---
_id: '2245'
abstract:
- lang: eng
text: 'Exogenous application of biologically important molecules for plant growth
promotion and/or regulation is very common both in plant research and horticulture.
Plant hormones such as auxins and cytokinins are classes of compounds which are
often applied exogenously. Nevertheless, plants possess a well-established machinery
to regulate the active pool of exogenously applied compounds by converting them
to metabolites and conjugates. Consequently, it is often very useful to know the
in vivo status of applied compounds to connect them with some of the regulatory
events in plant developmental processes. The in vivo status of applied compounds
can be measured by incubating plants with radiolabeled compounds, followed by
extraction, purification, and HPLC metabolic profiling of plant extracts. Recently
we have used this method to characterize the intracellularly localized PIN protein,
PIN5. Here we explain the method in detail, with a focus on general application. '
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the
in vivo status of exogenously applied auxins: A HPLC-based method to characterize
the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds.
Plant Chemical Genomics. Vol 1056. Methods in Molecular Biology. Springer;
2014:255-264. doi:10.1007/978-1-62703-592-7_23'
apa: 'Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., & Friml,
J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based
method to characterize the intracellularly localized auxin transporters. In G.
Hicks & S. Robert (Eds.), Plant Chemical Genomics (Vol. 1056, pp. 255–264).
Springer. https://doi.org/10.1007/978-1-62703-592-7_23'
chicago: 'Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and
Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based
Method to Characterize the Intracellularly Localized Auxin Transporters.” In Plant
Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64.
Methods in Molecular Biology. Springer, 2014. https://doi.org/10.1007/978-1-62703-592-7_23.'
ieee: 'S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml,
“Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method
to characterize the intracellularly localized auxin transporters,” in Plant
Chemical Genomics, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014,
pp. 255–264.'
ista: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing
the in vivo status of exogenously applied auxins: A HPLC-based method to characterize
the intracellularly localized auxin transporters. In: Plant Chemical Genomics.
Methods in Molecular Biology, vol. 1056, 255–264.'
mla: 'Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins:
A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.”
Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, vol.
1056, Springer, 2014, pp. 255–64, doi:10.1007/978-1-62703-592-7_23.'
short: S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:,
G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.
date_created: 2018-12-11T11:56:32Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-1-62703-592-7_23
editor:
- first_name: Glenn
full_name: Hicks, Glenn
last_name: Hicks
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
intvolume: ' 1056'
language:
- iso: eng
month: '01'
oa_version: None
page: 255 - 264
publication: Plant Chemical Genomics
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '4704'
quality_controlled: '1'
scopus_import: 1
series_title: Methods in Molecular Biology
status: public
title: 'Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method
to characterize the intracellularly localized auxin transporters'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1056
year: '2014'
...
---
_id: '2246'
abstract:
- lang: eng
text: 'Muller games are played by two players moving a token along a graph; the
winner is determined by the set of vertices that occur infinitely often. The central
algorithmic problem is to compute the winning regions for the players. Different
classes and representations of Muller games lead to problems of varying computational
complexity. One such class are parity games; these are of particular significance
in computational complexity, as they remain one of the few combinatorial problems
known to be in NP ∩ co-NP but not known to be in P. We show that winning regions
for a Muller game can be determined from the alternating structure of its traps.
To every Muller game we then associate a natural number that we call its trap
depth; this parameter measures how complicated the trap structure is. We present
algorithms for parity games that run in polynomial time for graphs of bounded
trap depth, and in general run in time exponential in the trap depth. '
author:
- first_name: Andrey
full_name: Grinshpun, Andrey
last_name: Grinshpun
- first_name: Pakawat
full_name: Phalitnonkiat, Pakawat
last_name: Phalitnonkiat
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
- first_name: Andrei
full_name: Tarfulea, Andrei
last_name: Tarfulea
citation:
ama: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller
and parity games. Theoretical Computer Science. 2014;521:73-91. doi:10.1016/j.tcs.2013.11.032
apa: Grinshpun, A., Phalitnonkiat, P., Rubin, S., & Tarfulea, A. (2014). Alternating
traps in Muller and parity games. Theoretical Computer Science. Elsevier.
https://doi.org/10.1016/j.tcs.2013.11.032
chicago: Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea.
“Alternating Traps in Muller and Parity Games.” Theoretical Computer Science.
Elsevier, 2014. https://doi.org/10.1016/j.tcs.2013.11.032.
ieee: A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps
in Muller and parity games,” Theoretical Computer Science, vol. 521. Elsevier,
pp. 73–91, 2014.
ista: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps
in Muller and parity games. Theoretical Computer Science. 521, 73–91.
mla: Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” Theoretical
Computer Science, vol. 521, Elsevier, 2014, pp. 73–91, doi:10.1016/j.tcs.2013.11.032.
short: A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer
Science 521 (2014) 73–91.
date_created: 2018-12-11T11:56:33Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:56:16Z
day: '13'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2013.11.032
intvolume: ' 521'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.3777
month: '02'
oa: 1
oa_version: Submitted Version
page: 73 - 91
publication: Theoretical Computer Science
publication_identifier:
issn:
- '03043975'
publication_status: published
publisher: Elsevier
publist_id: '4703'
quality_controlled: '1'
scopus_import: 1
status: public
title: Alternating traps in Muller and parity games
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 521
year: '2014'
...
---
_id: '2248'
abstract:
- lang: eng
text: 'Avian forelimb digit homology remains one of the standard themes in comparative
biology and EvoDevo research. In order to resolve the apparent contradictions
between embryological and paleontological evidence a variety of hypotheses have
been presented in recent years. The proposals range from excluding birds from
the dinosaur clade, to assignments of homology by different criteria, or even
assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail:
the frame shift hypothesis and the pyramid reduction hypothesis. While the former
postulates a homeotic shift of digit identities, the latter argues for a gradual
bilateral reduction of phalanges and digits. Here we present a new model that
integrates elements from both hypotheses with the existing experimental and fossil
evidence. We start from the main feature common to both earlier concepts, the
initiating ontogenetic event: reduction and loss of the anterior-most digit. It
is proposed that a concerted mechanism of molecular regulation and developmental
mechanics is capable of shifting the boundaries of hoxD expression in embryonic
forelimb buds as well as changing the digit phenotypes. Based on a distinction
between positional (topological) and compositional (phenotypic) homology criteria,
we argue that the identity of the avian digits is II, III, IV, despite a partially
altered phenotype. Finally, we introduce an alternative digit reduction scheme
that reconciles the current fossil evidence with the presented molecular-morphogenetic
model. Our approach identifies specific experiments that allow to test whether
gene expression can be shifted and digit phenotypes can be altered by induced
digit loss or digit gain.'
author:
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Brian
full_name: Metscher, Brian
last_name: Metscher
- first_name: Gerd
full_name: Müller, Gerd
last_name: Müller
citation:
ama: 'Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach
to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 2014;322(1):1-12. doi:10.1002/jez.b.22545'
apa: 'Capek, D., Metscher, B., & Müller, G. (2014). Thumbs down: A molecular-morphogenetic
approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. Wiley-Blackwell. https://doi.org/10.1002/jez.b.22545'
chicago: 'Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic
Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/jez.b.22545.'
ieee: 'D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic
approach to avian digit homology,” Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution, vol. 322, no. 1. Wiley-Blackwell, pp.
1–12, 2014.'
ista: 'Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic
approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 322(1), 1–12.'
mla: 'Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to
Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and
Developmental Evolution, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12,
doi:10.1002/jez.b.22545.'
short: 'D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution 322 (2014) 1–12.'
date_created: 2018-12-11T11:56:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:16Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/jez.b.22545
intvolume: ' 322'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 12
publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution'
publication_identifier:
issn:
- '15525007'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4701'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Thumbs down: A molecular-morphogenetic approach to avian digit homology'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 322
year: '2014'
...
---
_id: '2249'
abstract:
- lang: eng
text: The unfolded protein response (UPR) is a signaling network triggered by overload
of protein-folding demand in the endoplasmic reticulum (ER), a condition termed
ER stress. The UPR is critical for growth and development; nonetheless, connections
between the UPR and other cellular regulatory processes remain largely unknown.
Here, we identify a link between the UPR and the phytohormone auxin, a master
regulator of plant physiology. We show that ER stress triggers down-regulation
of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate
that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects
in the auxin response and levels. These data not only support that the plant IRE1
is required for auxin homeostasis, they also reveal a species-specific feature
of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation
is reduced in mutants of ER-localized auxin transporters, including PIN5, we define
a long-neglected biological significance of ER-based auxin regulation. We further
examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5
triple mutant enhances defects of UPR activation and auxin homeostasis in ire1
or pin5. Our results imply that the plant UPR has evolved a hormone-dependent
strategy for coordinating ER function with physiological processes.
author:
- first_name: Yani
full_name: Chen, Yani
last_name: Chen
- first_name: Kyaw
full_name: Aung, Kyaw
last_name: Aung
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Kathryn
full_name: Walicki, Kathryn
last_name: Walicki
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Federica
full_name: Brandizzí, Federica
last_name: Brandizzí
citation:
ama: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation
of the unfolded protein response and auxin signaling. Plant Journal. 2014;77(1):97-107.
doi:10.1111/tpj.12373
apa: Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., & Brandizzí, F.
(2014). Inter-regulation of the unfolded protein response and auxin signaling.
Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12373
chicago: Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica
Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.”
Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12373.
ieee: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation
of the unfolded protein response and auxin signaling,” Plant Journal, vol.
77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.
ista: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation
of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107.
mla: Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin
Signaling.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107,
doi:10.1111/tpj.12373.
short: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal
77 (2014) 97–107.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12373
intvolume: ' 77'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/
month: '01'
oa: 1
oa_version: Submitted Version
page: 97 - 107
publication: Plant Journal
publication_identifier:
issn:
- '09607412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4699'
quality_controlled: '1'
scopus_import: 1
status: public
title: Inter-regulation of the unfolded protein response and auxin signaling
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2014'
...
---
_id: '2250'
abstract:
- lang: eng
text: The genome sequences of new viruses often contain many "orphan"
or "taxon-specific" proteins apparently lacking homologs. However, because
viral proteins evolve very fast, commonly used sequence similarity detection methods
such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA
viruses characterized as "genus specific" by BLAST. More powerful methods
developed recently, such as HHblits or HHpred (available through web-based, user-friendly
interfaces), could detect distant homologs of a quarter of these proteins, suggesting
that these methods should be used to annotate viral genomes. In-depth manual analyses
of a subset of the remaining sequences, guided by contextual information such
as taxonomy, gene order, or domain cooccurrence, identified distant homologs of
another third. Thus, a combination of powerful automated methods and manual analyses
can uncover distant homologs of many proteins thought to be orphans. We expect
these methodological results to be also applicable to cellular organisms, since
they generally evolve much more slowly than RNA viruses. As an application, we
reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We
could identify homologs of most of its proteins thought to be orphans; in each
case, identifying homologs provided functional clues. We discovered that CBPV
encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase;
a putative membrane protein, SP24, with homologs in unrelated insect viruses and
insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses,
blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found
in negeviruses. SP24 and ORF2 are probably major structural components of the
virionsd.
author:
- first_name: Durga
full_name: Kuchibhatla, Durga
last_name: Kuchibhatla
- first_name: Westley
full_name: Sherman, Westley
last_name: Sherman
- first_name: Betty
full_name: Chung, Betty
last_name: Chung
- first_name: Shelley
full_name: Cook, Shelley
last_name: Cook
- first_name: Georg
full_name: Schneider, Georg
id: 329095A0-F248-11E8-B48F-1D18A9856A87
last_name: Schneider
- first_name: Birgit
full_name: Eisenhaber, Birgit
last_name: Eisenhaber
- first_name: David
full_name: Karlin, David
last_name: Karlin
citation:
ama: Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search
methods and in-depth manual analyses can identify remote homologs in many apparently
“orphan” viral proteins. Journal of Virology. 2014;88(1):10-20. doi:10.1128/JVI.02595-13
apa: Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber,
B., & Karlin, D. (2014). Powerful sequence similarity search methods and in-depth
manual analyses can identify remote homologs in many apparently “orphan” viral
proteins. Journal of Virology. ASM. https://doi.org/10.1128/JVI.02595-13
chicago: Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider,
Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods
and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
Viral Proteins.” Journal of Virology. ASM, 2014. https://doi.org/10.1128/JVI.02595-13.
ieee: D. Kuchibhatla et al., “Powerful sequence similarity search methods
and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’
viral proteins,” Journal of Virology, vol. 88, no. 1. ASM, pp. 10–20, 2014.
ista: Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin
D. 2014. Powerful sequence similarity search methods and in-depth manual analyses
can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal
of Virology. 88(1), 10–20.
mla: Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and
In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
Viral Proteins.” Journal of Virology, vol. 88, no. 1, ASM, 2014, pp. 10–20,
doi:10.1128/JVI.02595-13.
short: D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber,
D. Karlin, Journal of Virology 88 (2014) 10–20.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
ddc:
- '570'
department:
- _id: MD
doi: 10.1128/JVI.02595-13
file:
- access_level: open_access
checksum: 2c121b5e884992dfec5605bdf4e659da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:43Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5029'
file_name: IST-2016-417-v1+1_J._Virol.-2014-Kuchibhatla-10-20.pdf
file_size: 825756
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 88'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 10 - 20
publication: Journal of Virology
publication_identifier:
issn:
- 0022538X
publication_status: published
publisher: ASM
publist_id: '4698'
pubrep_id: '417'
quality_controlled: '1'
scopus_import: 1
status: public
title: Powerful sequence similarity search methods and in-depth manual analyses can
identify remote homologs in many apparently "orphan" viral proteins
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2014'
...
---
_id: '2251'
abstract:
- lang: eng
text: 'Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated
to be involved in memory consolidation. However, more recent work has investigated
SWRs that occur during active waking behaviour: findings that suggest that SWRs
may also play a role in cell assembly strengthening or spatial working memory.
Do such theories of SWR function apply to animal learning? This review discusses
how general theories linking SWRs to memory-related function may explain circuit
mechanisms related to rodent spatial learning and to the associated stabilization
of new cognitive maps.'
acknowledgement: CC BY 3.0
article_number: '20120528'
article_processing_charge: No
author:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: David
full_name: Dupret, David
last_name: Dupret
citation:
ama: Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London
Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528
apa: Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations
and learning-associated hippocampal maps. Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, The.
https://doi.org/10.1098/rstb.2012.0528
chicago: Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, The,
2014. https://doi.org/10.1098/rstb.2012.0528.
ieee: J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and
learning-associated hippocampal maps,” Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal
Society, The, 2014.
ista: Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences. 369(1635), 20120528.
mla: Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635,
20120528, Royal Society, The, 2014, doi:10.1098/rstb.2012.0528.
short: J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 369 (2014).
date_created: 2018-12-11T11:56:34Z
date_published: 2014-02-05T00:00:00Z
date_updated: 2021-01-12T06:56:18Z
day: '05'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1098/rstb.2012.0528
external_id:
pmid:
- '24366138'
file:
- access_level: open_access
checksum: 51beb33de71c9c19e0c205a20d206f9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:24Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5006'
file_name: IST-2016-527-v1+1_20120528.full.pdf
file_size: 771896
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 369'
issue: '1635'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
issn:
- '09628436'
publication_status: published
publisher: Royal Society, The
publist_id: '4697'
pubrep_id: '527'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sharp wave/ripple network oscillations and learning-associated hippocampal
maps
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 369
year: '2014'
...
---
_id: '2252'
abstract:
- lang: eng
text: The pattern of inheritance and mechanism of sex determination can have important
evolutionary consequences. We studied probabilistic sex determination in the ciliate
Tetrahymena thermophila, which was previously shown to cause evolution of skewed
sex ratios. We find that the genetic background alters the sex determination patterns
of mat alleles in heterozygotes and that allelic interaction can differentially
influence the expression probability of the 7 sexes. We quantify the dominance
relationships between several mat alleles and find that A-type alleles, which
specify sex I, are indeed recessive to B-type alleles, which are unable to specify
that sex. Our results provide additional support for the presence of modifier
loci and raise implications for the dynamics of sex ratios in populations of T.
thermophila.
article_processing_charge: No
author:
- first_name: Sujal
full_name: Phadke, Sujal
last_name: Phadke
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tuan
full_name: Pham, Tuan
last_name: Pham
- first_name: Stephanie
full_name: Pham, Stephanie
last_name: Pham
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance
relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal
of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
apa: Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic
background alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063
chicago: Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall.
“Genetic Background Alters Dominance Relationships between Mat Alleles in the
Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University
Press, 2014. https://doi.org/10.1093/jhered/est063.
ieee: S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background
alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press,
pp. 130–135, 2014.
ista: Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters
dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila.
Journal of Heredity. 105(1), 130–135.
mla: Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between
Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity,
vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
short: S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105
(2014) 130–135.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-08-25T14:45:42Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jhered/est063
intvolume: ' 105'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 130 - 135
publication: Journal of Heredity
publication_identifier:
issn:
- '00221503'
publication_status: published
publisher: Oxford University Press
publist_id: '4695'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic background alters dominance relationships between mat alleles in the
ciliate Tetrahymena Thermophila
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2014'
...
---
_id: '2253'
abstract:
- lang: eng
text: Plant growth is achieved predominantly by cellular elongation, which is thought
to be controlled on several levels by apoplastic auxin. Auxin export into the
apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN)
and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP)
classes; the latter were shown to depend on interaction with the FKBP42, TWISTED
DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical,
biochemical and cell biological analyses we demonstrate the importance of a putative
C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated
auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1
gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct)
show hypermorphic plant architecture, characterized by enhanced stem length and
leaf surface but reduced shoot branching. Greater hypocotyl length is the result
of enhanced cell elongation that correlates with reduced polar auxin transport
capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl
auxin accumulation, which is shown to result in elevated auxin-induced cell elongation
rates. Our data highlight the importance of C-terminal membrane anchoring for
TWD1 action, which is required for specific regulation of ABCB-mediated auxin
transport. These data support a model in which TWD1 controls lateral ABCB1-mediated
export into the apoplast, which is required for auxin-mediated cell elongation.
article_processing_charge: No
article_type: original
author:
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Daniel
full_name: Schenck, Daniel
last_name: Schenck
- first_name: Hartwig
full_name: Lüthen, Hartwig
last_name: Lüthen
- first_name: Alexander
full_name: Schulz, Alexander
last_name: Schulz
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its
in-plane membrane anchor leads to increased cell elongation and hypermorphic growth.
Plant Journal. 2014;77(1):108-118. doi:10.1111/tpj.12369
apa: Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., …
Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane
anchor leads to increased cell elongation and hypermorphic growth. Plant Journal.
Wiley-Blackwell. https://doi.org/10.1111/tpj.12369
chicago: Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel
Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression
of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell
Elongation and Hypermorphic Growth.” Plant Journal. Wiley-Blackwell, 2014.
https://doi.org/10.1111/tpj.12369.
ieee: A. Bailly et al., “Expression of TWISTED DWARF1 lacking its in-plane
membrane anchor leads to increased cell elongation and hypermorphic growth,” Plant
Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.
ista: Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml
J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane
anchor leads to increased cell elongation and hypermorphic growth. Plant Journal.
77(1), 108–118.
mla: Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane
Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant
Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:10.1111/tpj.12369.
short: A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz,
J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:18Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12369
intvolume: ' 77'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/tpj.12369
month: '01'
oa: 1
oa_version: Published Version
page: 108 - 118
project:
- _id: 256BDAB0-B435-11E9-9278-68D0E5697425
name: Innovationsförderung in der Grenzregion Österreich – Tschechische Republik
durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur
publication: Plant Journal
publication_identifier:
issn:
- '09607412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4694'
quality_controlled: '1'
scopus_import: 1
status: public
title: Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to
increased cell elongation and hypermorphic growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2014'
...
---
_id: '2254'
abstract:
- lang: eng
text: Theta-gamma network oscillations are thought to represent key reference signals
for information processing in neuronal ensembles, but the underlying synaptic
mechanisms remain unclear. To address this question, we performed whole-cell (WC)
patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in
the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials
at low frequency, consistent with sparse coding in the dentate gyrus. GCs were
exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs),
primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents
(IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence
with the field potential predominantly in the theta frequency band, whereas IPSCs
showed coherence primarily in the gamma range. Action potentials in GCs were phase
locked to network oscillations. Thus, theta-gamma-modulated synaptic currents
may provide a framework for sparse temporal coding of information in the dentate
gyrus.
author:
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- 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: Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal
granule cells in vivo define a mechanism for network oscillations. Neuron.
2014;81(1):140-152. doi:10.1016/j.neuron.2013.09.046
apa: Pernia-Andrade, A., & Jonas, P. M. (2014). Theta-gamma-modulated synaptic
currents in hippocampal granule cells in vivo define a mechanism for network oscillations.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.046
chicago: Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic
Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.09.046.
ieee: A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents
in hippocampal granule cells in vivo define a mechanism for network oscillations,”
Neuron, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.
ista: Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents
in hippocampal granule cells in vivo define a mechanism for network oscillations.
Neuron. 81(1), 140–152.
mla: Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic
Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.”
Neuron, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:10.1016/j.neuron.2013.09.046.
short: A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-08T00:00:00Z
date_updated: 2021-01-12T06:56:19Z
day: '08'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2013.09.046
ec_funded: 1
file:
- access_level: open_access
checksum: 438547cfcd9045a22f065f2019f07849
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:48Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4773'
file_name: IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf
file_size: 4373072
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 81'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 140 - 152
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '4692'
pubrep_id: '422'
quality_controlled: '1'
scopus_import: 1
status: public
title: Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo
define a mechanism for network oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2014'
...
---
_id: '2255'
abstract:
- lang: eng
text: Motivated by applications in biology, we present an algorithm for estimating
the length of tube-like shapes in 3-dimensional Euclidean space. In a first step,
we combine the tube formula of Weyl with integral geometric methods to obtain
an integral representation of the length, which we approximate using a variant
of the Koksma-Hlawka Theorem. In a second step, we use tools from computational
topology to decrease the dependence on small perturbations of the shape. We present
computational experiments that shed light on the stability and the convergence
rate of our algorithm.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal
of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x
apa: Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like
shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates
of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer,
2014. https://doi.org/10.1007/s10851-013-0468-x.
ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,”
Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp.
164–177, 2014.
ista: Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes.
Journal of Mathematical Imaging and Vision. 50(1), 164–177.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like
Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer,
2014, pp. 164–77, doi:10.1007/s10851-013-0468-x.
short: H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision
50 (2014) 164–177.
date_created: 2018-12-11T11:56:36Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s10851-013-0468-x
ec_funded: 1
file:
- access_level: open_access
checksum: 2f93f3e63a38a85cd4404d7953913b14
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:18Z
date_updated: 2020-07-14T12:45:35Z
file_id: '5204'
file_name: IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf
file_size: 3941391
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 164 - 177
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer
publist_id: '4691'
pubrep_id: '549'
quality_controlled: '1'
related_material:
record:
- id: '2843'
relation: earlier_version
status: public
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Stable length estimates of tube-like shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '2257'
abstract:
- lang: eng
text: 'Maximum entropy models are the least structured probability distributions
that exactly reproduce a chosen set of statistics measured in an interacting network.
Here we use this principle to construct probabilistic models which describe the
correlated spiking activity of populations of up to 120 neurons in the salamander
retina as it responds to natural movies. Already in groups as small as 10 neurons,
interactions between spikes can no longer be regarded as small perturbations in
an otherwise independent system; for 40 or more neurons pairwise interactions
need to be supplemented by a global interaction that controls the distribution
of synchrony in the population. Here we show that such “K-pairwise” models—being
systematic extensions of the previously used pairwise Ising models—provide an
excellent account of the data. We explore the properties of the neural vocabulary
by: 1) estimating its entropy, which constrains the population''s capacity to
represent visual information; 2) classifying activity patterns into a small set
of metastable collective modes; 3) showing that the neural codeword ensembles
are extremely inhomogenous; 4) demonstrating that the state of individual neurons
is highly predictable from the rest of the population, allowing the capacity for
error correction.'
acknowledgement: "\r\n\r\n\r\n\r\nThis work was funded by NSF grant IIS-0613435, NSF
grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508,
the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation,
ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES:
ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651."
article_number: e1003408
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for
collective behavior in a large network of sensory neurons. PLoS Computational
Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408
apa: Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry,
M. (2014). Searching for collective behavior in a large network of sensory neurons.
PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003408
chicago: Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek,
and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory
Neurons.” PLoS Computational Biology. Public Library of Science, 2014.
https://doi.org/10.1371/journal.pcbi.1003408.
ieee: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching
for collective behavior in a large network of sensory neurons,” PLoS Computational
Biology, vol. 10, no. 1. Public Library of Science, 2014.
ista: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching
for collective behavior in a large network of sensory neurons. PLoS Computational
Biology. 10(1), e1003408.
mla: Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network
of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408,
Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
short: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS
Computational Biology 10 (2014).
date_created: 2018-12-11T11:56:36Z
date_published: 2014-01-02T00:00:00Z
date_updated: 2024-02-21T13:46:14Z
day: '02'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1003408
file:
- access_level: open_access
checksum: c720222c5e924a4acb17f23b9381a6ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:46Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4965'
file_name: IST-2016-436-v1+1_journal.pcbi.1003408.pdf
file_size: 2194790
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/436
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '4689'
pubrep_id: '436'
quality_controlled: '1'
related_material:
record:
- id: '5562'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Searching for collective behavior in a large network of sensory neurons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '2261'
abstract:
- lang: eng
text: To reveal the full potential of human pluripotent stem cells, new methods
for rapid, site-specific genomic engineering are needed. Here, we describe a system
for precise genetic modification of human embryonic stem cells (ESCs) and induced
pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located
in a safe, intergenic, transcriptionally active region of chromosome 22, as the
recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient
cell lines were established by site-specific placement of a ‘landing pad’ cassette
carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous
or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE)
mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked
by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This
system provided complete control over content, direction and copy number of inserted
genes, with a specificity of 100%. A series of genes, including mCherry and various
combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted
in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from
a Parkinson’s disease patient and a normal sibling control. The DICE system offers
rapid, efficient and precise gene insertion in ESC and iPSC and is particularly
well suited for repeated modifications of the same locus.
acknowledgement: "California Institute for Regenerative Medicine [RT2-01880 and TR2-01756].
Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880
and TR2-01756]\r\nCC BY 3,0"
article_number: e34
author:
- first_name: Fangfang
full_name: Zhu, Fangfang
last_name: Zhu
- first_name: Matthew
full_name: Gamboa, Matthew
last_name: Gamboa
- first_name: Alfonso
full_name: Farruggio, Alfonso
last_name: Farruggio
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Bosiljka
full_name: Tasic, Bosiljka
last_name: Tasic
- first_name: Birgitt
full_name: Schüle, Birgitt
last_name: Schüle
- first_name: Yanru
full_name: Chen Tsai, Yanru
last_name: Chen Tsai
- first_name: Michele
full_name: Calos, Michele
last_name: Calos
citation:
ama: Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative
genomic editing in human pluripotent stem cells. Nucleic Acids Research.
2014;42(5). doi:10.1093/nar/gkt1290
apa: Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B.,
… Calos, M. (2014). DICE, an efficient system for iterative genomic editing in
human pluripotent stem cells. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gkt1290
chicago: Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka
Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient
System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” Nucleic
Acids Research. Oxford University Press, 2014. https://doi.org/10.1093/nar/gkt1290.
ieee: F. Zhu et al., “DICE, an efficient system for iterative genomic editing
in human pluripotent stem cells,” Nucleic Acids Research, vol. 42, no.
5. Oxford University Press, 2014.
ista: Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai
Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human
pluripotent stem cells. Nucleic Acids Research. 42(5), e34.
mla: Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing
in Human Pluripotent Stem Cells.” Nucleic Acids Research, vol. 42, no.
5, e34, Oxford University Press, 2014, doi:10.1093/nar/gkt1290.
short: F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y.
Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014).
date_created: 2018-12-11T11:56:38Z
date_published: 2014-03-05T00:00:00Z
date_updated: 2021-01-12T06:56:22Z
day: '05'
ddc:
- '571'
- '610'
department:
- _id: SiHi
doi: 10.1093/nar/gkt1290
file:
- access_level: open_access
checksum: e9268f5f96a820f04d7ebbf85927c3cb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:15Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4738'
file_name: IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf
file_size: 11044478
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '4684'
pubrep_id: '961'
quality_controlled: '1'
scopus_import: 1
status: public
title: DICE, an efficient system for iterative genomic editing in human pluripotent
stem cells
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2014'
...
---
_id: '2265'
abstract:
- lang: eng
text: Coordinated migration of newly-born neurons to their target territories is
essential for correct neuronal circuit assembly in the developing brain. Although
a cohort of signaling pathways has been implicated in the regulation of cortical
projection neuron migration, the precise molecular mechanisms and how a balanced
interplay of cell-autonomous and non-autonomous functions of candidate signaling
molecules controls the discrete steps in the migration process, are just being
revealed. In this chapter, I will focally review recent advances that improved
our understanding of the cell-autonomous and possible cell-nonautonomous functions
of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential
steps of cortical projection neuron migration. I will then elaborate on the emerging
concept that the Reelin signaling pathway, acts exactly at precise stages in the
course of cortical projection neuron migration. Lastly, I will discuss how finely
tuned transcriptional programs and downstream effectors govern particular aspects
in driving radial migration at discrete stages and how they regulate the precise
positioning of cortical projection neurons in the developing cerebral cortex.
alternative_title:
- Advances in Experimental Medicine and Biology
author:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Hippenmeyer S. Molecular pathways controlling the sequential steps of cortical
projection neuron migration. In: Nguyen L, ed. Cellular and Molecular Control
of Neuronal Migration. Vol 800. Springer; 2014:1-24. doi:10.1007/978-94-007-7687-6_1'
apa: Hippenmeyer, S. (2014). Molecular pathways controlling the sequential steps
of cortical projection neuron migration. In L. Nguyen (Ed.), Cellular and
Molecular Control of Neuronal Migration (Vol. 800, pp. 1–24). Springer. https://doi.org/10.1007/978-94-007-7687-6_1
chicago: Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps
of Cortical Projection Neuron Migration.” In Cellular and Molecular Control
of Neuronal Migration, edited by Laurent Nguyen, 800:1–24. Springer, 2014.
https://doi.org/10.1007/978-94-007-7687-6_1.
ieee: S. Hippenmeyer, “Molecular pathways controlling the sequential steps of cortical
projection neuron migration,” in Cellular and Molecular Control of Neuronal
Migration, vol. 800, L. Nguyen, Ed. Springer, 2014, pp. 1–24.
ista: 'Hippenmeyer S. 2014.Molecular pathways controlling the sequential steps of
cortical projection neuron migration. In: Cellular and Molecular Control of Neuronal
Migration. Advances in Experimental Medicine and Biology, vol. 800, 1–24.'
mla: Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of
Cortical Projection Neuron Migration.” Cellular and Molecular Control of Neuronal
Migration, edited by Laurent Nguyen, vol. 800, Springer, 2014, pp. 1–24, doi:10.1007/978-94-007-7687-6_1.
short: S. Hippenmeyer, in:, L. Nguyen (Ed.), Cellular and Molecular Control of
Neuronal Migration, Springer, 2014, pp. 1–24.
date_created: 2018-12-11T11:56:39Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:23Z
day: '01'
department:
- _id: SiHi
doi: 10.1007/978-94-007-7687-6_1
editor:
- first_name: Laurent
full_name: Nguyen, Laurent
last_name: Nguyen
intvolume: ' 800'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 24
publication: ' Cellular and Molecular Control of Neuronal Migration'
publication_status: published
publisher: Springer
publist_id: '4679'
quality_controlled: '1'
scopus_import: 1
status: public
title: Molecular pathways controlling the sequential steps of cortical projection
neuron migration
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 800
year: '2014'
...
---
_id: '2275'
abstract:
- lang: eng
text: "Energies with high-order non-submodular interactions have been shown to be
very useful in vision due to their high modeling power. Optimization of such energies,
however, is generally NP-hard. A naive approach that works for small problem instances
is exhaustive search, that is, enumeration of all possible labelings of the underlying
graph. We propose a general minimization approach for large graphs based on enumeration
of labelings of certain small patches. \r\nThis partial enumeration technique
reduces complex high-order energy formulations to pairwise Constraint Satisfaction
Problems with unary costs (uCSP), which can be efficiently solved using standard
methods like TRW-S. Our approach outperforms a number of existing state-of-the-art
algorithms on well known difficult problems (e.g. curvature regularization, stereo,
deconvolution); it gives near global minimum and better speed. \r\nOur main application
of interest is curvature regularization. In the context of segmentation, our partial
enumeration technique allows to evaluate curvature directly on small patches using
a novel integral geometry approach.\r\n"
author:
- first_name: Carl
full_name: Olsson, Carl
last_name: Olsson
- first_name: Johannes
full_name: Ulen, Johannes
last_name: Ulen
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Olsson C, Ulen J, Boykov Y, Kolmogorov V. Partial enumeration and curvature
regularization. In: IEEE; 2014:2936-2943. doi:10.1109/ICCV.2013.365'
apa: 'Olsson, C., Ulen, J., Boykov, Y., & Kolmogorov, V. (2014). Partial enumeration
and curvature regularization (pp. 2936–2943). Presented at the ICCV: International
Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.365'
chicago: Olsson, Carl, Johannes Ulen, Yuri Boykov, and Vladimir Kolmogorov. “Partial
Enumeration and Curvature Regularization,” 2936–43. IEEE, 2014. https://doi.org/10.1109/ICCV.2013.365.
ieee: 'C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and
curvature regularization,” presented at the ICCV: International Conference on
Computer Vision, Sydney, Australia, 2014, pp. 2936–2943.'
ista: 'Olsson C, Ulen J, Boykov Y, Kolmogorov V. 2014. Partial enumeration and curvature
regularization. ICCV: International Conference on Computer Vision, 2936–2943.'
mla: Olsson, Carl, et al. Partial Enumeration and Curvature Regularization.
IEEE, 2014, pp. 2936–43, doi:10.1109/ICCV.2013.365.
short: C. Olsson, J. Ulen, Y. Boykov, V. Kolmogorov, in:, IEEE, 2014, pp. 2936–2943.
conference:
end_date: 2013-12-08
location: Sydney, Australia
name: 'ICCV: International Conference on Computer Vision'
start_date: 2013-12-01
date_created: 2018-12-11T11:56:42Z
date_published: 2014-03-03T00:00:00Z
date_updated: 2021-01-12T06:56:28Z
day: '03'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/ICCV.2013.365
file:
- access_level: open_access
checksum: 4a74b5c92d6dcd2348c2c10ec8dd18bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:30Z
date_updated: 2020-07-14T12:45:36Z
file_id: '4754'
file_name: IST-2016-566-v1+1_iccv13_part_enumeration.pdf
file_size: 378601
relation: main_file
file_date_updated: 2020-07-14T12:45:36Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 2936 - 2943
publication_status: published
publisher: IEEE
publist_id: '4669'
pubrep_id: '566'
quality_controlled: '1'
scopus_import: 1
status: public
title: Partial enumeration and curvature regularization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2281'
abstract:
- lang: eng
text: We consider two-dimensional Bose-Einstein condensates with attractive interaction,
described by the Gross-Pitaevskii functional. Minimizers of this functional exist
only if the interaction strength a satisfies {Mathematical expression}, where
Q is the unique positive radial solution of {Mathematical expression} in {Mathematical
expression}. We present a detailed analysis of the behavior of minimizers as a
approaches a*, where all the mass concentrates at a global minimum of the trapping
potential.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yujin
full_name: Guo, Yujin
last_name: Guo
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Guo Y, Seiringer R. On the mass concentration for Bose-Einstein condensates
with attractive interactions. Letters in Mathematical Physics. 2014;104(2):141-156.
doi:10.1007/s11005-013-0667-9
apa: Guo, Y., & Seiringer, R. (2014). On the mass concentration for Bose-Einstein
condensates with attractive interactions. Letters in Mathematical Physics.
Springer. https://doi.org/10.1007/s11005-013-0667-9
chicago: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein
Condensates with Attractive Interactions.” Letters in Mathematical Physics.
Springer, 2014. https://doi.org/10.1007/s11005-013-0667-9.
ieee: Y. Guo and R. Seiringer, “On the mass concentration for Bose-Einstein condensates
with attractive interactions,” Letters in Mathematical Physics, vol. 104,
no. 2. Springer, pp. 141–156, 2014.
ista: Guo Y, Seiringer R. 2014. On the mass concentration for Bose-Einstein condensates
with attractive interactions. Letters in Mathematical Physics. 104(2), 141–156.
mla: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein
Condensates with Attractive Interactions.” Letters in Mathematical Physics,
vol. 104, no. 2, Springer, 2014, pp. 141–56, doi:10.1007/s11005-013-0667-9.
short: Y. Guo, R. Seiringer, Letters in Mathematical Physics 104 (2014) 141–156.
date_created: 2018-12-11T11:56:44Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2024-02-14T12:19:42Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s11005-013-0667-9
external_id:
arxiv:
- '1301.5682'
intvolume: ' 104'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1301.5682
month: '02'
oa: 1
oa_version: Preprint
page: 141 - 156
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4653'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mass concentration for Bose-Einstein condensates with attractive interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2014'
...
---
_id: '2285'
abstract:
- lang: eng
text: GABAergic inhibitory interneurons control fundamental aspects of neuronal
network function. Their functional roles are assumed to be defined by the identity
of their input synapses, the architecture of their dendritic tree, the passive
and active membrane properties and finally the nature of their postsynaptic targets.
Indeed, interneurons display a high degree of morphological and physiological
heterogeneity. However, whether their morphological and physiological characteristics
are correlated and whether interneuron diversity can be described by a continuum
of GABAergic cell types or by distinct classes has remained unclear. Here we perform
a detailed morphological and physiological characterization of GABAergic cells
in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased
and efficient sampling and classification we used knock-in mice expressing the
enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive
neurons and performed cluster analysis. We identified five interneuron classes,
each of them characterized by a distinct set of anatomical and physiological parameters.
Cross-correlation analysis further revealed a direct relation between morphological
and physiological properties indicating that dentate gyrus interneurons fall into
functionally distinct classes which may differentially control neuronal network
activity.
acknowledgement: 'Funded by Deutsche Forschungsgemeinschaft. Grant Numbers: SFB 505,
SFB 780, BA1582/2-1 Excellence Initiative of the German Research Foundation (Spemann
Graduate School). Grant Number: GSC-4 Lichtenberg Professorship-Award (VW-Foundation);
Schram-Foundation; Excellence Initiative Brain Links-Brain Tools. The authors thank
Drs. Jonas-Frederic Sauer and Claudio Elgueta for critically reading the manuscript.
They also thank Karin Winterhalter, Margit Northemann and Ulrich Nöller for technical
assistance.'
author:
- first_name: Jonas
full_name: Hosp, Jonas
last_name: Hosp
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Yuchio
full_name: Yanagawa, Yuchio
last_name: Yanagawa
- first_name: Kunihiko
full_name: Obata, Kunihiko
last_name: Obata
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Hosp J, Strüber M, Yanagawa Y, et al. Morpho-physiological criteria divide
dentate gyrus interneurons into classes. Hippocampus. 2014;23(2):189-203.
doi:10.1002/hipo.22214
apa: Hosp, J., Strüber, M., Yanagawa, Y., Obata, K., Vida, I., Jonas, P. M., &
Bartos, M. (2014). Morpho-physiological criteria divide dentate gyrus interneurons
into classes. Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.22214
chicago: Hosp, Jonas, Michael Strüber, Yuchio Yanagawa, Kunihiko Obata, Imre Vida,
Peter M Jonas, and Marlene Bartos. “Morpho-Physiological Criteria Divide Dentate
Gyrus Interneurons into Classes.” Hippocampus. Wiley-Blackwell, 2014. https://doi.org/10.1002/hipo.22214.
ieee: J. Hosp et al., “Morpho-physiological criteria divide dentate gyrus
interneurons into classes,” Hippocampus, vol. 23, no. 2. Wiley-Blackwell,
pp. 189–203, 2014.
ista: Hosp J, Strüber M, Yanagawa Y, Obata K, Vida I, Jonas PM, Bartos M. 2014.
Morpho-physiological criteria divide dentate gyrus interneurons into classes.
Hippocampus. 23(2), 189–203.
mla: Hosp, Jonas, et al. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons
into Classes.” Hippocampus, vol. 23, no. 2, Wiley-Blackwell, 2014, pp.
189–203, doi:10.1002/hipo.22214.
short: J. Hosp, M. Strüber, Y. Yanagawa, K. Obata, I. Vida, P.M. Jonas, M. Bartos,
Hippocampus 23 (2014) 189–203.
date_created: 2018-12-11T11:56:46Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:32Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1002/hipo.22214
file:
- access_level: open_access
checksum: ff6bc75a79dbc985a2e31b79253e6444
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:54Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5178'
file_name: IST-2016-461-v1+1_Hosp_et_al-2014-Hippocampus.pdf
file_size: 801589
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 189 - 203
publication: Hippocampus
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4646'
pubrep_id: '461'
quality_controlled: '1'
scopus_import: 1
status: public
title: Morpho-physiological criteria divide dentate gyrus interneurons into classes
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2014'
...
---
_id: '6853'
abstract:
- lang: eng
text: This monograph presents a short course in computational geometry and topology.
In the first part the book covers Voronoi diagrams and Delaunay triangulations,
then it presents the theory of alpha complexes which play a crucial role in biology.
The central part of the book is the homology theory and their computation, including
the theory of persistence which is indispensable for applications, e.g. shape
reconstruction. The target audience comprises researchers and practitioners in
mathematics, biology, neuroscience and computer science, but the book may also
be beneficial to graduate students of these fields.
alternative_title:
- SpringerBriefs in Applied Sciences and Technology
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. A Short Course in Computational Geometry and Topology.
1st ed. Cham: Springer Nature; 2014. doi:10.1007/978-3-319-05957-0'
apa: 'Edelsbrunner, H. (2014). A Short Course in Computational Geometry and Topology
(1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-05957-0'
chicago: 'Edelsbrunner, Herbert. A Short Course in Computational Geometry and
Topology. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham:
Springer Nature, 2014. https://doi.org/10.1007/978-3-319-05957-0.'
ieee: 'H. Edelsbrunner, A Short Course in Computational Geometry and Topology,
1st ed. Cham: Springer Nature, 2014.'
ista: 'Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology
1st ed., Cham: Springer Nature, IX, 110p.'
mla: Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology.
1st ed., Springer Nature, 2014, doi:10.1007/978-3-319-05957-0.
short: H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st
ed., Springer Nature, Cham, 2014.
date_created: 2019-09-06T09:22:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-03-04T07:47:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-319-05957-0
edition: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: IX, 110
place: Cham
publication_identifier:
eisbn:
- 9-783-3190-5957-0
eissn:
- 2191-5318
isbn:
- 9-783-3190-5956-3
issn:
- 2191-530X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: available as eBook via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106
- description: available via catalog IST BookList
relation: other
url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842
scopus_import: '1'
series_title: SpringerBriefs in Applied Sciences and Technology
status: public
title: A Short Course in Computational Geometry and Topology
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7038'
article_processing_charge: No
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Huszár K, Rolinek M. Playful Math - An Introduction to Mathematical Games.
IST Austria
apa: Huszár, K., & Rolinek, M. (n.d.). Playful Math - An introduction to
mathematical games. IST Austria.
chicago: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction
to Mathematical Games. IST Austria, n.d.
ieee: K. Huszár and M. Rolinek, Playful Math - An introduction to mathematical
games. IST Austria.
ista: Huszár K, Rolinek M. Playful Math - An introduction to mathematical games,
IST Austria, 5p.
mla: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical
Games. IST Austria.
short: K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games,
IST Austria, n.d.
date_created: 2019-11-18T15:57:05Z
date_published: 2014-06-30T00:00:00Z
date_updated: 2020-07-14T23:11:45Z
day: '30'
ddc:
- '510'
department:
- _id: VlKo
- _id: UlWa
file:
- access_level: open_access
checksum: 2b94e5e1f4c3fe8ab89b12806276fb09
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T15:57:51Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7039'
file_name: 2014_Playful_Math_Huszar.pdf
file_size: 511233
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication_status: draft
publisher: IST Austria
status: public
title: Playful Math - An introduction to mathematical games
type: working_paper
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '468'
abstract:
- lang: eng
text: Invasive alien parasites and pathogens are a growing threat to biodiversity
worldwide, which can contribute to the extinction of endemic species. On the Galápagos
Islands, the invasive parasitic fly Philornis downsi poses a major threat to the
endemic avifauna. Here, we investigated the influence of this parasite on the
breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea)
and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island
in 2010 and 2012. While the population of the small tree finch appeared to be
stable, the warbler finch has experienced a dramatic decline in population size
on Santa Cruz Island since 1997. We aimed to identify whether warbler finches
are particularly vulnerable during different stages of the breeding cycle. Contrary
to our prediction, breeding success was lower in the small tree finch than in
the warbler finch. In both species P. downsi had a strong negative impact on breeding
success and our data suggest that heavy rain events also lowered the fledging
success. On the one hand parents might be less efficient in compensating their
chicks' energy loss due to parasitism as they might be less efficient in foraging
on days of heavy rain. On the other hand, intense rainfalls might lead to increased
humidity and more rapid cooling of the nests. In the case of the warbler finch
we found that the control of invasive plant species with herbicides had a significant
additive negative impact on the breeding success. It is very likely that the availability
of insects (i.e. food abundance) is lower in such controlled areas, as herbicide
usage led to the removal of the entire understory. Predation seems to be a minor
factor in brood loss.
acknowledgement: The study was funded by the University of Vienna (Focus of Excellence
grant), the Galápagos Conservation Trust, and the Ethologische Gesellschaft e.V.
article_number: '0107518'
author:
- first_name: Arno
full_name: Cimadom, Arno
last_name: Cimadom
- first_name: Angel
full_name: Ulloa, Angel
last_name: Ulloa
- first_name: Patrick
full_name: Meidl, Patrick
id: 4709BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Meidl
- first_name: Markus
full_name: Zöttl, Markus
last_name: Zöttl
- first_name: Elisabet
full_name: Zöttl, Elisabet
last_name: Zöttl
- first_name: Birgit
full_name: Fessl, Birgit
last_name: Fessl
- first_name: Erwin
full_name: Nemeth, Erwin
last_name: Nemeth
- first_name: Michael
full_name: Dvorak, Michael
last_name: Dvorak
- first_name: Francesca
full_name: Cunninghame, Francesca
last_name: Cunninghame
- first_name: Sabine
full_name: Tebbich, Sabine
last_name: Tebbich
citation:
ama: Cimadom A, Ulloa A, Meidl P, et al. Invasive parasites habitat change and heavy
rainfall reduce breeding success in Darwin’s finches. PLoS One. 2014;9(9).
doi:10.1371/journal.pone.0107518
apa: Cimadom, A., Ulloa, A., Meidl, P., Zöttl, M., Zöttl, E., Fessl, B., … Tebbich,
S. (2014). Invasive parasites habitat change and heavy rainfall reduce breeding
success in Darwin’s finches. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107518
chicago: Cimadom, Arno, Angel Ulloa, Patrick Meidl, Markus Zöttl, Elisabet Zöttl,
Birgit Fessl, Erwin Nemeth, Michael Dvorak, Francesca Cunninghame, and Sabine
Tebbich. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding
Success in Darwin’s Finches.” PLoS One. Public Library of Science, 2014.
https://doi.org/10.1371/journal.pone.0107518.
ieee: A. Cimadom et al., “Invasive parasites habitat change and heavy rainfall
reduce breeding success in Darwin’s finches,” PLoS One, vol. 9, no. 9.
Public Library of Science, 2014.
ista: Cimadom A, Ulloa A, Meidl P, Zöttl M, Zöttl E, Fessl B, Nemeth E, Dvorak M,
Cunninghame F, Tebbich S. 2014. Invasive parasites habitat change and heavy rainfall
reduce breeding success in Darwin’s finches. PLoS One. 9(9), 0107518.
mla: Cimadom, Arno, et al. “Invasive Parasites Habitat Change and Heavy Rainfall
Reduce Breeding Success in Darwin’s Finches.” PLoS One, vol. 9, no. 9,
0107518, Public Library of Science, 2014, doi:10.1371/journal.pone.0107518.
short: A. Cimadom, A. Ulloa, P. Meidl, M. Zöttl, E. Zöttl, B. Fessl, E. Nemeth,
M. Dvorak, F. Cunninghame, S. Tebbich, PLoS One 9 (2014).
date_created: 2018-12-11T11:46:38Z
date_published: 2014-09-23T00:00:00Z
date_updated: 2021-01-12T08:00:48Z
day: '23'
ddc:
- '576'
department:
- _id: CampIT
doi: 10.1371/journal.pone.0107518
file:
- access_level: open_access
checksum: b24e7518ccd41effed0d7d9e2498f67f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:48Z
date_updated: 2020-07-14T12:46:34Z
file_id: '5103'
file_name: IST-2018-954-v1+1_2014_Meidl_Invasive_parasites.PDF
file_size: 489387
relation: main_file
file_date_updated: 2020-07-14T12:46:34Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7352'
pubrep_id: '954'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invasive parasites habitat change and heavy rainfall reduce breeding success
in Darwin's finches
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '475'
abstract:
- lang: eng
text: 'First cycle games (FCG) are played on a finite graph by two players who push
a token along the edges until a vertex is repeated, and a simple cycle is formed.
The winner is determined by some fixed property Y of the sequence of labels of
the edges (or nodes) forming this cycle. These games are traditionally of interest
because of their connection with infinite-duration games such as parity and mean-payoff
games. We study the memory requirements for winning strategies of FCGs and certain
associated infinite duration games. We exhibit a simple FCG that is not memoryless
determined (this corrects a mistake in Memoryless determinacy of parity and mean
payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims
that FCGs for which Y is closed under cyclic permutations are memoryless determined).
We show that θ (n)! memory (where n is the number of nodes in the graph), which
is always sufficient, may be necessary to win some FCGs. On the other hand, we
identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations,
and both Y and its complement are closed under concatenation) that are sufficient
to ensure that the corresponding FCGs and their associated infinite duration games
are memoryless determined. We demonstrate that many games considered in the literature,
such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity
side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE,
solving some families of FCGs is PSPACE-hard. '
alternative_title:
- EPTCS
author:
- first_name: Benjamin
full_name: Aminof, Benjamin
id: 4A55BD00-F248-11E8-B48F-1D18A9856A87
last_name: Aminof
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Aminof B, Rubin S. First cycle games. In: Electronic Proceedings in Theoretical
Computer Science, EPTCS. Vol 146. Open Publishing Association; 2014:83-90.
doi:10.4204/EPTCS.146.11'
apa: 'Aminof, B., & Rubin, S. (2014). First cycle games. In Electronic Proceedings
in Theoretical Computer Science, EPTCS (Vol. 146, pp. 83–90). Grenoble, France:
Open Publishing Association. https://doi.org/10.4204/EPTCS.146.11'
chicago: Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In Electronic
Proceedings in Theoretical Computer Science, EPTCS, 146:83–90. Open Publishing
Association, 2014. https://doi.org/10.4204/EPTCS.146.11.
ieee: B. Aminof and S. Rubin, “First cycle games,” in Electronic Proceedings
in Theoretical Computer Science, EPTCS, Grenoble, France, 2014, vol. 146,
pp. 83–90.
ista: 'Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical
Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.'
mla: Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” Electronic Proceedings
in Theoretical Computer Science, EPTCS, vol. 146, Open Publishing Association,
2014, pp. 83–90, doi:10.4204/EPTCS.146.11.
short: B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer
Science, EPTCS, Open Publishing Association, 2014, pp. 83–90.
conference:
end_date: 2014-04-06
location: Grenoble, France
name: 'SR: Strategic Reasoning'
start_date: 2014-04-05
date_created: 2018-12-11T11:46:41Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:00:53Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4204/EPTCS.146.11
ec_funded: 1
file:
- access_level: open_access
checksum: 4d7b4ab82980cca2b96ac7703992a8c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:08Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5260'
file_name: IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf
file_size: 100115
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 146'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 83 - 90
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Electronic Proceedings in Theoretical Computer Science, EPTCS
publication_status: published
publisher: Open Publishing Association
publist_id: '7345'
pubrep_id: '952'
quality_controlled: '1'
scopus_import: 1
status: public
title: First cycle games
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: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2014'
...