---
_id: '1086'
abstract:
- lang: eng
text: 'Characterisation of G protein-coupled receptors (GPCR) relies on the availability
of a toolbox of ligands that selectively modulate different functional states
of the receptors. To uncover such molecules, we explored a unique strategy for
ligand discovery that takes advantage of the evolutionary conservation of the
600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect
oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger),
identified and cloned its cognate receptor and determined its pharmacological
properties on the insect and human oxytocin/vasopressin receptors. Subsequently,
we identified a functional dichotomy: inotocin activated the insect inotocin and
the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement
of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist
([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over
the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further
investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor
interaction, which led to the identification of key residues of the receptors
that are important for ligand functionality and selectivity. These observations
could play an important role for development of oxytocin/vasopressin receptor
modulators that would enable clear distinction of the physiological and pathological
responses of the individual receptor subtypes.'
article_processing_charge: No
author:
- first_name: Maria
full_name: Di Giglio, Maria
last_name: Di Giglio
- first_name: Markus
full_name: Muttenthaler, Markus
last_name: Muttenthaler
- first_name: Kasper
full_name: Harpsøe, Kasper
last_name: Harpsøe
- first_name: Zita
full_name: Liutkeviciute, Zita
last_name: Liutkeviciute
- first_name: Peter
full_name: Keov, Peter
last_name: Keov
- first_name: Thomas
full_name: Eder, Thomas
last_name: Eder
- first_name: Thomas
full_name: Rattei, Thomas
last_name: Rattei
- first_name: Sarah
full_name: Arrowsmith, Sarah
last_name: Arrowsmith
- first_name: Susan
full_name: Wray, Susan
last_name: Wray
- first_name: Ales
full_name: Marek, Ales
last_name: Marek
- first_name: Tomas
full_name: Elbert, Tomas
last_name: Elbert
- first_name: Paul
full_name: Alewood, Paul
last_name: Alewood
- first_name: David
full_name: Gloriam, David
last_name: Gloriam
- first_name: Christian
full_name: Gruber, Christian
last_name: Gruber
citation:
ama: Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin
V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific
Reports. 2017;7:41002. doi:10.1038/srep41002
apa: Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P.,
Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor
antagonist from an evolutionary-related insect neuropeptide. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep41002
chicago: Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute,
Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin
V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific
Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41002.
ieee: M. Di Giglio et al., “Development of a human vasopressin V1a-receptor
antagonist from an evolutionary-related insect neuropeptide,” Scientific Reports,
vol. 7. Nature Publishing Group, p. 41002, 2017.
ista: Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei
T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017.
Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related
insect neuropeptide. Scientific Reports. 7, 41002.
mla: Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist
from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports,
vol. 7, Nature Publishing Group, 2017, p. 41002, doi:10.1038/srep41002.
short: M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T.
Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam,
C. Gruber, Scientific Reports 7 (2017) 41002.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:47:47Z
day: '01'
ddc:
- '570'
- '590'
doi: 10.1038/srep41002
external_id:
isi:
- '000393163800001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:59Z
date_updated: 2018-12-12T10:14:59Z
file_id: '5115'
file_name: IST-2017-790-v1+1_srep41002_1_.pdf
file_size: 1994139
relation: main_file
file_date_updated: 2018-12-12T10:14:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '41002'
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6291'
pubrep_id: '790'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related
insect neuropeptide
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1084'
abstract:
- lang: eng
text: 'BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis
controlling the response to antimicrobial peptides. In the presence of extracellular
bacitracin and nisin, respectively, the two response regulators (RRs) bind their
target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target
gene expression and ultimately antibiotic resistance. Despite high sequence similarity
between the RRs BceR and PsdR and their known binding sites, no cross-regulation
has been observed between them. We therefore investigated the specificity determinants
of PbceA and PpsdA that ensure the insulation of these two paralogous pathways
at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the
regulatory regions within these two promoters contain three important elements:
in addition to the known (main) binding site, we identified a linker region and
a secondary binding site that are crucial for functionality. Initial binding to
the high-affinity, low-specificity main binding site is a prerequisite for the
subsequent highly specific binding of a second RR dimer to the low-affinity secondary
binding site. In addition to this hierarchical cooperative binding, discrimination
requires a competition of the two RRs for their respective binding site mediated
by only slight differences in binding affinities.'
article_processing_charge: No
author:
- first_name: Chong
full_name: Fang, Chong
last_name: Fang
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Martin
full_name: Grafe, Martin
last_name: Grafe
- first_name: Ralf
full_name: Heermann, Ralf
last_name: Heermann
- first_name: Kirsten
full_name: Jung, Kirsten
last_name: Jung
- first_name: Susanne
full_name: Gebhard, Susanne
last_name: Gebhard
- first_name: Thorsten
full_name: Mascher, Thorsten
last_name: Mascher
citation:
ama: Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of
BceR like response regulators and their target promoters in Bacillus subtilis.
Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597
apa: Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S.,
& Mascher, T. (2017). Insulation and wiring specificity of BceR like response
regulators and their target promoters in Bacillus subtilis. Molecular Microbiology.
Wiley-Blackwell. https://doi.org/10.1111/mmi.13597
chicago: Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung,
Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR
like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular
Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.
ieee: C. Fang et al., “Insulation and wiring specificity of BceR like response
regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology,
vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.
ista: Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T.
2017. Insulation and wiring specificity of BceR like response regulators and their
target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.
mla: Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response
Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology,
vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.
short: C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T.
Mascher, Molecular Microbiology 104 (2017) 16–31.
date_created: 2018-12-11T11:50:03Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T11:48:43Z
day: '01'
department:
- _id: CaGu
doi: 10.1111/mmi.13597
external_id:
isi:
- '000398059200002'
intvolume: ' 104'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 16 - 31
publication: Molecular Microbiology
publication_identifier:
issn:
- ' 0950382X'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6294'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Insulation and wiring specificity of BceR like response regulators and their
target promoters in Bacillus subtilis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 104
year: '2017'
...
---
_id: '1079'
abstract:
- lang: eng
text: We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory
for atoms and molecules. We prove the nonexistence of minimizers for the energy
functional when the number of electrons is large and the total nuclear charge
is small. This nonexistence result also applies to external potentials decaying
faster than the Coulomb potential. In the case of arbitrary nuclear charges, we
obtain the nonexistence of stable minimizers and radial minimizers.
article_number: '6'
article_processing_charge: No
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Hanne
full_name: Van Den Bosch, Hanne
last_name: Van Den Bosch
citation:
ama: Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory
with small nuclear charges. Mathematical Physics, Analysis and Geometry.
2017;20(2). doi:10.1007/s11040-017-9238-0
apa: Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis
and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0
chicago: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis
and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0.
ieee: P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker
theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry,
vol. 20, no. 2. Springer, 2017.
ista: Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker
theory with small nuclear charges. Mathematical Physics, Analysis and Geometry.
20(2), 6.
mla: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von
Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis
and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.
short: P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20
(2017).
date_created: 2018-12-11T11:50:02Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:53:35Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s11040-017-9238-0
external_id:
isi:
- '000401270000004'
intvolume: ' 20'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.07368
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Mathematical Physics, Analysis and Geometry
publication_identifier:
issn:
- '13850172'
publication_status: published
publisher: Springer
publist_id: '6300'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear
charges
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2017'
...
---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2023-09-20T11:56:34Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2017'
...
---
_id: '1067'
abstract:
- lang: eng
text: Embryo morphogenesis relies on highly coordinated movements of different tissues.
However, remarkably little is known about how tissues coordinate their movements
to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements
first become apparent during “doming,” when the blastoderm begins to spread over
the yolk sac, a process involving coordinated epithelial surface cell layer expansion
and mesenchymal deep cell intercalations. Here, we find that active surface cell
expansion represents the key process coordinating tissue movements during doming.
By using a combination of theory and experiments, we show that epithelial surface
cells not only trigger blastoderm expansion by reducing tissue surface tension,
but also drive blastoderm thinning by inducing tissue contraction through radial
deep cell intercalations. Thus, coordinated tissue expansion and thinning during
doming relies on surface cells simultaneously controlling tissue surface tension
and radial tissue contraction.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Martin
full_name: Bock, Martin
last_name: Bock
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- 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: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical
basis of coordinated tissue spreading in zebrafish gastrulation. Developmental
Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010
apa: Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg,
C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish
gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010
chicago: Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume
Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue
Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017.
https://doi.org/10.1016/j.devcel.2017.01.010.
ieee: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg,
“The physical basis of coordinated tissue spreading in zebrafish gastrulation,”
Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.
ista: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017.
The physical basis of coordinated tissue spreading in zebrafish gastrulation.
Developmental Cell. 40(4), 354–366.
mla: Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading
in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press,
2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.
short: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg,
Developmental Cell 40 (2017) 354–366.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2023-09-20T12:06:27Z
day: '27'
ddc:
- '572'
- '597'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2017.01.010
ec_funded: 1
external_id:
isi:
- '000395368300007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:57Z
date_updated: 2018-12-12T10:10:57Z
file_id: '4849'
file_name: IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf
file_size: 6866187
relation: main_file
file_date_updated: 2018-12-12T10:10:57Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 354 - 366
project:
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6320'
pubrep_id: '869'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The physical basis of coordinated tissue spreading in zebrafish gastrulation
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2017'
...
---
_id: '1074'
abstract:
- lang: eng
text: Recently it has become feasible to detect long blocks of nearly identical
sequence shared between pairs of genomes. These IBD blocks are direct traces of
recent coalescence events and, as such, contain ample signal to infer recent demography.
Here, we examine sharing of such blocks in two-dimensional populations with local
migration. Using a diffusion approximation to trace genetic ancestry, we derive
analytical formulae for patterns of isolation by distance of IBD blocks, which
can also incorporate recent population density changes. We introduce an inference
scheme that uses a composite likelihood approach to fit these formulae. We then
extensively evaluate our theory and inference method on a range of scenarios using
simulated data. We first validate the diffusion approximation by showing that
the theoretical results closely match the simulated block sharing patterns. We
then demonstrate that our inference scheme can accurately and robustly infer dispersal
rate and effective density, as well as bounds on recent dynamics of population
density. To demonstrate an application, we use our estimation scheme to explore
the fit of a diffusion model to Eastern European samples in the POPRES data set.
We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last
centuries, combined with accelerating population growth, can explain the observed
exponential decay of block sharing with increasing pairwise sample distance.
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- 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: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351.
doi:10.1534/genetics.116.196220
apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography
from isolation by distance of long shared sequence blocks. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.116.196220
chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent
Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics.
Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.
ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from
isolation by distance of long shared sequence blocks,” Genetics, vol. 205,
no. 3. Genetics Society of America, pp. 1335–1351, 2017.
ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.
mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance
of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society
of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.
short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T12:00:56Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
intvolume: ' 205'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6307'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1076'
abstract:
- lang: eng
text: Signatures of the Coulomb corrections in the photoelectron momentum distribution
during laser-induced ionization of atoms or ions in tunneling and multiphoton
regimes are investigated analytically in the case of a one-dimensional problem.
A high-order Coulomb-corrected strong-field approximation is applied, where the
exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov
state including the second-order corrections to the eikonal. Although without
high-order corrections our theory coincides with the known analytical R-matrix
(ARM) theory, we propose a simplified procedure for the matrix element derivation.
Rather than matching the eikonal Coulomb-Volkov wave function with the bound state
as in the ARM theory to remove the Coulomb singularity, we calculate the matrix
element via the saddle-point integration method by time as well as by coordinate,
and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron
momentum distribution with respect to the ARM theory due to high-order corrections
is analyzed for tunneling and multiphoton regimes. The relation of the quantum
corrections to the tunneling delay time is discussed.
article_number: '023403'
article_processing_charge: No
author:
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Jiří
full_name: Daněk, Jiří
last_name: Daněk
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Karen
full_name: Hatsagortsyan, Karen
last_name: Hatsagortsyan
- first_name: Christoph
full_name: Keitel, Christoph
last_name: Keitel
citation:
ama: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization
via a high-order Coulomb-corrected strong-field approximation. Physical Review
A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403
apa: Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C.
(2017). Strong-field ionization via a high-order Coulomb-corrected strong-field
approximation. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403
chicago: Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan,
and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.
ieee: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation,”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2.
American Physical Society, 2017.
ista: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation. Physical
Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.
mla: Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.
short: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical
Review A - Atomic, Molecular, and Optical Physics 95 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:57:23Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.95.023403
ec_funded: 1
external_id:
isi:
- '000400571700011'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.07018
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_identifier:
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
publist_id: '6305'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong-field ionization via a high-order Coulomb-corrected strong-field approximation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '1072'
abstract:
- lang: eng
text: Given a finite set of points in Rn and a radius parameter, we study the Čech,
Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized
discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel
sets of generalized discrete Morse functions, we prove that the four complexes
are simple-homotopy equivalent by a sequence of simplicial collapses, which are
explicitly described by a single discrete gradient field.
acknowledgement: This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP),
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR
109 “Discretization in Geometry and Dynamics”.
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions
of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991
apa: Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay
complexes. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/6991
chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and
Delaunay Complexes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.
ieee: U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,”
Transactions of the American Mathematical Society, vol. 369, no. 5. American
Mathematical Society, pp. 3741–3762, 2017.
ista: Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes.
Transactions of the American Mathematical Society. 369(5), 3741–3762.
mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay
Complexes.” Transactions of the American Mathematical Society, vol. 369,
no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.
short: U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society
369 (2017) 3741–3762.
date_created: 2018-12-11T11:49:59Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-09-20T12:05:56Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/6991
ec_funded: 1
external_id:
arxiv:
- '1312.1231'
isi:
- '000398030400024'
intvolume: ' 369'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.1231
month: '05'
oa: 1
oa_version: Preprint
page: 3741 - 3762
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '6311'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Morse theory of Čech and delaunay complexes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 369
year: '2017'
...
---
_id: '1073'
abstract:
- lang: eng
text: Let X and Y be finite simplicial sets (e.g. finite simplicial complexes),
both equipped with a free simplicial action of a finite group G. Assuming that
Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes
the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|;
the existence of such a map can be decided even for dimX≤2d+1. This yields the
first algorithm for deciding topological embeddability of a k-dimensional finite
simplicial complex into Rn under the condition k≤23n−1. More generally, we present
an algorithm that, given a lifting-extension problem satisfying an appropriate
stability assumption, computes the set of all homotopy classes of solutions. This
result is new even in the non-equivariant situation.
article_processing_charge: No
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
citation:
ama: Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension
problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6
apa: Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of
the lifting extension problem. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-016-9855-6
chicago: Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability
of the Lifting Extension Problem.” Discrete & Computational Geometry.
Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.
ieee: M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting
extension problem,” Discrete & Computational Geometry, vol. 54, no.
4. Springer, pp. 915–965, 2017.
ista: Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting
extension problem. Discrete & Computational Geometry. 54(4), 915–965.
mla: Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.”
Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017,
pp. 915–65, doi:10.1007/s00454-016-9855-6.
short: M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54
(2017) 915–965.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:01:28Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-016-9855-6
external_id:
isi:
- '000400072700008'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1307.6444
month: '06'
oa: 1
oa_version: Submitted Version
page: 915 - 965
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6309'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic solvability of the lifting extension problem
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1061'
abstract:
- lang: eng
text: 'Background: Metabolic engineering and synthetic biology of cyanobacteria
offer a promising sustainable alternative approach for fossil-based ethylene production,
by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly
into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis
sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce
ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae
pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the
ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene.
Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene
production through the integration of a codon-optimized version of the efe gene
under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\''-AGGAGG-3\'')
as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased
ethylene production twofold by RBS screening and further investigated improving
ethylene production from a single gene copy of efe, using multiple tandem promoters
and by putting our best construct on an RSF1010-based broad-host-self-replicating
plasmid, which has a higher copy number than the genome. Moreover, to raise the
intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene
is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced
the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the
glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however,
surprisingly, ethylene production was lower in this strain than in the wild-type
background. Conclusion: Making use of different RBS sequences, production of ethylene
ranging over a 20-fold difference has been achieved. However, a further increase
of production through multiple tandem promoters and a broad-host plasmid was not
achieved speculating that the transcription strength and the gene copy number
are not the limiting factors in our system.'
article_number: '34'
article_processing_charge: No
author:
- first_name: Vinod
full_name: Veetil, Vinod
last_name: Veetil
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
citation:
ama: Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis
sp PCC 6803 strains. Microbial Cell Factories. 2017;16(1). doi:10.1186/s12934-017-0645-5
apa: Veetil, V., Angermayr, A., & Hellingwerf, K. (2017). Ethylene production
with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories.
BioMed Central. https://doi.org/10.1186/s12934-017-0645-5
chicago: Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production
with Engineered Synechocystis Sp PCC 6803 Strains.” Microbial Cell Factories.
BioMed Central, 2017. https://doi.org/10.1186/s12934-017-0645-5.
ieee: V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered
Synechocystis sp PCC 6803 strains,” Microbial Cell Factories, vol. 16,
no. 1. BioMed Central, 2017.
ista: Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered
Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.
mla: Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp
PCC 6803 Strains.” Microbial Cell Factories, vol. 16, no. 1, 34, BioMed
Central, 2017, doi:10.1186/s12934-017-0645-5.
short: V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).
date_created: 2018-12-11T11:49:56Z
date_published: 2017-02-23T00:00:00Z
date_updated: 2023-09-20T12:09:21Z
day: '23'
ddc:
- '579'
doi: 10.1186/s12934-017-0645-5
extern: '1'
external_id:
isi:
- '000397733000001'
pmid:
- '28231787'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:50Z
date_updated: 2018-12-12T10:16:50Z
file_id: '5240'
file_name: IST-2017-792-v1+1_s12934-017-0645-5.pdf
file_size: 1361313
relation: main_file
file_date_updated: 2018-12-12T10:16:50Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Microbial Cell Factories
publication_identifier:
issn:
- '14752859'
publication_status: published
publisher: BioMed Central
publist_id: '6325'
pubrep_id: '792'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ethylene production with engineered Synechocystis sp PCC 6803 strains
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2017'
...
---
_id: '1065'
abstract:
- lang: eng
text: 'We consider the problem of reachability in pushdown graphs. We study the
problem for pushdown graphs with constant treewidth. Even for pushdown graphs
with treewidth 1, for the reachability problem we establish the following: (i)
the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem
would contradict the k-clique conjecture and imply faster combinatorial algorithms
for cliques in graphs.'
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: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information
Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003
apa: Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant
treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003
chicago: Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with
Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.
ieee: K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,”
Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.
ista: Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth.
Information Processing Letters. 122, 25–29.
mla: Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant
Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp.
25–29, doi:10.1016/j.ipl.2017.02.003.
short: K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:18Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: HeEd
doi: 10.1016/j.ipl.2017.02.003
ec_funded: 1
external_id:
isi:
- '000399506600005'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2019-10-15T07:44:51Z
file_id: '4998'
file_name: IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf
file_size: 247657
relation: main_file
file_date_updated: 2019-10-15T07:44:51Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 25 - 29
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'
publication: Information Processing Letters
publication_identifier:
issn:
- '00200190'
publication_status: published
publisher: Elsevier
publist_id: '6323'
pubrep_id: '991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pushdown reachability with constant treewidth
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2017'
...
---
_id: '1062'
abstract:
- lang: eng
text: Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates
the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that
MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’
to the less frequent ‘burst’ firing. This latter is evident in a small fraction
of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available
or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted.
Burst firing causes large increases of Ca2+‐entry and potentiates CA release by
∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the
aim to uncover a physiological role for burst‐firing we investigated the effects
of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0
and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts.
Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase
of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive
TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo
7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that
support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures
of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could
be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of
the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold),
showing that the action of protons on vesicle release is mainly a result of the
ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide
direct evidence suggesting that MCCs respond to low pHo with sustained depolarization,
burst firing and enhanced CA‐secretion, thus mimicking the physiological response
of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and
muscle fatigue.
article_processing_charge: No
author:
- first_name: Laura
full_name: Guarina, Laura
last_name: Guarina
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing
and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 2017;595(8):2587-2609.
doi:10.1113/JP273735
apa: Guarina, L., Vandael, D. H., Carabelli, V., & Carbone, E. (2017). Low pH
inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK
channels while preserving Cav1 channels in mouse chromaffin cells. Journal
of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP273735
chicago: Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone.
“Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1
and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” Journal
of Physiology. Wiley-Blackwell, 2017. https://doi.org/10.1113/JP273735.
ieee: L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts
burst firing and catecholamine release by blocking TASK-1 and BK channels while
preserving Cav1 channels in mouse chromaffin cells,” Journal of Physiology,
vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.
ista: Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst
firing and catecholamine release by blocking TASK-1 and BK channels while preserving
Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.
mla: Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine
Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse
Chromaffin Cells.” Journal of Physiology, vol. 595, no. 8, Wiley-Blackwell,
2017, pp. 2587–609, doi:10.1113/JP273735.
short: L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology
595 (2017) 2587–2609.
date_created: 2018-12-11T11:49:56Z
date_published: 2017-04-15T00:00:00Z
date_updated: 2023-09-20T12:09:47Z
day: '15'
doi: 10.1113/JP273735
extern: '1'
external_id:
isi:
- '000399430300022'
intvolume: ' 595'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: '2587 - 2609 '
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6326'
quality_controlled: '1'
status: public
title: Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1
and BK channels while preserving Cav1 channels in mouse chromaffin cells
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 595
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T12:10:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '1066'
abstract:
- lang: eng
text: "Simulation is an attractive alternative to language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. 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. 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 in general, whereas the (quantitative) simulation reduces to quantitative
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, yet they still admit pseudo-polynomial
time algorithms."
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: 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. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative
fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
“Quantitative Fair Simulation Games.” Information and Computation. Elsevier,
2017. https://doi.org/10.1016/j.ic.2016.10.006.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair
simulation games,” Information and Computation, vol. 254, no. 2. Elsevier,
pp. 143–166, 2017.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation
games. Information and Computation. 254(2), 143–166.
mla: Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information
and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation
254 (2017) 143–166.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:07:48Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2016.10.006
ec_funded: 1
external_id:
isi:
- '000402025600002'
intvolume: ' 254'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 143 - 166
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '6322'
quality_controlled: '1'
related_material:
record:
- id: '5428'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Quantitative fair simulation games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 254
year: '2017'
...
---
_id: '1023'
abstract:
- lang: eng
text: We consider products of independent square non-Hermitian random matrices.
More precisely, let X1,…, Xn be independent N × N random matrices with independent
entries (real or complex with independent real and imaginary parts) with zero
mean and variance 1/N. Soshnikov-O’Rourke [19] and Götze-Tikhomirov [15] showed
that the empirical spectral distribution of the product of n random matrices with
iid entries converges to (equation found). We prove that if the entries of the
matrices X1,…, Xn are independent (but not necessarily identically distributed)
and satisfy uniform subexponential decay condition, then in the bulk the convergence
of the ESD of X1,…, Xn to (0.1) holds up to the scale N–1/2+ε.
article_number: '22'
article_processing_charge: No
author:
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Nemish Y. Local law for the product of independent non-Hermitian random matrices
with independent entries. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP38
apa: Nemish, Y. (2017). Local law for the product of independent non-Hermitian random
matrices with independent entries. Electronic Journal of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/17-EJP38
chicago: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian
Random Matrices with Independent Entries.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP38.
ieee: Y. Nemish, “Local law for the product of independent non-Hermitian random
matrices with independent entries,” Electronic Journal of Probability,
vol. 22. Institute of Mathematical Statistics, 2017.
ista: Nemish Y. 2017. Local law for the product of independent non-Hermitian random
matrices with independent entries. Electronic Journal of Probability. 22, 22.
mla: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random
Matrices with Independent Entries.” Electronic Journal of Probability,
vol. 22, 22, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP38.
short: Y. Nemish, Electronic Journal of Probability 22 (2017).
date_created: 2018-12-11T11:49:44Z
date_published: 2017-02-06T00:00:00Z
date_updated: 2023-09-22T09:27:51Z
day: '06'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/17-EJP38
external_id:
isi:
- '000396611900022'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:29Z
date_updated: 2018-12-12T10:15:29Z
file_id: '5149'
file_name: IST-2017-802-v1+1_euclid.ejp.1487991681.pdf
file_size: 742275
relation: main_file
file_date_updated: 2018-12-12T10:15:29Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6370'
pubrep_id: '802'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law for the product of independent non-Hermitian random matrices with
independent entries
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2017'
...
---
_id: '1022'
abstract:
- lang: eng
text: We introduce a multiscale topological description of the Megaparsec web-like
cosmic matter distribution. Betti numbers and topological persistence offer a
powerful means of describing the rich connectivity structure of the cosmic web
and of its multiscale arrangement of matter and galaxies. Emanating from algebraic
topology and Morse theory, Betti numbers and persistence diagrams represent an
extension and deepening of the cosmologically familiar topological genus measure
and the related geometric Minkowski functionals. In addition to a description
of the mathematical background, this study presents the computational procedure
for computing Betti numbers and persistence diagrams for density field filtrations.
The field may be computed starting from a discrete spatial distribution of galaxies
or simulation particles. The main emphasis of this study concerns an extensive
and systematic exploration of the imprint of different web-like morphologies and
different levels of multiscale clustering in the corresponding computed Betti
numbers and persistence diagrams. To this end, we use Voronoi clustering models
as templates for a rich variety of web-like configurations and the fractal-like
Soneira-Peebles models exemplify a range of multiscale configurations. We have
identified the clear imprint of cluster nodes, filaments, walls, and voids in
persistence diagrams, along with that of the nested hierarchy of structures in
multiscale point distributions. We conclude by outlining the potential of persistent
topology for understanding the connectivity structure of the cosmic web, in large
simulations of cosmic structure formation and in the challenging context of the
observed galaxy distribution in large galaxy surveys.
acknowledgement: Part of this work has been supported by the 7th Framework Programme
for Research of the European Commission, under FETOpen grant number 255827 (CGL
Computational Geometry Learning) and ERC advanced grant, URSAT (Understanding Random
Systems via Algebraic Topology) number 320422.
article_processing_charge: No
author:
- first_name: Pratyush
full_name: Pranav, Pratyush
last_name: Pranav
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Rien
full_name: Van De Weygaert, Rien
last_name: Van De Weygaert
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Bernard
full_name: Jones, Bernard
last_name: Jones
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Pranav P, Edelsbrunner H, Van De Weygaert R, et al. The topology of the cosmic
web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical
Society. 2017;465(4):4281-4310. doi:10.1093/mnras/stw2862
apa: Pranav, P., Edelsbrunner, H., Van De Weygaert, R., Vegter, G., Kerber, M.,
Jones, B., & Wintraecken, M. (2017). The topology of the cosmic web in terms
of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society.
Oxford University Press. https://doi.org/10.1093/mnras/stw2862
chicago: Pranav, Pratyush, Herbert Edelsbrunner, Rien Van De Weygaert, Gert Vegter,
Michael Kerber, Bernard Jones, and Mathijs Wintraecken. “The Topology of the Cosmic
Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical
Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2862.
ieee: P. Pranav et al., “The topology of the cosmic web in terms of persistent
Betti numbers,” Monthly Notices of the Royal Astronomical Society, vol.
465, no. 4. Oxford University Press, pp. 4281–4310, 2017.
ista: Pranav P, Edelsbrunner H, Van De Weygaert R, Vegter G, Kerber M, Jones B,
Wintraecken M. 2017. The topology of the cosmic web in terms of persistent Betti
numbers. Monthly Notices of the Royal Astronomical Society. 465(4), 4281–4310.
mla: Pranav, Pratyush, et al. “The Topology of the Cosmic Web in Terms of Persistent
Betti Numbers.” Monthly Notices of the Royal Astronomical Society, vol.
465, no. 4, Oxford University Press, 2017, pp. 4281–310, doi:10.1093/mnras/stw2862.
short: P. Pranav, H. Edelsbrunner, R. Van De Weygaert, G. Vegter, M. Kerber, B.
Jones, M. Wintraecken, Monthly Notices of the Royal Astronomical Society 465 (2017)
4281–4310.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:40:55Z
day: '01'
department:
- _id: HeEd
doi: 10.1093/mnras/stw2862
external_id:
isi:
- '000395170200039'
intvolume: ' 465'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.04519
month: '01'
oa: 1
oa_version: Submitted Version
page: 4281 - 4310
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- '00358711'
publication_status: published
publisher: Oxford University Press
publist_id: '6373'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The topology of the cosmic web in terms of persistent Betti numbers
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 465
year: '2017'
...
---
_id: '1026'
abstract:
- lang: eng
text: The optogenetic revolution enabled spatially-precise and temporally-precise
control over protein function, signaling pathway activation, and animal behavior
with tremendous success in the dissection of signaling networks and neural circuits.
Very recently, optogenetic methods have been paired with optical reporters in
novel drug screening platforms. In these all-optical platforms, light remotely
activated ion channels and kinases thereby obviating the use of electrophysiology
or reagents. Consequences were remarkable operational simplicity, throughput,
and cost-effectiveness that culminated in the identification of new drug candidates.
These blueprints for all-optical assays also revealed potential pitfalls and inspire
all-optical variants of other screens, such as those that aim at better understanding
dynamic drug action or orphan protein function.
acknowledgement: This work was supported by grants of the European Union Seventh Framework
Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the
Austrian Science Fund FWF (W1232 MolecularDrugTargets).
article_processing_charge: No
article_type: original
author:
- first_name: Viviana
full_name: Agus, Viviana
last_name: Agus
- 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: 'Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and
applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006'
apa: 'Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening:
Technologies and applications. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.006'
chicago: 'Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology. Elsevier,
2017. https://doi.org/10.1016/j.copbio.2017.02.006.'
ieee: 'V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies
and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier,
pp. 8–14, 2017.'
ista: 'Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies
and applications. Current Opinion in Biotechnology. 48, 8–14.'
mla: 'Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology, vol.
48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.'
short: V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-22T09:26:06Z
day: '01'
department:
- _id: HaJa
doi: 10.1016/j.copbio.2017.02.006
ec_funded: 1
external_id:
isi:
- '000418313200003'
intvolume: ' 48'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 8 - 14
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Current Opinion in Biotechnology
publication_identifier:
issn:
- '09581669'
publication_status: published
publisher: Elsevier
publist_id: '6365'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Optogenetic methods in drug screening: Technologies and applications'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2017'
...
---
_id: '1020'
abstract:
- lang: eng
text: Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such
as the one extracted form cotton or woodpulp, have been used by humankind for
hundreds of years to make textiles and paper. Here we show how, by engineering
light-matter interaction, we can optimize light scattering using exclusively cellulose
nanocrystals. The produced material is sustainable, biocompatible, and when compared
to ordinary microfiber-based paper, it shows enhanced scattering strength (×4),
yielding a transport mean free path as low as 3.5 μm in the visible light range.
The experimental results are in a good agreement with the theoretical predictions
obtained with a diffusive model for light propagation.
acknowledgement: This research was funded by the EPSRC (EP/M027961/1), the Leverhulme
Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship
(BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All
data created during this research are provided in full in the results section and
Supporting Information. They are openly available from figshare and can be accessed
at ref 30.
article_processing_charge: No
author:
- first_name: Soraya
full_name: Caixeiro, Soraya
last_name: Caixeiro
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Olimpia
full_name: Onelli, Olimpia
last_name: Onelli
- first_name: Silvia
full_name: Vignolini, Silvia
last_name: Vignolini
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
citation:
ama: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose
based nanostructures for enhanced light scattering. ACS Applied Materials and
Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986
apa: Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017).
Disordered cellulose based nanostructures for enhanced light scattering. ACS
Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986
chicago: Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and
Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light
Scattering.” ACS Applied Materials and Interfaces. American Chemical Society,
2017. https://doi.org/10.1021/acsami.6b15986.
ieee: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered
cellulose based nanostructures for enhanced light scattering,” ACS Applied
Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890,
2017.
ista: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered
cellulose based nanostructures for enhanced light scattering. ACS Applied Materials
and Interfaces. 9(9), 7885–7890.
mla: Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced
Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9,
American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986.
short: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied
Materials and Interfaces 9 (2017) 7885–7890.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-03-08T00:00:00Z
date_updated: 2023-09-22T09:40:14Z
day: '08'
department:
- _id: JoFi
doi: 10.1021/acsami.6b15986
external_id:
isi:
- '000396186000002'
intvolume: ' 9'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01415
month: '03'
oa: 1
oa_version: Submitted Version
page: 7885 - 7890
publication: ACS Applied Materials and Interfaces
publication_identifier:
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
publist_id: '6372'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disordered cellulose based nanostructures for enhanced light scattering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2017'
...
---
_id: '1021'
abstract:
- lang: eng
text: Most flows in nature and engineering are turbulent because of their large
velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian
flows, for which the angular velocity decreases radially but the angular momentum
increases, are however laminar at Reynolds numbers exceeding one million. This
is in apparent contradiction to direct numerical simulations showing that in these
experiments turbulence transition is triggered by the axial boundaries. We here
show numerically that as the Reynolds number increases, turbulence becomes progressively
confined to the boundary layers and the flow in the bulk fully relaminarizes.
Our findings support that turbulence is unlikely to occur in isothermal constant-density
quasi-Keplerian flows.
article_processing_charge: No
author:
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi
Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109
apa: Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments
on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University
Press. https://doi.org/10.1017/jfm.2017.109
chicago: Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments
on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University
Press, 2017. https://doi.org/10.1017/jfm.2017.109.
ieee: J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments
on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge
University Press, pp. 21–34, 2017.
ista: Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on
quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34.
mla: Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments
on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge
University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109.
short: J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-04-25T00:00:00Z
date_updated: 2023-09-22T09:39:46Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.109
external_id:
isi:
- '000398179100006'
intvolume: ' 817'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05527
month: '04'
oa: 1
oa_version: Submitted Version
page: 21 - 34
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6371'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary layer turbulence in experiments on quasi Keplerian flows
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 817
year: '2017'
...
---
_id: '1025'
abstract:
- lang: eng
text: Many organ surfaces are covered by a protective epithelial-cell layer. It
emerges that such layers are maintained by cell stretching that triggers cell
division mediated by the force-sensitive ion-channel protein Piezo1. See Letter
p.118
article_processing_charge: No
author:
- 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: 'Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44.
doi:10.1038/nature21502'
apa: 'Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature21502'
chicago: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature.
Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.'
ieee: 'C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature,
vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.'
ista: 'Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643),
43–44.'
mla: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature,
vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.'
short: C.-P.J. Heisenberg, Nature 543 (2017) 43–44.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-02T00:00:00Z
date_updated: 2023-09-22T09:26:59Z
day: '02'
department:
- _id: CaHe
doi: 10.1038/nature21502
external_id:
isi:
- '000395671500025'
intvolume: ' 543'
isi: 1
issue: '7643'
language:
- iso: eng
month: '03'
oa_version: None
page: 43 - 44
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6367'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell biology: Stretched divisions'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 543
year: '2017'
...
---
_id: '1017'
abstract:
- lang: eng
text: The development of the vertebrate central nervous system is reliant on a complex
cascade of biological processes that include mitotic division, relocation of migrating
neurons, and the extension of dendritic and axonal processes. Each of these cellular
events requires the diverse functional repertoire of the microtubule cytoskeleton
for the generation of forces, assembly of macromolecular complexes and transport
of molecules and organelles. The tubulins are a multi-gene family that encode
for the constituents of microtubules, and have been implicated in a spectrum of
neurological disorders. Evidence is building that different tubulins tune the
functional properties of the microtubule cytoskeleton dependent on the cell type,
developmental profile and subcellular localisation. Here we review of the origins
of the functional specification of the tubulin gene family in the developing brain
at a transcriptional, translational, and post-transcriptional level. We remind
the reader that tubulins are not just loading controls for your average Western
blot.
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Ines
full_name: Leca, Ines
last_name: Leca
- first_name: Thomas
full_name: Gstrein, Thomas
last_name: Gstrein
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: David
full_name: Keays, David
last_name: Keays
citation:
ama: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development:
The origins of functional specification. Molecular and Cellular Neuroscience.
2017;84:58-67. doi:10.1016/j.mcn.2017.03.002'
apa: 'Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017).
Tubulins and brain development: The origins of functional specification. Molecular
and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002'
chicago: 'Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays.
“Tubulins and Brain Development: The Origins of Functional Specification.” Molecular
and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.'
ieee: 'M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and
brain development: The origins of functional specification,” Molecular and
Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.'
ista: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain
development: The origins of functional specification. Molecular and Cellular Neuroscience.
84, 58–67.'
mla: 'Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional
Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic
Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.'
short: M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular
Neuroscience 84 (2017) 58–67.
date_created: 2018-12-11T11:49:42Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-22T09:42:15Z
day: '01'
ddc:
- '571'
department:
- _id: SiHi
doi: 10.1016/j.mcn.2017.03.002
external_id:
isi:
- '000415140700007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:19Z
date_updated: 2018-12-12T10:09:19Z
file_id: '4742'
file_name: IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf
file_size: 1436377
relation: main_file
file_date_updated: 2018-12-12T10:09:19Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 58 - 67
publication: Molecular and Cellular Neuroscience
publication_identifier:
issn:
- '10447431'
publication_status: published
publisher: Academic Press
publist_id: '6377'
pubrep_id: '806'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tubulins and brain development: The origins of functional specification'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 84
year: '2017'
...
---
_id: '1015'
abstract:
- lang: eng
text: 'Vortices are commonly observed in the context of classical hydrodynamics:
from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon
such as a tornado, all classical vortices are characterized by an arbitrary circulation
value of the local velocity field. On the other hand the appearance of vortices
with quantized circulation represents one of the fundamental signatures of macroscopic
quantum phenomena. In two-dimensional superfluids quantized vortices play a key
role in determining finite-temperature properties, as the superfluid phase and
the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless
transition. Very recent experiments with two-dimensional superfluid fermions motivate
the present work: we present theoretical results based on the renormalization
group showing that the universal jump of the superfluid density and the critical
temperature crucially depend on the interaction strength, providing a strong benchmark
for forthcoming investigations.'
article_number: '45702'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
citation:
ama: Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold
Fermi gases. Scientific Reports. 2017;7. doi:10.1038/srep45702
apa: Bighin, G., & Salasnich, L. (2017). Vortices and antivortices in two-dimensional
ultracold Fermi gases. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep45702
chicago: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional
Ultracold Fermi Gases.” Scientific Reports. Nature Publishing Group, 2017.
https://doi.org/10.1038/srep45702.
ieee: G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional
ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group,
2017.
ista: Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional
ultracold Fermi gases. Scientific Reports. 7, 45702.
mla: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional
Ultracold Fermi Gases.” Scientific Reports, vol. 7, 45702, Nature Publishing
Group, 2017, doi:10.1038/srep45702.
short: G. Bighin, L. Salasnich, Scientific Reports 7 (2017).
date_created: 2018-12-11T11:49:42Z
date_published: 2017-04-04T00:00:00Z
date_updated: 2023-09-22T09:43:10Z
day: '04'
ddc:
- '539'
department:
- _id: MiLe
doi: 10.1038/srep45702
external_id:
isi:
- '000398148100001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:32Z
date_updated: 2018-12-12T10:12:32Z
file_id: '4950'
file_name: IST-2017-809-v1+1_srep45702.pdf
file_size: 478289
relation: main_file
file_date_updated: 2018-12-12T10:12:32Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6380'
pubrep_id: '809'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vortices and antivortices in two-dimensional ultracold Fermi gases
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1016'
abstract:
- lang: eng
text: The integrity and dynamic properties of the microtubule cytoskeleton are indispensable
for the development of the mammalian brain. Consequently, mutations in the genes
that encode the structural component (the α/β-tubulin heterodimer) can give rise
to severe, sporadic neurodevelopmental disorders. These are commonly referred
to as the tubulinopathies. Here we report the addition of recessive quadrupedalism,
also known as Uner Tan syndrome (UTS), to the growing list of diseases caused
by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic
TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to
the identifying quadrupedal locomotion, all three patients showed severe cerebellar
hypoplasia. None, however, displayed the basal ganglia malformations typically
associated with TUBB2B mutations. Functional analysis of the R390Q substitution
revealed that it did not affect the ability of β-tubulin to fold or become assembled
into the α/β-heterodimer, nor did it influence the incorporation of mutant-containing
heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2
did not affect growth under basal conditions, but did result in increased sensitivity
to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation
on microtubule function. The TUBB2B mutation described here represents an unusual
recessive mode of inheritance for missense-mediated tubulinopathies and reinforces
the sensitivity of the developing cerebellum to microtubule defects.
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Thai
full_name: Nguyen, Thai
last_name: Nguyen
- first_name: Anjana
full_name: Srivatsan, Anjana
last_name: Srivatsan
- first_name: Ines
full_name: Leca, Ines
last_name: Leca
- first_name: Guoling
full_name: Tian, Guoling
last_name: Tian
- first_name: Tanja
full_name: Fritz, Tanja
last_name: Fritz
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Jennifer
full_name: Mcevoy Venneri, Jennifer
last_name: Mcevoy Venneri
- first_name: James
full_name: Kiely, James
last_name: Kiely
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Uner
full_name: Tan, Uner
last_name: Tan
- first_name: Richard
full_name: Kolodner, Richard
last_name: Kolodner
- first_name: Nicholas
full_name: Cowan, Nicholas
last_name: Cowan
- first_name: David
full_name: Keays, David
last_name: Keays
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Breuss M, Nguyen T, Srivatsan A, et al. Uner Tan syndrome caused by a homozygous
TUBB2B mutation affecting microtubule stability. Human Molecular Genetics.
2017;26(2):258-269. doi:10.1093/hmg/ddw383
apa: Breuss, M., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., … Gleeson,
J. (2017). Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting
microtubule stability. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/ddw383
chicago: Breuss, Martin, Thai Nguyen, Anjana Srivatsan, Ines Leca, Guoling Tian,
Tanja Fritz, Andi H Hansen, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B
Mutation Affecting Microtubule Stability.” Human Molecular Genetics. Oxford
University Press, 2017. https://doi.org/10.1093/hmg/ddw383.
ieee: M. Breuss et al., “Uner Tan syndrome caused by a homozygous TUBB2B
mutation affecting microtubule stability,” Human Molecular Genetics, vol.
26, no. 2. Oxford University Press, pp. 258–269, 2017.
ista: Breuss M, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev
D, Mcevoy Venneri J, Kiely J, Rosti R, Scott E, Tan U, Kolodner R, Cowan N, Keays
D, Gleeson J. 2017. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting
microtubule stability. Human Molecular Genetics. 26(2), 258–269.
mla: Breuss, Martin, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation
Affecting Microtubule Stability.” Human Molecular Genetics, vol. 26, no.
2, Oxford University Press, 2017, pp. 258–69, doi:10.1093/hmg/ddw383.
short: M. Breuss, T. Nguyen, A. Srivatsan, I. Leca, G. Tian, T. Fritz, A.H. Hansen,
D. Musaev, J. Mcevoy Venneri, J. Kiely, R. Rosti, E. Scott, U. Tan, R. Kolodner,
N. Cowan, D. Keays, J. Gleeson, Human Molecular Genetics 26 (2017) 258–269.
date_created: 2018-12-11T11:49:42Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:42:42Z
day: '01'
department:
- _id: SiHi
doi: 10.1093/hmg/ddw383
external_id:
isi:
- '000397066400002'
intvolume: ' 26'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 258 - 269
publication: Human Molecular Genetics
publication_identifier:
issn:
- '09646906'
publication_status: published
publisher: Oxford University Press
publist_id: '6379'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule
stability
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 26
year: '2017'
...
---
_id: '1018'
abstract:
- lang: eng
text: In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory
processes, including those activated by cytokinins. The crosstalk between cytokinin
response and light is known for a long time. However, the molecular mechanism
underlying the interactionbetween light and cytokinin signaling remains elusive.
In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH)
gene whose activity is indispensable for spatiotemporally correct expression of
CYTOKININ INDEPENDENT-1 (CKI1), encoding the constitutively active sensor histidine
kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE 1 (HY1)
which encodes the key protein in the biosynthesis of phytochromobilin, a cofactor
of photoconvertiblephytochromes. Our analysis confirmed the light-dependent regulation
oftheCKI1 expression pattern. We show that CKI1 expression is under the control
of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator
of CKI1 expression, presumably via the phyA-regulated transcription factors PHYTOCHROME
INTERACTING FACTOR 3 (PIF3) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Changes in
CKI1 expression observed in lph/hy1-7 and phy mutants correlatewithmisregulation
of MSP signaling, changedcytokinin sensitivity and developmental aberrations,previously
shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate
novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook
development during skotomorphogenesis. Based on these results, we propose that
the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying
the well-known interaction between light- and cytokinin-controlled plant development.
article_processing_charge: No
author:
- first_name: Tereza
full_name: Dobisova, Tereza
last_name: Dobisova
- first_name: Vendula
full_name: Hrdinova, Vendula
last_name: Hrdinova
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Sarka
full_name: Michlickova, Sarka
last_name: Michlickova
- first_name: Ivana
full_name: Urbankova, Ivana
last_name: Urbankova
- first_name: Romana
full_name: Hejatkova, Romana
last_name: Hejatkova
- first_name: Petra
full_name: Zadnikova, Petra
last_name: Zadnikova
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
citation:
ama: Dobisova T, Hrdinova V, Cuesta C, et al. Light regulated expression of sensor
histidine kinase CKI1 controls cytokinin related development. Plant Physiology.
2017;174(1):387-404. doi:10.1104/pp.16.01964
apa: Dobisova, T., Hrdinova, V., Cuesta, C., Michlickova, S., Urbankova, I., Hejatkova,
R., … Hejátko, J. (2017). Light regulated expression of sensor histidine kinase
CKI1 controls cytokinin related development. Plant Physiology. American
Society of Plant Biologists. https://doi.org/10.1104/pp.16.01964
chicago: Dobisova, Tereza, Vendula Hrdinova, Candela Cuesta, Sarka Michlickova,
Ivana Urbankova, Romana Hejatkova, Petra Zadnikova, Markéta Pernisová, Eva Benková,
and Jan Hejátko. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls
Cytokinin Related Development.” Plant Physiology. American Society of Plant
Biologists, 2017. https://doi.org/10.1104/pp.16.01964.
ieee: T. Dobisova et al., “Light regulated expression of sensor histidine
kinase CKI1 controls cytokinin related development,” Plant Physiology,
vol. 174, no. 1. American Society of Plant Biologists, pp. 387–404, 2017.
ista: Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R,
Zadnikova P, Pernisová M, Benková E, Hejátko J. 2017. Light regulated expression
of sensor histidine kinase CKI1 controls cytokinin related development. Plant
Physiology. 174(1), 387–404.
mla: Dobisova, Tereza, et al. “Light Regulated Expression of Sensor Histidine Kinase
CKI1 Controls Cytokinin Related Development.” Plant Physiology, vol. 174,
no. 1, American Society of Plant Biologists, 2017, pp. 387–404, doi:10.1104/pp.16.01964.
short: T. Dobisova, V. Hrdinova, C. Cuesta, S. Michlickova, I. Urbankova, R. Hejatkova,
P. Zadnikova, M. Pernisová, E. Benková, J. Hejátko, Plant Physiology 174 (2017)
387–404.
date_created: 2018-12-11T11:49:43Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2023-09-22T09:41:48Z
day: '17'
department:
- _id: EvBe
doi: 10.1104/pp.16.01964
external_id:
isi:
- '000402057200028'
intvolume: ' 174'
isi: 1
issue: '1'
language:
- iso: eng
month: '05'
oa_version: None
page: 387 - 404
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6375'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light regulated expression of sensor histidine kinase CKI1 controls cytokinin
related development
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 174
year: '2017'
...
---
_id: '1019'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor
of tissue-specific gene expression in Drosophila melanogaster. Heredity.
2017;119(1):27-34. doi:10.1038/hdy.2017.12
apa: Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12
chicago: Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage
Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12.
ieee: E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,”
Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.
ista: Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general
inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity.
119(1), 27–34.
mla: Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific
Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1,
Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12.
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.
date_created: 2018-12-11T11:49:43Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-22T09:41:21Z
day: '01'
department:
- _id: BeVi
doi: 10.1038/hdy.2017.12
external_id:
isi:
- '000405397800004'
intvolume: ' 119'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 27 - 34
publication: Heredity
publication_identifier:
issn:
- 0018067X
publication_status: published
publisher: Nature Publishing Group
publist_id: '6374'
quality_controlled: '1'
related_material:
record:
- id: '9861'
relation: research_data
status: public
scopus_import: '1'
status: public
title: X-linkage is not a general inhibitor of tissue-specific gene expression in
Drosophila melanogaster
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 119
year: '2017'
...
---
_id: '1014'
abstract:
- lang: eng
text: 'We consider the large-scale regularity of solutions to second-order linear
elliptic equations with random coefficient fields. In contrast to previous works
on regularity theory for random elliptic operators, our interest is in the regularity
at the boundary: We consider problems posed on the half-space with homogeneous
Dirichlet boundary conditions and derive an associated C1,α-type large-scale regularity
theory in the form of a corresponding decay estimate for the homogenization-adapted
tilt-excess. This regularity theory entails an associated Liouville-type theorem.
The results are based on the existence of homogenization correctors adapted to
the half-space setting, which we construct-by an entirely deterministic argument-as
a modification of the homogenization corrector on the whole space. This adaption
procedure is carried out inductively on larger scales, crucially relying on the
regularity theory already established on smaller scales.'
article_processing_charge: No
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Claudia
full_name: Raithel, Claudia
last_name: Raithel
citation:
ama: Fischer JL, Raithel C. Liouville principles and a large-scale regularity theory
for random elliptic operators on the half-space. SIAM Journal on Mathematical
Analysis. 2017;49(1):82-114. doi:10.1137/16M1070384
apa: Fischer, J. L., & Raithel, C. (2017). Liouville principles and a large-scale
regularity theory for random elliptic operators on the half-space. SIAM Journal
on Mathematical Analysis. Society for Industrial and Applied Mathematics .
https://doi.org/10.1137/16M1070384
chicago: Fischer, Julian L, and Claudia Raithel. “Liouville Principles and a Large-Scale
Regularity Theory for Random Elliptic Operators on the Half-Space.” SIAM Journal
on Mathematical Analysis. Society for Industrial and Applied Mathematics ,
2017. https://doi.org/10.1137/16M1070384.
ieee: J. L. Fischer and C. Raithel, “Liouville principles and a large-scale regularity
theory for random elliptic operators on the half-space,” SIAM Journal on Mathematical
Analysis, vol. 49, no. 1. Society for Industrial and Applied Mathematics ,
pp. 82–114, 2017.
ista: Fischer JL, Raithel C. 2017. Liouville principles and a large-scale regularity
theory for random elliptic operators on the half-space. SIAM Journal on Mathematical
Analysis. 49(1), 82–114.
mla: Fischer, Julian L., and Claudia Raithel. “Liouville Principles and a Large-Scale
Regularity Theory for Random Elliptic Operators on the Half-Space.” SIAM Journal
on Mathematical Analysis, vol. 49, no. 1, Society for Industrial and Applied
Mathematics , 2017, pp. 82–114, doi:10.1137/16M1070384.
short: J.L. Fischer, C. Raithel, SIAM Journal on Mathematical Analysis 49 (2017)
82–114.
date_created: 2018-12-11T11:49:41Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-09-22T09:43:36Z
day: '12'
doi: 10.1137/16M1070384
extern: '1'
external_id:
isi:
- '000396681800004'
intvolume: ' 49'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.04328
month: '01'
oa: 1
oa_version: Submitted Version
page: 82 - 114
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
issn:
- '00361410'
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '6381'
quality_controlled: '1'
status: public
title: Liouville principles and a large-scale regularity theory for random elliptic
operators on the half-space
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 49
year: '2017'
...
---
_id: '9861'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: 'Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
2017. doi:10.5061/dryad.02f6r'
apa: 'Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data
from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r'
chicago: 'Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch.
“Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression
in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.'
ieee: 'E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.”
Dryad, 2017.'
ista: 'Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,
Dryad, 10.5061/dryad.02f6r.'
mla: 'Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor
of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017,
doi:10.5061/dryad.02f6r.'
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).
date_created: 2021-08-10T08:12:52Z
date_published: 2017-02-14T00:00:00Z
date_updated: 2023-09-22T09:41:20Z
day: '14'
department:
- _id: BeVi
doi: 10.5061/dryad.02f6r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.02f6r
month: '02'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1019'
relation: used_in_publication
status: public
status: public
title: 'Data from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1006'
abstract:
- lang: eng
text: 'Background: The phenomenon of immune priming, i.e. enhanced protection following
a secondary exposure to a pathogen, has now been demonstrated in a wide range
of invertebrate species. Despite accumulating phenotypic evidence, knowledge of
its mechanistic underpinnings is currently very limited. Here we used the system
of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus
thuringiensis (Bt) to further our molecular understanding of the oral immune priming
phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants)
of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon
later challenge exposure, using a whole-transcriptome sequencing approach. Results:
Whereas gene expression of individuals primed with the orally non-pathogenic strain
showed minor changes to controls, we found that priming with the pathogenic strain
induced regulation of a large set of distinct genes, many of which are known immune
candidates. Intriguingly, the immune repertoire activated upon priming and subsequent
challenge qualitatively differed from the one mounted upon infection with Bt without
previous priming. Moreover, a large subset of priming-specific genes showed an
inverse regulation compared to their regulation upon challenge only. Conclusions:
Our data demonstrate that gene expression upon infection is strongly affected
by previous immune priming. We hypothesise that this shift in gene expression
indicates activation of a more targeted and efficient response towards a previously
encountered pathogen, in anticipation of potential secondary encounter.'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: Greenwood J, Milutinovic B, Peuß R, et al. Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.
BMC Genomics. 2017;18(1):329. doi:10.1186/s12864-017-3705-7
apa: Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Oral immune priming with Bacillus thuringiensis induces
a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics.
BioMed Central. https://doi.org/10.1186/s12864-017-3705-7
chicago: Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Oral Immune
Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of
Tribolium Castaneum Larvae.” BMC Genomics. BioMed Central, 2017. https://doi.org/10.1186/s12864-017-3705-7.
ieee: J. Greenwood et al., “Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae,” BMC
Genomics, vol. 18, no. 1. BioMed Central, p. 329, 2017.
ista: Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Oral immune priming with Bacillus thuringiensis induces a shift
in the gene expression of Tribolium castaneum larvae. BMC Genomics. 18(1), 329.
mla: Greenwood, Jenny, et al. “Oral Immune Priming with Bacillus Thuringiensis Induces
a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics,
vol. 18, no. 1, BioMed Central, 2017, p. 329, doi:10.1186/s12864-017-3705-7.
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, BMC Genomics 18 (2017) 329.
date_created: 2018-12-11T11:49:39Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1186/s12864-017-3705-7
external_id:
isi:
- '000400625200004'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:46Z
date_updated: 2018-12-12T10:16:46Z
file_id: '5236'
file_name: IST-2017-814-v1+1_s12864-017-3705-7.pdf
file_size: 2379672
relation: main_file
file_date_updated: 2018-12-12T10:16:46Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '329'
publication: BMC Genomics
publication_identifier:
issn:
- '14712164'
publication_status: published
publisher: BioMed Central
publist_id: '6392'
pubrep_id: '814'
quality_controlled: '1'
related_material:
record:
- id: '9859'
relation: research_data
status: public
- id: '9860'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Oral immune priming with Bacillus thuringiensis induces a shift in the gene
expression of Tribolium castaneum larvae
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2017'
...
---
_id: '1011'
abstract:
- lang: eng
text: Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly
equivalent, are standard models for interprocedural analysis. Yet RSMs are more
convenient as they (a) explicitly model function calls and returns, and (b) specify
many natural parameters for algorithmic analysis, e.g., the number of entries
and exits. We consider a general framework where RSM transitions are labeled from
a semiring and path properties are algebraic with semiring operations, which can
model, e.g., interprocedural reachability and dataflow analysis problems. Our
main contributions are new algorithms for several fundamental problems. As compared
to a direct translation of RSMs to PDSs and the best-known existing bounds of
PDSs, our analysis algorithm improves the complexity for finite-height semirings
(that subsumes reachability and standard dataflow properties). We further consider
the problem of extracting distance values from the representation structures computed
by our algorithm, and give efficient algorithms that distinguish the complexity
of a one-time preprocessing from the complexity of each individual query. Another
advantage of our algorithm is that our improvements carry over to the concurrent
setting, where we improve the bestknown complexity for the context-bounded analysis
of concurrent RSMs. Finally, we provide a prototype implementation that gives
a significant speed-up on several benchmarks from the SLAM/SDV project.
alternative_title:
- LNCS
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: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Samarth
full_name: Mishra, Samarth
last_name: Mishra
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. Faster algorithms for weighted
recursive state machines. In: Yang H, ed. Vol 10201. Springer; 2017:287-313. doi:10.1007/978-3-662-54434-1_11'
apa: 'Chatterjee, K., Kragl, B., Mishra, S., & Pavlogiannis, A. (2017). Faster
algorithms for weighted recursive state machines. In H. Yang (Ed.) (Vol. 10201,
pp. 287–313). Presented at the ESOP: European Symposium on Programming, Uppsala,
Sweden: Springer. https://doi.org/10.1007/978-3-662-54434-1_11'
chicago: Chatterjee, Krishnendu, Bernhard Kragl, Samarth Mishra, and Andreas Pavlogiannis.
“Faster Algorithms for Weighted Recursive State Machines.” edited by Hongseok
Yang, 10201:287–313. Springer, 2017. https://doi.org/10.1007/978-3-662-54434-1_11.
ieee: 'K. Chatterjee, B. Kragl, S. Mishra, and A. Pavlogiannis, “Faster algorithms
for weighted recursive state machines,” presented at the ESOP: European Symposium
on Programming, Uppsala, Sweden, 2017, vol. 10201, pp. 287–313.'
ista: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. 2017. Faster algorithms
for weighted recursive state machines. ESOP: European Symposium on Programming,
LNCS, vol. 10201, 287–313.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Weighted Recursive
State Machines. Edited by Hongseok Yang, vol. 10201, Springer, 2017, pp. 287–313,
doi:10.1007/978-3-662-54434-1_11.
short: K. Chatterjee, B. Kragl, S. Mishra, A. Pavlogiannis, in:, H. Yang (Ed.),
Springer, 2017, pp. 287–313.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'ESOP: European Symposium on Programming'
start_date: 2017-04-22
date_created: 2018-12-11T11:49:41Z
date_published: 2017-03-19T00:00:00Z
date_updated: 2023-09-22T09:44:50Z
day: '19'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-54434-1_11
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
external_id:
isi:
- '000681702400011'
intvolume: ' 10201'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.04914
month: '03'
oa: 1
oa_version: Submitted Version
page: 287 - 313
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster algorithms for weighted recursive state machines
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10201
year: '2017'
...
---
_id: '1004'
abstract:
- lang: eng
text: The fundamental tasks of the root system are, besides anchoring, mediating
interactions between plant and soil and providing the plant with water and nutrients.
The architecture of the root system is controlled by endogenous mechanisms that
constantly integrate environmental signals, such as availability of nutrients
and water. Extremely important for efficient soil exploitation and survival under
less favorable conditions is the developmental flexibility of the root system
that is largely determined by its postembryonic branching capacity. Modulation
of initiation and outgrowth of lateral roots provides roots with an exceptional
plasticity, allows optimal adjustment to underground heterogeneity, and enables
effective soil exploitation and use of resources. Here we discuss recent advances
in understanding the molecular mechanisms that shape the plant root system and
integrate external cues to adapt to the changing environment.
article_processing_charge: No
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current
Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010
apa: Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching.
Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010
chicago: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010.
ieee: K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current
Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017.
ista: Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current
Opinion in Genetics & Development. 45, 82–89.
mla: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017,
pp. 82–89, doi:10.1016/j.gde.2017.03.010.
short: K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017)
82–89.
date_created: 2018-12-11T11:49:38Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-22T09:48:15Z
day: '01'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1016/j.gde.2017.03.010
external_id:
isi:
- '000404880400013'
pmid:
- '28391060'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T08:00:36Z
date_updated: 2019-04-17T08:00:36Z
file_id: '6336'
file_name: Otvos_Benkova_CurOpDevBiol_2017.pdf
file_size: 364133
relation: main_file
success: 1
file_date_updated: 2019-04-17T08:00:36Z
has_accepted_license: '1'
intvolume: ' 45'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 82 - 89
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Current Opinion in Genetics & Development
publication_identifier:
issn:
- 0959437X
publication_status: published
publisher: Elsevier
publist_id: '6394'
pubrep_id: '1017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatiotemporal mechanisms of root branching
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2017'
...
---
_id: '1010'
abstract:
- lang: eng
text: 'We prove a local law in the bulk of the spectrum for random Gram matrices
XX∗, a generalization of sample covariance matrices, where X is a large matrix
with independent, centered entries with arbitrary variances. The limiting eigenvalue
density that generalizes the Marchenko-Pastur law is determined by solving a system
of nonlinear equations. Our entrywise and averaged local laws are on the optimal
scale with the optimal error bounds. They hold both in the square case (hard edge)
and in the properly rectangular case (soft edge). In the latter case we also establish
a macroscopic gap away from zero in the spectrum of XX∗. '
article_number: '25'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic
Journal of Probability. 2017;22. doi:10.1214/17-EJP42
apa: Alt, J., Erdös, L., & Krüger, T. H. (2017). Local law for random Gram matrices.
Electronic Journal of Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/17-EJP42
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Law for Random
Gram Matrices.” Electronic Journal of Probability. Institute of Mathematical
Statistics, 2017. https://doi.org/10.1214/17-EJP42.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local law for random Gram matrices,”
Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics,
2017.
ista: Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic
Journal of Probability. 22, 25.
mla: Alt, Johannes, et al. “Local Law for Random Gram Matrices.” Electronic Journal
of Probability, vol. 22, 25, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP42.
short: J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017).
date_created: 2018-12-11T11:49:40Z
date_published: 2017-03-08T00:00:00Z
date_updated: 2023-09-22T09:45:23Z
day: '08'
ddc:
- '510'
- '539'
department:
- _id: LaEr
doi: 10.1214/17-EJP42
ec_funded: 1
external_id:
arxiv:
- '1606.07353'
isi:
- '000396611900025'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:39Z
date_updated: 2018-12-12T10:13:39Z
file_id: '5024'
file_name: IST-2017-807-v1+1_euclid.ejp.1488942016.pdf
file_size: 639384
relation: main_file
file_date_updated: 2018-12-12T10:13:39Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6386'
pubrep_id: '807'
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Local law for random Gram matrices
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2017'
...
---
_id: '1009'
abstract:
- lang: eng
text: A standard objective in partially-observable Markov decision processes (POMDPs)
is to find a policy that maximizes the expected discounted-sum payoff. However,
such policies may still permit unlikely but highly undesirable outcomes, which
is problematic especially in safety-critical applications. Recently, there has
been a surge of interest in POMDPs where the goal is to maximize the probability
to ensure that the payoff is at least a given threshold, but these approaches
do not consider any optimization beyond satisfying this threshold constraint.
In this work we go beyond both the “expectation” and “threshold” approaches and
consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we
are given a threshold t and the objective is to find a policy σ such that a) each
possible outcome of σ yields a discounted-sum payoff of at least t, and b) the
expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies
satisfying a). We present a practical approach to tackle the GPO problem and evaluate
it on standard POMDP benchmarks.
acknowledgement: 'he research leading to these results was supported by the Austrian
Science Fund (FWF) NFN Grant no. S11407-N23 (RiSE/SHiNE); two ERC Starting grants
(279307: Graph Games, 279499: inVEST); the Vienna Science and Tech- nology Fund
(WWTF) through project ICT15-003; and the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. [291734].'
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: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Guillermo
full_name: Pérez, Guillermo
last_name: Pérez
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
- first_name: Djordje
full_name: Zikelic, Djordje
last_name: Zikelic
citation:
ama: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. Optimizing expectation
with guarantees in POMDPs. In: Proceedings of the 31st AAAI Conference on Artificial
Intelligence. Vol 5. AAAI Press; 2017:3725-3732.'
apa: 'Chatterjee, K., Novotný, P., Pérez, G., Raskin, J., & Zikelic, D. (2017).
Optimizing expectation with guarantees in POMDPs. In Proceedings of the 31st
AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3725–3732). San Francisco,
CA, United States: AAAI Press.'
chicago: Chatterjee, Krishnendu, Petr Novotný, Guillermo Pérez, Jean Raskin, and
Djordje Zikelic. “Optimizing Expectation with Guarantees in POMDPs.” In Proceedings
of the 31st AAAI Conference on Artificial Intelligence, 5:3725–32. AAAI Press,
2017.
ieee: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, and D. Zikelic, “Optimizing
expectation with guarantees in POMDPs,” in Proceedings of the 31st AAAI Conference
on Artificial Intelligence, San Francisco, CA, United States, 2017, vol. 5,
pp. 3725–3732.
ista: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. 2017. Optimizing expectation
with guarantees in POMDPs. Proceedings of the 31st AAAI Conference on Artificial
Intelligence. AAAI: Conference on Artificial Intelligence vol. 5, 3725–3732.'
mla: Chatterjee, Krishnendu, et al. “Optimizing Expectation with Guarantees in POMDPs.”
Proceedings of the 31st AAAI Conference on Artificial Intelligence, vol.
5, AAAI Press, 2017, pp. 3725–32.
short: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, D. Zikelic, in:, Proceedings
of the 31st AAAI Conference on Artificial Intelligence, AAAI Press, 2017, pp.
3725–3732.
conference:
end_date: 2017-02-10
location: San Francisco, CA, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2017-02-04
date_created: 2018-12-11T11:49:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:46:41Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
isi:
- '000485630703107'
intvolume: ' 5'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092
month: '01'
oa: 1
oa_version: Submitted Version
page: 3725 - 3732
project:
- _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: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '6387'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing expectation with guarantees in POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2017'
...
---
_id: '9859'
abstract:
- lang: eng
text: 'Lists of all differentially expressed genes in the different priming-challenge
treatments (compared to the fully naïve control; xlsx file). Relevant columns
include the following: sample_1 and sample_2 – treatment groups being compared;
Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change)
– log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated
compared with sample 2, positive means sample 2 upregulated compared with sample
1; cuffdiff test_statistic – test statistic of differential expression test; p_value
– p-value of differential expression test; q_value (FDR correction) – adjusted
P-value of differential expression test. (XLSX 598 kb)'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 1: Table S1. of
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression
of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d1.v1'
apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Additional file 1: Table S1. of Oral immune priming with
Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum
larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1'
chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional
File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a
Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature,
2017. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1.'
ieee: 'J. Greenwood et al., “Additional file 1: Table S1. of Oral immune
priming with Bacillus thuringiensis induces a shift in the gene expression of
Tribolium castaneum larvae.” Springer Nature, 2017.'
ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Additional file 1: Table S1. of Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,
Springer Nature, 10.6084/m9.figshare.c.3756974_d1.v1.'
mla: 'Greenwood, Jenny, et al. Additional File 1: Table S1. of Oral Immune Priming
with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium
Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d1.v1.'
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, (2017).
date_created: 2021-08-10T07:59:02Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.c.3756974_d1.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '1006'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9860'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 5: Table S3. of
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression
of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d5.v1'
apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Additional file 5: Table S3. of Oral immune priming with
Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum
larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1'
chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional
File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a
Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature,
2017. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1.'
ieee: 'J. Greenwood et al., “Additional file 5: Table S3. of Oral immune
priming with Bacillus thuringiensis induces a shift in the gene expression of
Tribolium castaneum larvae.” Springer Nature, 2017.'
ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Additional file 5: Table S3. of Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,
Springer Nature, 10.6084/m9.figshare.c.3756974_d5.v1.'
mla: 'Greenwood, Jenny, et al. Additional File 5: Table S3. of Oral Immune Priming
with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium
Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d5.v1.'
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, (2017).
date_created: 2021-08-10T08:07:12Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.c.3756974_d5.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '1006'
relation: used_in_publication
status: public
status: public
title: 'Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1002'
abstract:
- lang: eng
text: " We present an interactive design system to create functional mechanical
\ objects. Our computational approach allows novice users to retarget an existing
mechanical template to a user-specified input shape. Our proposed representation
for a mechanical template encodes a parameterized mechanism, mechanical constraints
that ensure a physically valid configuration, spatial relationships of mechanical
parts to the user-provided shape, and functional constraints that specify an intended
functionality. We provide an intuitive interface and optimization-in-the-loop
approach for finding a valid configuration of the mechanism and the shape to
ensure that higher-level functional goals are met. Our algorithm interactively
optimizes the mechanism while the user manipulates the placement of mechanical
components and the shape. Our system allows users to efficiently explore various
design choices and to synthesize customized mechanical objects that can be fabricated
with rapid prototyping technologies. We demonstrate the efficacy of our approach
by retargeting various mechanical templates to different shapes and fabricating
the resulting functional mechanical objects.\r\n"
alternative_title:
- ACM Transactions on Graphics
article_number: '81'
article_processing_charge: No
author:
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Duygu
full_name: Ceylan, Duygu
last_name: Ceylan
- first_name: Wilmot
full_name: Li, Wilmot
last_name: Li
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. Functionality-aware retargeting
of mechanisms to 3D shapes. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073710'
apa: 'Zhang, R., Auzinger, T., Ceylan, D., Li, W., & Bickel, B. (2017). Functionality-aware
retargeting of mechanisms to 3D shapes (Vol. 36). Presented at the SIGGRAPH: Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States : ACM. https://doi.org/10.1145/3072959.3073710'
chicago: Zhang, Ran, Thomas Auzinger, Duygu Ceylan, Wilmot Li, and Bernd Bickel.
“Functionality-Aware Retargeting of Mechanisms to 3D Shapes,” Vol. 36. ACM, 2017.
https://doi.org/10.1145/3072959.3073710.
ieee: 'R. Zhang, T. Auzinger, D. Ceylan, W. Li, and B. Bickel, “Functionality-aware
retargeting of mechanisms to 3D shapes,” presented at the SIGGRAPH: Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States , 2017, vol. 36, no.
4.'
ista: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. 2017. Functionality-aware
retargeting of mechanisms to 3D shapes. SIGGRAPH: Computer Graphics and Interactive
Techniques, ACM Transactions on Graphics, vol. 36, 81.'
mla: Zhang, Ran, et al. Functionality-Aware Retargeting of Mechanisms to 3D Shapes.
Vol. 36, no. 4, 81, ACM, 2017, doi:10.1145/3072959.3073710.
short: R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017.
conference:
end_date: 2017-08-03
location: 'Los Angeles, CA, United States '
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques'
start_date: 2017-07-30
date_created: 2018-12-11T11:49:38Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:49:31Z
day: '01'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3072959.3073710
ec_funded: 1
external_id:
isi:
- '000406432100049'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:05Z
date_updated: 2018-12-12T10:09:05Z
file_id: '4728'
file_name: IST-2018-1050-v1+1_MechRet.pdf
file_size: 25463895
relation: main_file
file_date_updated: 2018-12-12T10:09:05Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
issn:
- '07300301'
publication_status: published
publisher: ACM
publist_id: '6396'
pubrep_id: '1050'
quality_controlled: '1'
related_material:
record:
- id: '8386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functionality-aware retargeting of mechanisms to 3D shapes
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1001'
abstract:
- lang: eng
text: We present a computational approach for designing CurveUps, curvy shells that
form from an initially flat state. They consist of small rigid tiles that are
tightly held together by two pre-stretched elastic sheets attached to them. Our
method allows the realization of smooth, doubly curved surfaces that can be fabricated
as a flat piece. Once released, the restoring forces of the pre-stretched sheets
support the object to take shape in 3D. CurveUps are structurally stable in their
target configuration. The design process starts with a target surface. Our method
generates a tile layout in 2D and optimizes the distribution, shape, and attachment
areas of the tiles to obtain a configuration that is fabricable and in which the
curved up state closely matches the target. Our approach is based on an efficient
approximate model and a local optimization strategy for an otherwise intractable
nonlinear optimization problem. We demonstrate the effectiveness of our approach
for a wide range of shapes, all realized as physical prototypes.
alternative_title:
- ACM Transactions on Graphics
article_number: '64'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Eder
full_name: Miguel, Eder
last_name: Miguel
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Guseinov R, Miguel E, Bickel B. CurveUps: Shaping objects from flat plates
with tension-actuated curvature. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073709'
apa: 'Guseinov, R., Miguel, E., & Bickel, B. (2017). CurveUps: Shaping objects
from flat plates with tension-actuated curvature (Vol. 36). Presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles,
CA, United States: ACM. https://doi.org/10.1145/3072959.3073709'
chicago: 'Guseinov, Ruslan, Eder Miguel, and Bernd Bickel. “CurveUps: Shaping Objects
from Flat Plates with Tension-Actuated Curvature,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073709.'
ieee: 'R. Guseinov, E. Miguel, and B. Bickel, “CurveUps: Shaping objects from flat
plates with tension-actuated curvature,” presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States, 2017, vol. 36, no. 4.'
ista: 'Guseinov R, Miguel E, Bickel B. 2017. CurveUps: Shaping objects from flat
plates with tension-actuated curvature. SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 64.'
mla: 'Guseinov, Ruslan, et al. CurveUps: Shaping Objects from Flat Plates with
Tension-Actuated Curvature. Vol. 36, no. 4, 64, ACM, 2017, doi:10.1145/3072959.3073709.'
short: R. Guseinov, E. Miguel, B. Bickel, in:, ACM, 2017.
conference:
end_date: 2017-08-25
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2017-08-19
date_created: 2018-12-11T11:49:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:49:58Z
day: '01'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3072959.3073709
ec_funded: 1
external_id:
isi:
- '000406432100032'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:24Z
date_updated: 2018-12-12T10:10:24Z
file_id: '4811'
file_name: IST-2018-1053-v1+1_CurveUp.pdf
file_size: 36159696
relation: main_file
file_date_updated: 2018-12-12T10:10:24Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_status: published
publisher: ACM
publist_id: '6397'
pubrep_id: '1053'
quality_controlled: '1'
related_material:
record:
- id: '8366'
relation: dissertation_contains
status: public
status: public
title: 'CurveUps: Shaping objects from flat plates with tension-actuated curvature'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1003'
abstract:
- lang: eng
text: Network games (NGs) are played on directed graphs and are extensively used
in network design and analysis. Search problems for NGs include finding special
strategy profiles such as a Nash equilibrium and a globally optimal solution.
The networks modeled by NGs may be huge. In formal verification, abstraction has
proven to be an extremely effective technique for reasoning about systems with
big and even infinite state spaces. We describe an abstraction-refinement methodology
for reasoning about NGs. Our methodology is based on an abstraction function that
maps the state space of an NG to a much smaller state space. We search for a global
optimum and a Nash equilibrium by reasoning on an under- and an overapproximation
defined on top of this smaller state space. When the approximations are too coarse
to find such profiles, we refine the abstraction function. Our experimental results
demonstrate the efficiency of the methodology.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning
about network games. In: AAAI Press; 2017:70-76. doi:10.24963/ijcai.2017/11'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). An abstraction-refinement
methodology for reasoning about network games (pp. 70–76). Presented at the IJCAI:
International Joint Conference on Artificial Intelligence , Melbourne, Australia:
AAAI Press. https://doi.org/10.24963/ijcai.2017/11'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement
Methodology for Reasoning about Network Games,” 70–76. AAAI Press, 2017. https://doi.org/10.24963/ijcai.2017/11.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology
for reasoning about network games,” presented at the IJCAI: International Joint
Conference on Artificial Intelligence , Melbourne, Australia, 2017, pp. 70–76.'
ista: 'Avni G, Guha S, Kupferman O. 2017. An abstraction-refinement methodology
for reasoning about network games. IJCAI: International Joint Conference on Artificial
Intelligence , 70–76.'
mla: Avni, Guy, et al. An Abstraction-Refinement Methodology for Reasoning about
Network Games. AAAI Press, 2017, pp. 70–76, doi:10.24963/ijcai.2017/11.
short: G. Avni, S. Guha, O. Kupferman, in:, AAAI Press, 2017, pp. 70–76.
conference:
end_date: 2017-08-25
location: Melbourne, Australia
name: 'IJCAI: International Joint Conference on Artificial Intelligence '
start_date: 2017-08-19
date_created: 2018-12-11T11:49:38Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T09:49:00Z
day: '30'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.24963/ijcai.2017/11
external_id:
isi:
- '000764137500011'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:58Z
date_updated: 2018-12-12T10:16:58Z
file_id: '5249'
file_name: IST-2017-818-v1+1_allIJCAI_CR.pdf
file_size: 365172
relation: main_file
file_date_updated: 2018-12-12T10:16:58Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 70 - 76
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '10450823'
publication_status: published
publisher: AAAI Press
publist_id: '6395'
pubrep_id: '818'
quality_controlled: '1'
related_material:
record:
- id: '6006'
relation: later_version
status: public
scopus_import: '1'
status: public
title: An abstraction-refinement methodology for reasoning about network games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1000'
abstract:
- lang: eng
text: 'We study probabilistic models of natural images and extend the autoregressive
family of PixelCNN models by incorporating latent variables. Subsequently, we
describe two new generative image models that exploit different image transformations
as latent variables: a quantized grayscale view of the image or a multi-resolution
image pyramid. The proposed models tackle two known shortcomings of existing PixelCNN
models: 1) their tendency to focus on low-level image details, while largely ignoring
high-level image information, such as object shapes, and 2) their computationally
costly procedure for image sampling. We experimentally demonstrate benefits of
our LatentPixelCNN models, in particular showing that they produce much more realistically
looking image samples than previous state-of-the-art probabilistic models. '
acknowledgement: We thank Tim Salimans for spotting a mistake in our preliminary arXiv
manuscript. This work was funded by the European Research Council under the European
Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.
article_processing_charge: No
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Lampert C. PixelCNN models with auxiliary variables for natural
image modeling. In: 34th International Conference on Machine Learning.
Vol 70. JMLR; 2017:1905-1914.'
apa: 'Kolesnikov, A., & Lampert, C. (2017). PixelCNN models with auxiliary variables
for natural image modeling. In 34th International Conference on Machine Learning
(Vol. 70, pp. 1905–1914). Sydney, Australia: JMLR.'
chicago: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary
Variables for Natural Image Modeling.” In 34th International Conference on
Machine Learning, 70:1905–14. JMLR, 2017.
ieee: A. Kolesnikov and C. Lampert, “PixelCNN models with auxiliary variables for
natural image modeling,” in 34th International Conference on Machine Learning,
Sydney, Australia, 2017, vol. 70, pp. 1905–1914.
ista: 'Kolesnikov A, Lampert C. 2017. PixelCNN models with auxiliary variables for
natural image modeling. 34th International Conference on Machine Learning. ICML:
International Conference on Machine Learning vol. 70, 1905–1914.'
mla: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary
Variables for Natural Image Modeling.” 34th International Conference on Machine
Learning, vol. 70, JMLR, 2017, pp. 1905–14.
short: A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine
Learning, JMLR, 2017, pp. 1905–1914.
conference:
end_date: 2017-08-11
location: Sydney, Australia
name: 'ICML: International Conference on Machine Learning'
start_date: 2017-08-06
date_created: 2018-12-11T11:49:37Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-22T09:50:41Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1612.08185'
isi:
- '000683309501102'
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.08185
month: '08'
oa: 1
oa_version: Submitted Version
page: 1905 - 1914
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: 34th International Conference on Machine Learning
publication_identifier:
isbn:
- 978-151085514-4
publication_status: published
publisher: JMLR
publist_id: '6398'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PixelCNN models with auxiliary variables for natural image modeling
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 70
year: '2017'
...
---
_id: '998'
abstract:
- lang: eng
text: 'A major open problem on the road to artificial intelligence is the development
of incrementally learning systems that learn about more and more concepts over
time from a stream of data. In this work, we introduce a new training strategy,
iCaRL, that allows learning in such a class-incremental way: only the training
data for a small number of classes has to be present at the same time and new
classes can be added progressively. iCaRL learns strong classifiers and a data
representation simultaneously. This distinguishes it from earlier works that were
fundamentally limited to fixed data representations and therefore incompatible
with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet
ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period
of time where other strategies quickly fail. '
article_processing_charge: No
author:
- first_name: Sylvestre Alvise
full_name: Rebuffi, Sylvestre Alvise
last_name: Rebuffi
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. iCaRL: Incremental classifier
and representation learning. In: Vol 2017. IEEE; 2017:5533-5542. doi:10.1109/CVPR.2017.587'
apa: 'Rebuffi, S. A., Kolesnikov, A., Sperl, G., & Lampert, C. (2017). iCaRL:
Incremental classifier and representation learning (Vol. 2017, pp. 5533–5542).
Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States: IEEE. https://doi.org/10.1109/CVPR.2017.587'
chicago: 'Rebuffi, Sylvestre Alvise, Alexander Kolesnikov, Georg Sperl, and Christoph
Lampert. “ICaRL: Incremental Classifier and Representation Learning,” 2017:5533–42.
IEEE, 2017. https://doi.org/10.1109/CVPR.2017.587.'
ieee: 'S. A. Rebuffi, A. Kolesnikov, G. Sperl, and C. Lampert, “iCaRL: Incremental
classifier and representation learning,” presented at the CVPR: Computer Vision
and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 5533–5542.'
ista: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. 2017. iCaRL: Incremental classifier
and representation learning. CVPR: Computer Vision and Pattern Recognition vol.
2017, 5533–5542.'
mla: 'Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation
Learning. Vol. 2017, IEEE, 2017, pp. 5533–42, doi:10.1109/CVPR.2017.587.'
short: S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
date_created: 2018-12-11T11:49:37Z
date_published: 2017-04-14T00:00:00Z
date_updated: 2023-09-22T09:51:58Z
day: '14'
department:
- _id: ChLa
- _id: ChWo
doi: 10.1109/CVPR.2017.587
ec_funded: 1
external_id:
isi:
- '000418371405066'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.07725
month: '04'
oa: 1
oa_version: Submitted Version
page: 5533 - 5542
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6400'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'iCaRL: Incremental classifier and representation learning'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '990'
abstract:
- lang: eng
text: Assortative mating is an important driver of speciation in populations with
gene flow and is predicted to evolve under certain conditions in few-locus models.
However, the evolution of assortment is less understood for mating based on quantitative
traits, which are often characterized by high genetic variability and extensive
linkage disequilibrium between trait loci. We explore this scenario for a two-deme
model with migration, by considering a single polygenic trait subject to divergent
viability selection across demes, as well as assortative mating and sexual selection
within demes, and investigate how trait divergence is shaped by various evolutionary
forces. Our analysis reveals the existence of sharp thresholds of assortment strength,
at which divergence increases dramatically. We also study the evolution of assortment
via invasion of modifiers of mate discrimination and show that the ES assortment
strength has an intermediate value under a range of migration-selection parameters,
even in diverged populations, due to subtle effects which depend sensitively on
the extent of phenotypic variation within these populations. The evolutionary
dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal
models. We further investigate the sensitivity of our results to the assumptions
of the hypergeometric model, using individual-based simulations.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- 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: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a
polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252
apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative
mating in a polygenic trait model of speciation with gene flow. Evolution;
International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252
chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.
ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow,” Evolution; International
Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493,
2017.
ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 71(6), 1478–1493.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell,
2017, pp. 1478–93, doi:10.1111/evo.13252.
short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution
71 (2017) 1478–1493.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:55:13Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13252
ec_funded: 1
external_id:
isi:
- '000403014800005'
pmid:
- '28419447'
file:
- access_level: open_access
checksum: 6d4c38cb1347fd43620d1736c6df5c79
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6329'
file_name: 2017_Evolution_Sachdeva_supplement.pdf
file_size: 625260
relation: main_file
- access_level: open_access
checksum: f1d90dd8831b44baf49b4dd176f263af
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6330'
file_name: 2017_Evolution_Sachdeva_article.pdf
file_size: 520110
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: '1478 - 1493 '
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6409'
pubrep_id: '977'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence and evolution of assortative mating in a polygenic trait model of
speciation with gene flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '988'
abstract:
- lang: eng
text: The current-phase relation (CPR) of a Josephson junction (JJ) determines how
the supercurrent evolves with the superconducting phase difference across the
junction. Knowledge of the CPR is essential in order to understand the response
of a JJ to various external parameters. Despite the rising interest in ultraclean
encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we
use a fully gate-tunable graphene superconducting quantum intereference device
(SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in
the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently
controlling the critical current of the JJs, we can operate the SQUID either in
a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us
to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found
to be skewed, deviating significantly from a sinusoidal form. The skewness can
be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance
oscillations of the ballistic graphene cavity. We compare our experiments with
tight-binding calculations that include realistic graphene-superconductor interfaces
and find a good qualitative agreement.
article_processing_charge: No
author:
- first_name: Gaurav
full_name: Nanda, Gaurav
last_name: Nanda
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Péter
full_name: Rakyta, Péter
last_name: Rakyta
- first_name: Andor
full_name: Kormányos, Andor
last_name: Kormányos
- first_name: Reinhold
full_name: Kleiner, Reinhold
last_name: Kleiner
- first_name: Dieter
full_name: Koelle, Dieter
last_name: Koelle
- first_name: Kazuo
full_name: Watanabe, Kazuo
last_name: Watanabe
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Lieven
full_name: Vandersypen, Lieven
last_name: Vandersypen
- first_name: Srijit
full_name: Goswami, Srijit
last_name: Goswami
citation:
ama: Nanda G, Aguilera Servin JL, Rakyta P, et al. Current-phase relation of ballistic
graphene Josephson junctions. Nano Letters. 2017;17(6):3396-3401. doi:10.1021/acs.nanolett.7b00097
apa: Nanda, G., Aguilera Servin, J. L., Rakyta, P., Kormányos, A., Kleiner, R.,
Koelle, D., … Goswami, S. (2017). Current-phase relation of ballistic graphene
Josephson junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b00097
chicago: Nanda, Gaurav, Juan L Aguilera Servin, Péter Rakyta, Andor Kormányos, Reinhold
Kleiner, Dieter Koelle, Kazuo Watanabe, Takashi Taniguchi, Lieven Vandersypen,
and Srijit Goswami. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b00097.
ieee: G. Nanda et al., “Current-phase relation of ballistic graphene Josephson
junctions,” Nano Letters, vol. 17, no. 6. American Chemical Society, pp.
3396–3401, 2017.
ista: Nanda G, Aguilera Servin JL, Rakyta P, Kormányos A, Kleiner R, Koelle D, Watanabe
K, Taniguchi T, Vandersypen L, Goswami S. 2017. Current-phase relation of ballistic
graphene Josephson junctions. Nano Letters. 17(6), 3396–3401.
mla: Nanda, Gaurav, et al. “Current-Phase Relation of Ballistic Graphene Josephson
Junctions.” Nano Letters, vol. 17, no. 6, American Chemical Society, 2017,
pp. 3396–401, doi:10.1021/acs.nanolett.7b00097.
short: G. Nanda, J.L. Aguilera Servin, P. Rakyta, A. Kormányos, R. Kleiner, D. Koelle,
K. Watanabe, T. Taniguchi, L. Vandersypen, S. Goswami, Nano Letters 17 (2017)
3396–3401.
date_created: 2018-12-11T11:49:33Z
date_published: 2017-05-05T00:00:00Z
date_updated: 2023-09-22T09:56:21Z
day: '05'
ddc:
- '621'
department:
- _id: NanoFab
doi: 10.1021/acs.nanolett.7b00097
external_id:
isi:
- '000403631600011'
file:
- access_level: open_access
checksum: 22021daa90cf13b01becd776838acb7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:50Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5037'
file_name: IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf
file_size: 508638
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '6'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 3396 - 3401
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6412'
pubrep_id: '826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Current-phase relation of ballistic graphene Josephson junctions
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2017'
...
---
_id: '993'
abstract:
- lang: eng
text: In real-world applications, observations are often constrained to a small
fraction of a system. Such spatial subsampling can be caused by the inaccessibility
or the sheer size of the system, and cannot be overcome by longer sampling. Spatial
subsampling can strongly bias inferences about a system’s aggregated properties.
To overcome the bias, we derive analytically a subsampling scaling framework that
is applicable to different observables, including distributions of neuronal avalanches,
of number of people infected during an epidemic outbreak, and of node degrees.
We demonstrate how to infer the correct distributions of the underlying full system,
how to apply it to distinguish critical from subcritical systems, and how to disentangle
subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal
avalanche models and to recordings from developing neural networks. We show that
only mature, but not young networks follow power-law scaling, indicating self-organization
to criticality during development.
article_number: '15140'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Anna
full_name: Levina (Martius), Anna
id: 35AF8020-F248-11E8-B48F-1D18A9856A87
last_name: Levina (Martius)
- first_name: Viola
full_name: Priesemann, Viola
last_name: Priesemann
citation:
ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications.
2017;8. doi:10.1038/ncomms15140
apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140
chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.
ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications.
8, 15140.
mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140.
short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-05-04T00:00:00Z
date_updated: 2023-09-22T09:54:07Z
day: '04'
ddc:
- '005'
- '571'
department:
- _id: GaTk
- _id: JoCs
doi: 10.1038/ncomms15140
ec_funded: 1
external_id:
isi:
- '000400560700001'
file:
- access_level: open_access
checksum: 9880212f8c4c53404c7c6fbf9023c53a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:05Z
date_updated: 2020-07-14T12:48:19Z
file_id: '5122'
file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf
file_size: 746224
relation: main_file
file_date_updated: 2020-07-14T12:48:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '05'
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: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6406'
pubrep_id: '819'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subsampling scaling
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '995'
abstract:
- lang: eng
text: Recently it was shown that an impurity exchanging orbital angular momentum
with a surrounding bath can be described in terms of the angulon quasiparticle
[Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor
dressed by a many-particle field of boson excitations, and can be formed out of,
for example, a molecule or a nonspherical atom in superfluid helium, or out of
an electron coupled to lattice phonons or a Bose condensate. Here we develop an
approach to the angulon based on the path-integral formalism, which sets the ground
for a systematic, perturbative treatment of the angulon problem. The resulting
perturbation series can be interpreted in terms of Feynman diagrams, from which,
in turn, one can derive a set of diagrammatic rules. These rules extend the machinery
of the graphical theory of angular momentum - well known from theoretical atomic
spectroscopy - to the case where an environment with an infinite number of degrees
of freedom is present. In particular, we show that each diagram can be interpreted
as a 'skeleton', which enforces angular momentum conservation, dressed by an additional
many-body contribution. This connection between the angulon theory and the graphical
theory of angular momentum is particularly important as it allows to systematically
and substantially simplify the analytical representation of each diagram. In order
to exemplify the technique, we calculate the 1- and 2-loop contributions to the
angulon self-energy, the spectral function, and the quasiparticle weight. The
diagrammatic theory we develop paves the way to investigate next-to-leading order
quantities in a more compact way compared to the variational approaches.
article_number: '085410'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting
with a many-particle environment. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410
apa: Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum
impurities interacting with a many-particle environment. Physical Review B
- Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410
chicago: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital
Quantum Impurities Interacting with a Many-Particle Environment.” Physical
Review B - Condensed Matter and Materials Physics. American Physical Society,
2017. https://doi.org/10.1103/PhysRevB.96.085410.
ieee: G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017.
ista: Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment. Physical Review B - Condensed Matter
and Materials Physics. 96(8), 085410.
mla: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum
Impurities Interacting with a Many-Particle Environment.” Physical Review B
- Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American
Physical Society, 2017, doi:10.1103/PhysRevB.96.085410.
short: G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials
Physics 96 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-08-07T00:00:00Z
date_updated: 2023-09-22T09:53:17Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.96.085410
external_id:
isi:
- '000407017100009'
intvolume: ' 96'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02616
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic approach to orbital quantum impurities interacting with a many-particle
environment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '989'
abstract:
- lang: eng
text: We present a generalized optimal transport model in which the mass-preserving
constraint for the L2-Wasserstein distance is relaxed by introducing a source
term in the continuity equation. The source term is also incorporated in the path
energy by means of its squared L2-norm in time of a functional with linear growth
in space. This extension of the original transport model enables local density
modulations, which is a desirable feature in applications such as image warping
and blending. A key advantage of the use of a functional with linear growth in
space is that it allows for singular sources and sinks, which can be supported
on points or lines. On a technical level, the L2-norm in time ensures a disintegration
of the source in time, which we use to obtain the well-posedness of the model
and the existence of geodesic paths. The numerical discretization is based on
the proximal splitting approach [18] and selected numerical test cases show the
potential of the proposed approach. Furthermore, the approach is applied to the
warping and blending of textures.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Martin
full_name: Rumpf, Martin
last_name: Rumpf
- first_name: Stefan
full_name: Simon, Stefan
last_name: Simon
citation:
ama: 'Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation.
In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577.
doi:10.1007/978-3-319-58771-4_45'
apa: 'Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing
with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.)
(Vol. 10302, pp. 563–577). Presented at the SSVM: Scale Space and Variational
Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45'
chicago: Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing
with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm
Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45.
ieee: J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity
modulation,” presented at the SSVM: Scale Space and Variational Methods in Computer
Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577.
ista: Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity
modulation. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS,
vol. 10302, 563–577.
mla: Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation.
Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45.
short: J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.),
Springer, 2017, pp. 563–577.
conference:
end_date: 2017-06-08
location: Kolding, Denmark
name: 'SSVM: Scale Space and Variational Methods in Computer Vision'
start_date: 2017-06-04
date_created: 2018-12-11T11:49:34Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T09:55:50Z
day: '18'
department:
- _id: JaMa
doi: 10.1007/978-3-319-58771-4_45
editor:
- first_name: François
full_name: Lauze, François
last_name: Lauze
- first_name: Yiqiu
full_name: Dong, Yiqiu
last_name: Dong
- first_name: Anders
full_name: Bjorholm Dahl, Anders
last_name: Bjorholm Dahl
external_id:
isi:
- '000432210900045'
intvolume: ' 10302'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 563 - 577
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6410'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transport based image morphing with intensity modulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10302
year: '2017'
...
---
_id: '994'
abstract:
- lang: eng
text: The formation of vortices is usually considered to be the main mechanism of
angular momentum disposal in superfluids. Recently, it was predicted that a superfluid
can acquire angular momentum via an alternative, microscopic route -- namely,
through interaction with rotating impurities, forming so-called `angulon quasiparticles'
[Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to
transfer of a small number of angular momentum quanta from the impurity to the
superfluid, as opposed to vortex instabilities, where angular momentum is quantized
in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules)
represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically
3D as well, as opposed to a merely planar rotation which is inherent to vortices.
Herein we show that the angulon theory can explain the anomalous broadening of
the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid
helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities
in experiment.
article_processing_charge: No
author:
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Cherepanov I, Lemeshko M. Fingerprints of angulon instabilities in the spectra
of matrix-isolated molecules. Physical Review Materials. 2017;1(3). doi:10.1103/PhysRevMaterials.1.035602
apa: Cherepanov, I., & Lemeshko, M. (2017). Fingerprints of angulon instabilities
in the spectra of matrix-isolated molecules. Physical Review Materials.
American Physical Society. https://doi.org/10.1103/PhysRevMaterials.1.035602
chicago: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities
in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevMaterials.1.035602.
ieee: I. Cherepanov and M. Lemeshko, “Fingerprints of angulon instabilities in the
spectra of matrix-isolated molecules,” Physical Review Materials, vol.
1, no. 3. American Physical Society, 2017.
ista: Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the
spectra of matrix-isolated molecules. Physical Review Materials. 1(3).
mla: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities
in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials,
vol. 1, no. 3, American Physical Society, 2017, doi:10.1103/PhysRevMaterials.1.035602.
short: I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-08-08T00:00:00Z
date_updated: 2023-09-22T09:53:42Z
day: '08'
department:
- _id: MiLe
doi: 10.1103/PhysRevMaterials.1.035602
ec_funded: 1
external_id:
isi:
- '000416564000004'
intvolume: ' 1'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.09220
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Materials
publication_status: published
publisher: American Physical Society
publist_id: '6405'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1
year: '2017'
...
---
_id: '991'
abstract:
- lang: eng
text: Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for
lysosome fusion, but its function at fast synapses is controversial. The paper
by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held
in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains,
resulting in reliable and temporally precise high-frequency transmission. Thus,
a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse.
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696.
doi:10.1016/j.neuron.2017.05.011'
apa: 'Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011'
chicago: 'Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.”
Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.'
ieee: 'C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron,
vol. 94, no. 4. Elsevier, pp. 694–696, 2017.'
ista: 'Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4),
694–696.'
mla: 'Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron,
vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011.'
short: C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2023-09-22T09:54:37Z
day: '17'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2017.05.011
external_id:
isi:
- '000401415100002'
intvolume: ' 94'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 694 - 696
publication: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '6408'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Synaptotagmins: That’s why so many'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 94
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- 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: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T10:01:17Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
file:
- access_level: open_access
checksum: 59cdd4400fb41280122d414fea971546
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:49Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5306'
file_name: IST-2017-841-v1+1_elife-25192-v2.pdf
file_size: 2441529
relation: main_file
- access_level: open_access
checksum: b69024880558b858eb8c5d47a92b6377
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5307'
file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf
file_size: 3752660
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- 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: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-22T10:00:49Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
file:
- access_level: open_access
checksum: 29a1b5db458048d3bd5c67e0e2a56818
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:14Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5064'
file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf
file_size: 998157
relation: main_file
- access_level: open_access
checksum: 7b78401e52a576cf3e6bbf8d0abadc17
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:15Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5065'
file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf
file_size: 9715993
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
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
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6459'
pubrep_id: '864'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '962'
abstract:
- lang: eng
text: 'We present a new algorithm for model counting of a class of string constraints.
In addition to the classic operation of concatenation, our class includes some
recursively defined operations such as Kleene closure, and replacement of substrings.
Additionally, our class also includes length constraints on the string expressions,
which means, by requiring reasoning about numbers, that we face a multi-sorted
logic. In the end, our string constraints are motivated by their use in programming
for web applications. Our algorithm comprises two novel features: the ability
to use a technique of (1) partial derivatives for constraints that are already
in a solved form, i.e. a form where its (string) satisfiability is clearly displayed,
and (2) non-progression, where cyclic reasoning in the reduction process may be
terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally
compare our model counter with two recent works on model counting of similar constraints,
SMC [18] and ABC [5], to demonstrate its superior performance.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Minh
full_name: Trinh, Minh
last_name: Trinh
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: Joxan
full_name: Jaffar, Joxan
last_name: Jaffar
citation:
ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings.
In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21'
apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined
strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented
at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21'
chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined
Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer,
2017. https://doi.org/10.1007/978-3-319-63390-9_21.
ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined
strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany,
2017, vol. 10427, pp. 399–418.'
ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings.
CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.'
mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings.
Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418,
doi:10.1007/978-3-319-63390-9_21.
short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 399–418.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:49:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:58:02Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63390-9_21
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
isi:
- '000431900900021'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 399 - 418
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6443'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model counting for recursively-defined strings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10427
year: '2017'
...
---
_id: '953'
abstract:
- lang: eng
text: 'The role of natural selection in the evolution of adaptive phenotypes has
undergone constant probing by evolutionary biologists, employing both theoretical
and empirical approaches. As Darwin noted, natural selection can act together
with other processes, including random changes in the frequencies of phenotypic
differences that are not under strong selection, and changes in the environment,
which may reflect evolutionary changes in the organisms themselves. As understanding
of genetics developed after 1900, the new genetic discoveries were incorporated
into evolutionary biology. The resulting general principles were summarized by
Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine
how recent advances in genetics, developmental biology and molecular biology,
including epigenetics, relate to today''s understanding of the evolution of adaptations.
We illustrate how careful genetic studies have repeatedly shown that apparently
puzzling results in a wide diversity of organisms involve processes that are consistent
with neo-Darwinism. They do not support important roles in adaptation for processes
such as directed mutation or the inheritance of acquired characters, and therefore
no radical revision of our understanding of the mechanism of adaptive evolution
is needed.'
article_number: '20162864'
article_processing_charge: No
author:
- first_name: Deborah
full_name: Charlesworth, Deborah
last_name: Charlesworth
- 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: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences.
2017;284(1855). doi:10.1098/rspb.2016.2864
apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources
of adaptive evolution. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864
chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The
Sources of Adaptive Evolution.” Proceedings of the Royal Society of London
Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.
ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive
evolution,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 284, no. 1855. Royal Society, The, 2017.
ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855),
20162864.
mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 284, no.
1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.
short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society
of London Series B Biological Sciences 284 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-22T10:01:48Z
day: '31'
department:
- _id: NiBa
doi: 10.1098/rspb.2016.2864
external_id:
isi:
- '000405148800021'
pmid:
- '28566483'
intvolume: ' 284'
isi: 1
issue: '1855'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6462'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sources of adaptive evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 284
year: '2017'
...