydrological impact of climate change on two climatically
contrasting watersheds in the Greater Himalaya, the Baltoro and Langtang watersheds
that drain into the Indus and Ganges rivers, respectively. We show that the largest
uncertainty in future runoff is a result of variations in projected precipitation
between climate models. In both watersheds, strong, but highly variable, increases
in future runoff are projected and, despite the different characteristics of the
watersheds, their responses are surprisingly similar. In both cases, glaciers
will recede but net glacier melt runoff is on a rising limb at least until 2050.
In combination with a positive change in precipitation, water availability during
this century is not likely to decline. We conclude that river basins that depend
on monsoon rains and glacier melt will continue to sustain the increasing water
demands expected in these areas10.
article_processing_charge: No
article_type: letter_note
author:
- first_name: W. W.
full_name: Immerzeel, W. W.
last_name: Immerzeel
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M. F. P.
full_name: Bierkens, M. F. P.
last_name: Bierkens
citation:
ama: Immerzeel WW, Pellicciotti F, Bierkens MFP. Rising river flows throughout the
twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience.
2013;6(9):742-745. doi:10.1038/ngeo1896
apa: Immerzeel, W. W., Pellicciotti, F., & Bierkens, M. F. P. (2013). Rising
river flows throughout the twenty-first century in two Himalayan glacierized watersheds.
Nature Geoscience. Springer Nature. https://doi.org/10.1038/ngeo1896
chicago: Immerzeel, W. W., Francesca Pellicciotti, and M. F. P. Bierkens. “Rising
River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.”
Nature Geoscience. Springer Nature, 2013. https://doi.org/10.1038/ngeo1896.
ieee: W. W. Immerzeel, F. Pellicciotti, and M. F. P. Bierkens, “Rising river flows
throughout the twenty-first century in two Himalayan glacierized watersheds,”
Nature Geoscience, vol. 6, no. 9. Springer Nature, pp. 742–745, 2013.
ista: Immerzeel WW, Pellicciotti F, Bierkens MFP. 2013. Rising river flows throughout
the twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience.
6(9), 742–745.
mla: Immerzeel, W. W., et al. “Rising River Flows throughout the Twenty-First Century
in Two Himalayan Glacierized Watersheds.” Nature Geoscience, vol. 6, no.
9, Springer Nature, 2013, pp. 742–45, doi:10.1038/ngeo1896.
short: W.W. Immerzeel, F. Pellicciotti, M.F.P. Bierkens, Nature Geoscience 6 (2013)
742–745.
date_created: 2023-02-20T08:17:17Z
date_published: 2013-09-13T00:00:00Z
date_updated: 2023-02-21T10:46:37Z
day: '13'
doi: 10.1038/ngeo1896
extern: '1'
intvolume: ' 6'
issue: '9'
keyword:
- General Earth and Planetary Sciences
language:
- iso: eng
month: '09'
oa_version: None
page: 742-745
publication: Nature Geoscience
publication_identifier:
eissn:
- 1752-0908
issn:
- 1752-0894
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rising river flows throughout the twenty-first century in two Himalayan glacierized
watersheds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '12641'
abstract:
- lang: eng
text: We investigate the sensitivity of a distributed enhanced temperature-index
(ETI) melt model, in order to understand which parameters have the largest influence
on model outputs and thus need to be accurately known. We use melt and meteorological
data from two Alpine glaciers and one glacier in the Andes of Chile. Sensitivity
analysis is conducted in a systematic way in terms of parameters and the different
conditions (day, night, clear-sky, overcast), melt seasons and glaciers examined.
The sensitivity of total melt to changes in individual parameters is calculated
using a local method around the optimal value of the parameters. We verify that
the parameters are optimal at the distributed scale and assess the model uncertainty
induced by uncertainty in the parameters using a Monte Carlo technique. Model
sensitivity to parameters is consistent across melt seasons, glaciers, different
conditions and the daily statistics examined. The parameters to which the model
is most sensitive are the shortwave-radiation factor, the temperature lapse rate
for extrapolation of air temperature, the albedo parameters, the temperature threshold
and the cloud transmittance factor parameters. A parameter uncertainty of 5% results
in a model uncertainty of 5.6% of mean melt on Haut Glacier d’Arolla, Switzerland.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Heynen, Martin
last_name: Heynen
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
citation:
ama: Heynen M, Pellicciotti F, Carenzo M. Parameter sensitivity of a distributed
enhanced temperature-index melt model. Annals of Glaciology. 2013;54(63):311-321.
doi:10.3189/2013aog63a537
apa: Heynen, M., Pellicciotti, F., & Carenzo, M. (2013). Parameter sensitivity
of a distributed enhanced temperature-index melt model. Annals of Glaciology.
International Glaciological Society. https://doi.org/10.3189/2013aog63a537
chicago: Heynen, Martin, Francesca Pellicciotti, and Marco Carenzo. “Parameter Sensitivity
of a Distributed Enhanced Temperature-Index Melt Model.” Annals of Glaciology.
International Glaciological Society, 2013. https://doi.org/10.3189/2013aog63a537.
ieee: M. Heynen, F. Pellicciotti, and M. Carenzo, “Parameter sensitivity of a distributed
enhanced temperature-index melt model,” Annals of Glaciology, vol. 54,
no. 63. International Glaciological Society, pp. 311–321, 2013.
ista: Heynen M, Pellicciotti F, Carenzo M. 2013. Parameter sensitivity of a distributed
enhanced temperature-index melt model. Annals of Glaciology. 54(63), 311–321.
mla: Heynen, Martin, et al. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index
Melt Model.” Annals of Glaciology, vol. 54, no. 63, International Glaciological
Society, 2013, pp. 311–21, doi:10.3189/2013aog63a537.
short: M. Heynen, F. Pellicciotti, M. Carenzo, Annals of Glaciology 54 (2013) 311–321.
date_created: 2023-02-20T08:17:21Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-21T10:43:42Z
day: '01'
doi: 10.3189/2013aog63a537
extern: '1'
intvolume: ' 54'
issue: '63'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2013aog63a537
month: '08'
oa: 1
oa_version: Published Version
page: 311-321
publication: Annals of Glaciology
publication_identifier:
eissn:
- 1727-5644
issn:
- 0260-3055
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter sensitivity of a distributed enhanced temperature-index melt model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2013'
...