---
_id: '6848'
abstract:
- lang: eng
text: Proton-translocating transhydrogenase (also known as nicotinamide nucleotide
transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner
mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride
between NADH and NADP+, coupled to the translocation of one proton across the
membrane. Its main physiological function is the generation of NADPH, which is
a substrate in anabolic reactions and a regulator of oxidative status; however,
NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid
deficiency in humans and metabolic abnormalities in mice, similar to those observed
in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve
a rotation of around 180° of the entire NADP(H)-binding domain that alternately
participates in hydride transfer and proton-channel gating. However, owing to
the lack of high-resolution structures of intact NNT, the details of this process
remain unclear5,6. Here we present the cryo-electron microscopy structure of intact
mammalian NNT in different conformational states. We show how the NADP(H)-binding
domain opens the proton channel to the opposite sides of the membrane, and we
provide structures of these two states. We also describe the catalytically important
interfaces and linkers between the membrane and the soluble domains and their
roles in nucleotide exchange. These structures enable us to propose a revised
mechanism for a coupling process in NNT that is consistent with a large body of
previous biochemical work. Our results are relevant to the development of currently
unavailable NNT inhibitors, which may have therapeutic potential in ischaemia
reperfusion injury, metabolic syndrome and some cancers7,8,9.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: " We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their
assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing
was performed at the IST high-performance computing cluster.\r\nThis project has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement no. 665385."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2
apa: Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial
proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019.
https://doi.org/10.1038/s41586-019-1519-2.
ieee: D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating
transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295,
2019.
ista: Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 573(7773), 291–295.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer
Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.
short: D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.
date_created: 2019-09-04T06:21:41Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2024-03-25T23:30:08Z
day: '12'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-019-1519-2
ec_funded: 1
external_id:
isi:
- '000485415400061'
pmid:
- '31462775'
file:
- access_level: open_access
checksum: 52728cda5210a3e9b74cc204e8aed3d5
content_type: application/pdf
creator: lsazanov
date_created: 2020-11-26T16:33:44Z
date_updated: 2020-11-26T16:33:44Z
file_id: '8821'
file_name: Manuscript_final_acc_withFigs_SI_opt_red.pdf
file_size: 3066206
relation: main_file
success: 1
file_date_updated: 2020-11-26T16:33:44Z
has_accepted_license: '1'
intvolume: ' 573'
isi: 1
issue: '7773'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 291–295
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/
record:
- id: '8340'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of mitochondrial proton-translocating transhydrogenase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 573
year: '2019'
...
---
_id: '6849'
abstract:
- lang: eng
text: 'Brain function is mediated by complex dynamical interactions between excitatory
and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons)
are one of the least studied types, despite being suspected to play important
roles in cognitive processes. We studied the network effects of optogenetic silencing
of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states.
The cell firing pattern in response to light pulses allowed us to classify the
recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal
cell and interneurons, and the inhibited interneurons corresponding to the CCK
group. The light application, which inhibited the activity of CCK interneurons
triggered wider changes in the firing dynamics of cells. We observed rate changes
(i.e. remapping) of pyramidal cells during the exploration session in which the
light was applied relative to the previous control session that was not restricted
neither in time nor space to the light delivery. Also, the disinhibited pyramidal
cells had higher increase in bursting than in single spike firing rate as a result
of CCK silencing. In addition, the firing activity patterns during exploratory
periods were more weakly reactivated in sleep for those periods in which CCK-interneuron
were silenced than in the unaffected periods. Furthermore, light pulses during
sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK
neurons during exploration suppressed the reactivation of waking firing patterns
in sleep and CCK interneuron activity was also required during sleep for the normal
reactivation of waking patterns. These findings demonstrate the involvement of
CCK cells in reactivation-related memory consolidation. An important part of our
analysis was to test the relationship of the identified CCKinterneurons to brain
oscillations. Our findings showed that these cells exhibited different oscillatory
behaviour during anaesthesia and natural waking and sleep conditions. We showed
that: 1) Contrary to the past studies performed under anaesthesia, the identified
CCKinterneurons fired on the descending portion of the theta phase in waking exploration.
2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3)
Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons
increased around the peak activity of the sharp-wave ripple (SWR) events in natural
sleep, which is congruent with new reports about their functional connectivity.
We also found that light driven CCK-interneuron silencing altered the dynamics
on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted
their preferred theta phases when the light was applied, while interneurons responses
were less consistent. 2) As a population, pyramidal cells negatively shifted their
preferred activity during gamma oscillations, albeit we did not find gamma modulation
differences related to the light application when pyramidal cells were subdivided
into the disinhibited and unaffected groups. 3) During the peak of SWR events,
all but the CCK-interneurons had a reduction in their relative firing rate change
during the light application as compared to the change observed at SWR initiation.
Finally, regarding to the place field activity of the recorded pyramidal neurons,
we showed that the disinhibited pyramidal cells had reduced place field similarity,
coherence and spatial information, but only during the light application. The
mechanisms behind such observed behaviours might involve eCB signalling and plastic
changes in CCK-interneuron synapses. In conclusion, the observed changes related
to the light-mediated silencing of CCKinterneurons have unravelled characteristics
of this interneuron subpopulation that might change the understanding not only
of their particular network interactions, but also of the current theories about
the emergence of certain cognitive processes such as place coding needed for navigation
or hippocampus-dependent memory consolidation. '
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
citation:
ama: Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal
network dynamics. 2019. doi:10.15479/AT:ISTA:6849
apa: Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating
hippocampal network dynamics. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6849
chicago: Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating
Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:6849.
ieee: D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal
network dynamics,” Institute of Science and Technology Austria, 2019.
ista: Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal
network dynamics. Institute of Science and Technology Austria.
mla: Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.
short: D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics, Institute of Science and Technology Austria, 2019.
date_created: 2019-09-06T06:54:16Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2023-09-19T10:01:12Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6849
file:
- access_level: closed
checksum: 244dc4f74dbfc94f414156092298831f
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: drangel
date_created: 2019-09-09T13:09:45Z
date_updated: 2021-02-10T23:30:09Z
embargo_to: open_access
file_id: '6865'
file_name: Thesis_Damaris_Rangel_source.docx
file_size: 18253100
relation: source_file
- access_level: open_access
checksum: 59c73be40eeaa1c4db24067270151555
content_type: application/pdf
creator: drangel
date_created: 2019-09-09T13:09:52Z
date_updated: 2020-09-11T22:30:04Z
embargo: 2020-09-10
file_id: '6866'
file_name: Thesis_Damaris_Rangel_pdfa.pdf
file_size: 2160109
relation: main_file
request_a_copy: 0
file_date_updated: 2021-02-10T23:30:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '97'
publication_identifier:
isbn:
- '9783990780039'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5914'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The role of CCK-interneurons in regulating hippocampal network dynamics
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6855'
abstract:
- lang: eng
text: Many traits of interest are highly heritable and genetically complex, meaning
that much of the variation they exhibit arises from differences at numerous loci
in the genome. Complex traits and their evolution have been studied for more than
a century, but only in the last decade have genome-wide association studies (GWASs)
in humans begun to reveal their genetic basis. Here, we bring these threads of
research together to ask how findings from GWASs can further our understanding
of the processes that give rise to heritable variation in complex traits and of
the genetic basis of complex trait evolution in response to changing selection
pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary
thinking helps us to interpret findings from GWASs and informs related efforts
of practical importance.
article_processing_charge: No
author:
- first_name: Guy
full_name: Sella, Guy
last_name: Sella
- 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: Sella G, Barton NH. Thinking about the evolution of complex traits in the era
of genome-wide association studies. Annual Review of Genomics and Human Genetics.
2019;20:461-493. doi:10.1146/annurev-genom-083115-022316
apa: Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex
traits in the era of genome-wide association studies. Annual Review of Genomics
and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316
chicago: Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex
Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics
and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.
ieee: G. Sella and N. H. Barton, “Thinking about the evolution of complex traits
in the era of genome-wide association studies,” Annual Review of Genomics and
Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.
ista: Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in
the era of genome-wide association studies. Annual Review of Genomics and Human
Genetics. 20, 461–493.
mla: Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex
Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics
and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.
short: G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019)
461–493.
date_created: 2019-09-07T14:28:29Z
date_published: 2019-07-05T00:00:00Z
date_updated: 2023-08-29T07:49:38Z
day: '05'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1146/annurev-genom-083115-022316
external_id:
isi:
- '000485148400020'
pmid:
- '31283361'
file:
- access_level: open_access
checksum: 23d3978cf4739a89ce2c3e779f9305ca
content_type: application/pdf
creator: dernst
date_created: 2019-09-09T07:22:12Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6862'
file_name: 2019_AnnualReview_Sella.pdf
file_size: 411491
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 461-493
pmid: 1
publication: Annual Review of Genomics and Human Genetics
publication_identifier:
eissn:
- 1545-293X
issn:
- 1527-8204
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thinking about the evolution of complex traits in the era of genome-wide association
studies
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2019'
...
---
_id: '6856'
abstract:
- lang: eng
text: 'Plant mating systems play a key role in structuring genetic variation both
within and between species. In hybrid zones, the outcomes and dynamics of hybridization
are usually interpreted as the balance between gene flow and selection against
hybrids. Yet, mating systems can introduce selective forces that alter these expectations;
with diverse outcomes for the level and direction of gene flow depending on variation
in outcrossing and whether the mating systems of the species pair are the same
or divergent. We present a survey of hybridization in 133 species pairs from 41
plant families and examine how patterns of hybridization vary with mating system.
We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and
the frequency of reproductive isolating barriers vary in relation to mating system/s
of the species pair. We combine these results with a simulation model and examples
from the literature to address two general themes: (i) the two‐way interaction
between introgression and the evolution of reproductive systems, and (ii) how
mating system can facilitate or restrict interspecific gene flow. We conclude
that examining mating system with hybridization provides unique opportunities
to understand divergence and the processes underlying reproductive isolation.'
article_processing_charge: No
article_type: original
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- 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: Yaniv
full_name: Brandvain, Yaniv
last_name: Brandvain
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Sarah
full_name: Yakimowski, Sarah
last_name: Yakimowski
- first_name: Tanmay
full_name: Dixit, Tanmay
last_name: Dixit
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
- first_name: Eva
full_name: Cereghetti, Eva
id: 71AA91B4-05ED-11EA-8BEB-F5833E63BD63
last_name: Cereghetti
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: 'Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid
zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist.
2019;224(3):1035-1047. doi:10.1111/nph.16180'
apa: 'Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit,
T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180'
chicago: 'Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse,
Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field.
“Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries
to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.'
ieee: 'M. Pickup et al., “Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no.
3. Wiley, pp. 1035–1047, 2019.'
ista: 'Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer
C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.'
mla: 'Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation,
Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no.
3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.'
short: M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit,
C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.
date_created: 2019-09-07T14:35:40Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-18T08:47:08Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/nph.16180
ec_funded: 1
external_id:
pmid:
- '31505037'
file:
- access_level: open_access
checksum: 21e4c95599bbcaf7c483b89954658672
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:15:05Z
date_updated: 2020-07-14T12:47:42Z
file_id: '7011'
file_name: 2019_NewPhytologist_Pickup.pdf
file_size: 1511958
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1035-1047
pmid: 1
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Mating system variation in hybrid zones: Facilitation, barriers and asymmetries
to gene flow'
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: 224
year: '2019'
...
---
_id: '6857'
abstract:
- lang: eng
text: "Gene Drives are regarded as future tools with a high potential for population
control. Due to their inherent ability to overcome the rules of Mendelian inheritance,
gene drives (GD) may spread genes rapidly through populations of sexually reproducing
organisms. A release of organisms carrying a GD would constitute a paradigm shift
in the handling of genetically modified organisms because gene drive organisms
(GDO) are designed to drive their transgenes into wild populations and thereby
increase the number of GDOs. The rapid development in this field and its focus
on wild populations demand a prospective risk assessment with a focus on exposure
related aspects. Presently, it is unclear how adequate risk management could be
guaranteed to limit the spread of GDs in time and space, in order to avoid potential
adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the
“Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute
of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight
into the potential population dynamic behavior of GDs and appropriate measures
of control. Scientists from France, Germany, England, and the USA discussed both
topics in this meeting on April 4–5, 2019. This article summarizes results of
the workshop."
article_number: '1900151'
article_processing_charge: No
article_type: original
author:
- first_name: B
full_name: Giese, B
last_name: Giese
- first_name: J L
full_name: Friess, J L
last_name: Friess
- first_name: 'M F '
full_name: 'Schetelig, M F '
last_name: Schetelig
- 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: Philip
full_name: Messer, Philip
last_name: Messer
- first_name: Florence
full_name: Debarre, Florence
last_name: Debarre
- first_name: H
full_name: Meimberg, H
last_name: Meimberg
- first_name: N
full_name: Windbichler, N
last_name: Windbichler
- first_name: C
full_name: Boete, C
last_name: Boete
citation:
ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory
matters – A report from the workshop “Evaluation of spatial and temporal control
of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151'
apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre,
F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report
from the workshop “Evaluation of spatial and temporal control of Gene Drives”,
4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151'
chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer,
Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics
and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and
Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays.
Wiley, 2019. https://doi.org/10.1002/bies.201900151.'
ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A
report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’,
4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.'
ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg
H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters
– A report from the workshop “Evaluation of spatial and temporal control of Gene
Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.'
mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report
from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’,
4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley,
2019, doi:10.1002/bies.201900151.'
short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre,
H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).
date_created: 2019-09-07T14:40:03Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:56:26Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/bies.201900151
external_id:
isi:
- '000489502000001'
file:
- access_level: open_access
checksum: 8cc7551bff70b2658f8d5630f228ee12
content_type: application/pdf
creator: dernst
date_created: 2019-10-11T06:59:26Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6939'
file_name: 2019_BioEssays_Giese.pdf
file_size: 193248
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BioEssays
publication_identifier:
eissn:
- 1521-1878
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop
“Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2019'
...
---
_id: '6858'
article_processing_charge: No
article_type: review
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Is speciation driven by cycles of mixing and isolation? National
Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113
apa: Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation?
National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113
chicago: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.
ieee: N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National
Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.
ista: Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National
Science Review. 6(2), 291–292.
mla: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review, vol. 6, no. 2, Oxford University Press, 2019,
pp. 291–92, doi:10.1093/nsr/nwy113.
short: N.H. Barton, National Science Review 6 (2019) 291–292.
date_created: 2019-09-07T14:43:02Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-29T07:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/nsr/nwy113
external_id:
isi:
- '000467957400025'
file:
- access_level: open_access
checksum: 571d60fa21a568607d1fd04e119da88c
content_type: application/pdf
creator: dernst
date_created: 2020-10-02T09:16:44Z
date_updated: 2020-10-02T09:16:44Z
file_id: '8595'
file_name: 2019_NSR_Barton.pdf
file_size: 106463
relation: main_file
success: 1
file_date_updated: 2020-10-02T09:16:44Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 291-292
publication: National Science Review
publication_identifier:
eissn:
- 2053-714X
issn:
- 2095-5138
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Is speciation driven by cycles of mixing and isolation?
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2019'
...
---
_id: '6859'
abstract:
- lang: eng
text: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found
in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation
across theplasma membrane using the rotary-catalysis mechanism. They belong to
the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type
ATP synthasesin overall architecture. We solved cryo–electron microscopy structures
of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs,
in three rotationalstates and two substates. These structures indicate substantial
flexibility betweenV1and Voin a working enzyme, which results from mechanical
competition between centralshaft rotation and resistance from the peripheral stalks.
We also describedetails of adenosine diphosphate inhibition release, V1-Votorque
transmission, andproton translocation, which are relevant for the entire V-type
ATPase family.
acknowledged_ssus:
- _id: ScienComp
article_number: eaaw9144
article_processing_charge: No
author:
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus
thermophilus V/A-type ATPase. Science. 2019;365(6455). doi:10.1126/science.aaw9144
apa: Zhou, L., & Sazanov, L. A. (2019). Structure and conformational plasticity
of the intact Thermus thermophilus V/A-type ATPase. Science. AAAS. https://doi.org/10.1126/science.aaw9144
chicago: Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity
of the Intact Thermus Thermophilus V/A-Type ATPase.” Science. AAAS, 2019.
https://doi.org/10.1126/science.aaw9144.
ieee: L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the
intact Thermus thermophilus V/A-type ATPase,” Science, vol. 365, no. 6455.
AAAS, 2019.
ista: Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact
Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144.
mla: Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity
of the Intact Thermus Thermophilus V/A-Type ATPase.” Science, vol. 365,
no. 6455, eaaw9144, AAAS, 2019, doi:10.1126/science.aaw9144.
short: L. Zhou, L.A. Sazanov, Science 365 (2019).
date_created: 2019-09-07T19:04:45Z
date_published: 2019-08-23T00:00:00Z
date_updated: 2023-08-29T07:52:02Z
day: '23'
department:
- _id: LeSa
doi: 10.1126/science.aaw9144
external_id:
isi:
- '000482464000043'
pmid:
- '31439765'
intvolume: ' 365'
isi: 1
issue: '6455'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/
scopus_import: '1'
status: public
title: Structure and conformational plasticity of the intact Thermus thermophilus
V/A-type ATPase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 365
year: '2019'
...
---
_id: '6867'
abstract:
- lang: eng
text: A novel magnetic scratch method achieves repeatability, reproducibility and
geometric control greater than pipette scratch assays and closely approximating
the precision of cell exclusion assays while inducing the cell injury inherently
necessary for wound healing assays. The magnetic scratch is affordable, easily
implemented and standardisable and thus may contribute toward better comparability
of data generated in different studies and laboratories.
article_number: '12625'
article_processing_charge: No
author:
- first_name: M.
full_name: Fenu, M.
last_name: Fenu
- first_name: T.
full_name: Bettermann, T.
last_name: Bettermann
- first_name: C.
full_name: Vogl, C.
last_name: Vogl
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: J.
full_name: Schramel, J.
last_name: Schramel
- first_name: F.
full_name: Jenner, F.
last_name: Jenner
- first_name: I.
full_name: Ribitsch, I.
last_name: Ribitsch
citation:
ama: Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for
standardisation of wound-healing assays. Scientific Reports. 2019;9(1).
doi:10.1038/s41598-019-48930-7
apa: Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner,
F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation
of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7
chicago: Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel,
F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation
of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7.
ieee: M. Fenu et al., “A novel magnet-based scratch method for standardisation
of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature,
2019.
ista: Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch
I. 2019. A novel magnet-based scratch method for standardisation of wound-healing
assays. Scientific Reports. 9(1), 12625.
mla: Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of
Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer
Nature, 2019, doi:10.1038/s41598-019-48930-7.
short: M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner,
I. Ribitsch, Scientific Reports 9 (2019).
date_created: 2019-09-15T22:00:42Z
date_published: 2019-09-02T00:00:00Z
date_updated: 2023-08-29T07:55:15Z
day: '02'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1038/s41598-019-48930-7
external_id:
isi:
- '000483697800007'
pmid:
- '31477739'
file:
- access_level: open_access
checksum: 9cfd986d4108e288cc72276ef047ab0c
content_type: application/pdf
creator: dernst
date_created: 2019-09-16T12:42:40Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6879'
file_name: 2019_ScientificReports_Fenu.pdf
file_size: 3523795
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A novel magnet-based scratch method for standardisation of wound-healing assays
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6868'
abstract:
- lang: eng
text: "Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control
electrical rhythmicity and excitability in the heart and brain, but the function
of HCN channels at the subcellular level in axons remains poorly understood. Here,
we show that the action potential conduction velocity in both myelinated and unmyelinated
central axons can be bidirectionally modulated by a HCN channel blocker, cyclic
adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar
mossy fiber boutons show that HCN channels ensure reliable high-frequency firing
and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration
13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating
subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2
channels control conduction velocity primarily by altering the resting membrane
potential\r\nand are associated with significant metabolic costs. These results
suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity
to finely tune energy consumption and temporal delays across axons in the brain."
article_number: e42766
article_processing_charge: No
article_type: original
author:
- first_name: Niklas
full_name: Byczkowicz, Niklas
last_name: Byczkowicz
- first_name: Abdelmoneim
full_name: Eshra, Abdelmoneim
last_name: Eshra
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Andrea
full_name: Trevisiol, Andrea
last_name: Trevisiol
- first_name: Johannes
full_name: Hirrlinger, Johannes
last_name: Hirrlinger
- first_name: Maarten Hp
full_name: Kole, Maarten Hp
last_name: Kole
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Stefan
full_name: Hallermann, Stefan
last_name: Hallermann
citation:
ama: Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated
neuromodulation can control action potential velocity and fidelity in central
axons. eLife. 2019;8. doi:10.7554/eLife.42766
apa: Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger,
J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation
can control action potential velocity and fidelity in central axons. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.42766
chicago: Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber,
Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and
Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential
Velocity and Fidelity in Central Axons.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/eLife.42766.
ieee: N. Byczkowicz et al., “HCN channel-mediated neuromodulation can control
action potential velocity and fidelity in central axons,” eLife, vol. 8.
eLife Sciences Publications, 2019.
ista: Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger
J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation
can control action potential velocity and fidelity in central axons. eLife. 8,
e42766.
mla: Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control
Action Potential Velocity and Fidelity in Central Axons.” ELife, vol. 8,
e42766, eLife Sciences Publications, 2019, doi:10.7554/eLife.42766.
short: N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger,
M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019).
date_created: 2019-09-15T22:00:43Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2023-08-30T06:17:06Z
day: '09'
ddc:
- '570'
department:
- _id: RySh
doi: 10.7554/eLife.42766
external_id:
isi:
- '000485663900001'
file:
- access_level: open_access
checksum: c350b7861ef0fb537cae8a3232aec016
content_type: application/pdf
creator: dernst
date_created: 2019-09-16T13:14:33Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6880'
file_name: 2019_eLife_Byczkowicz.pdf
file_size: 4008137
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: HCN channel-mediated neuromodulation can control action potential velocity
and fidelity in central axons
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6877'
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell.
2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047
apa: Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic
debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047
chicago: Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove
Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.
ieee: A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,”
Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.
ista: Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris.
Cell. 179(1), 51–53.
mla: Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic
Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.
short: A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.
date_created: 2019-09-15T22:00:46Z
date_published: 2019-09-19T00:00:00Z
date_updated: 2024-03-25T23:30:22Z
day: '19'
department:
- _id: MiSi
doi: 10.1016/j.cell.2019.08.047
external_id:
isi:
- '000486618500011'
pmid:
- '31539498'
intvolume: ' 179'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 51-53
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The neural crest pitches in to remove apoptotic debris
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 179
year: '2019'
...
---
_id: '6884'
abstract:
- lang: eng
text: 'In two-player games on graphs, the players move a token through a graph to
produce a finite or infinite path, which determines the qualitative winner or
quantitative payoff of the game. We study bidding games in which the players bid
for the right to move the token. Several bidding rules were studied previously.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the "bank" rather than the
other player. Taxman bidding spans the spectrum between Richman and poorman bidding.
They are parameterized by a constant tau in [0,1]: portion tau of the winning
bid is paid to the other player, and portion 1-tau to the bank. While finite-duration
(reachability) taxman games have been studied before, we present, for the first
time, results on infinite-duration taxman games. It was previously shown that
both Richman and poorman infinite-duration games with qualitative objectives reduce
to reachability games, and we show a similar result here. Our most interesting
results concern quantitative taxman games, namely mean-payoff games, where poorman
and Richman bidding differ significantly. A central quantity in these games is
the ratio between the two players'' initial budgets. While in poorman mean-payoff
games, the optimal payoff of a player depends on the initial ratio, in Richman
bidding, the payoff depends only on the structure of the game. In both games the
optimal payoffs can be found using (different) probabilistic connections with
random-turn games in which in each turn, instead of bidding, a coin is tossed
to determine which player moves. While the value with Richman bidding equals the
value of a random-turn game with an un-biased coin, with poorman bidding, the
bias in the coin is the initial ratio of the budgets. We give a complete classification
of mean-payoff taxman games that is based on a probabilistic connection: the value
of a taxman bidding game with parameter tau and initial ratio r, equals the value
of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau).
Thus, we show that Richman bidding is the exception; namely, for every tau <1,
the value of the game depends on the initial ratio. Our proof technique simplifies
and unifies the previous proof techniques for both Richman and poorman bidding. '
alternative_title:
- LIPIcs
article_number: '11'
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
citation:
ama: 'Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol
138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11'
apa: 'Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in
graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical
Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11'
chicago: Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in
Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.
https://doi.org/10.4230/LIPICS.MFCS.2019.11.
ieee: 'G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,”
presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer
Science, Aachen, Germany, 2019, vol. 138.'
ista: 'Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games.
MFCS: nternational Symposium on Mathematical Foundations of Computer Science,
LIPIcs, vol. 138, 11.'
mla: Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11.
short: G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019.
conference:
end_date: 2019-08-30
location: Aachen, Germany
name: 'MFCS: nternational Symposium on Mathematical Foundations of Computer Science'
start_date: 2019-08-26
date_created: 2019-09-18T08:04:26Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-07T14:08:34Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPICS.MFCS.2019.11
ec_funded: 1
external_id:
arxiv:
- '1905.03835'
file:
- access_level: open_access
checksum: 6346e116a4f4ed1414174d96d2c4fbd7
content_type: application/pdf
creator: kschuh
date_created: 2019-09-27T11:45:15Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6913'
file_name: 2019_LIPIcs_Avni.pdf
file_size: 554457
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 138'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '9239'
relation: later_version
status: public
scopus_import: 1
status: public
title: Bidding mechanisms in graph 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2019'
...
---
_id: '6885'
abstract:
- lang: eng
text: 'A vector addition system with states (VASS) consists of a finite set of states
and counters. A configuration is a state and a value for each counter; a transition
changes the state and each counter is incremented, decremented, or left unchanged.
While qualitative properties such as state and configuration reachability have
been studied for VASS, we consider the long-run average cost of infinite computations
of VASS. The cost of a configuration is for each state, a linear combination of
the counter values. In the special case of uniform cost functions, the linear
combination is the same for all states. The (regular) long-run emptiness problem
is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped)
computation such that the long-run average value of the cost function does not
exceed the threshold. For uniform cost functions, we show that the regular long-run
emptiness problem is (a) decidable in polynomial time for integer-valued VASS,
and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative
counters). For general cost functions, we show that the problem is (c) NP-complete
for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most
interesting result is for (c) integer-valued VASS with general cost functions,
where we establish a connection between the regular long-run emptiness problem
and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness
problem is equally hard as the regular problem in all cases except (c), where
it remains open. '
alternative_title:
- LIPIcs
article_number: '27'
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
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition
systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2019. doi:10.4230/LIPICS.CONCUR.2019.27'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average
behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR:
International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average
Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27.
ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of
vector addition systems with states,” presented at the CONCUR: International Conference
on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.'
ista: 'Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector
addition systems with states. CONCUR: International Conference on Concurrency
Theory, LIPIcs, vol. 140, 27.'
mla: Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition
Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:06:14Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:09:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPICS.CONCUR.2019.27
file:
- access_level: open_access
checksum: 4985e26e1572d1575d64d38acabd71d6
content_type: application/pdf
creator: kschuh
date_created: 2019-09-27T12:09:35Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6914'
file_name: 2019_LIPIcs_Chatterjee.pdf
file_size: 538120
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Long-run average behavior of vector addition systems with states
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2019'
...
---
_id: '6886'
abstract:
- lang: eng
text: 'In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner of the game. Such games
are central in formal methods since they model the interaction between a non-terminating
system and its environment. In bidding games the players bid for the right to
move the token: in each round, the players simultaneously submit bids, and the
higher bidder moves the token and pays the other player. Bidding games are known
to have a clean and elegant mathematical structure that relies on the ability
of the players to submit arbitrarily small bids. Many applications, however, require
a fixed granularity for the bids, which can represent, for example, the monetary
value expressed in cents. We study, for the first time, the combination of discrete-bidding
and infinite-duration games. Our most important result proves that these games
form a large determined subclass of concurrent games, where determinacy is the
strong property that there always exists exactly one player who can guarantee
winning the game. In particular, we show that, in contrast to non-discrete bidding
games, the mechanism with which tied bids are resolved plays an important role
in discrete-bidding games. We study several natural tie-breaking mechanisms and
show that, while some do not admit determinacy, most natural mechanisms imply
determinacy for every pair of initial budgets. '
alternative_title:
- LIPIcs
article_number: '20'
article_processing_charge: No
arxiv: 1
author:
- first_name: Milad
full_name: Aghajohari, Milad
last_name: Aghajohari
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration
games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20'
apa: 'Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding
infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference
on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20'
chicago: Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding
Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20.
ieee: 'M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding
infinite-duration games,” presented at the CONCUR: International Conference on
Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.'
ista: 'Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding
infinite-duration games. CONCUR: International Conference on Concurrency Theory,
LIPIcs, vol. 140, 20.'
mla: Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration
Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019,
doi:10.4230/LIPICS.CONCUR.2019.20.
short: M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:06:58Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2022-01-26T08:27:10Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPICS.CONCUR.2019.20
external_id:
arxiv:
- '1905.03588'
file:
- access_level: open_access
checksum: 4df6d3575c506edb17215adada03cc8e
content_type: application/pdf
creator: kschuh
date_created: 2019-09-27T12:21:38Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6915'
file_name: 2019_LIPIcs_Aghajohari.pdf
file_size: 741425
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Determinacy in discrete-bidding infinite-duration games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 140
year: '2019'
...
---
_id: '6887'
abstract:
- lang: eng
text: 'The fundamental model-checking problem, given as input a model and a specification,
asks for the algorithmic verification of whether the model satisfies the specification.
Two classical models for reactive systems are graphs and Markov decision processes
(MDPs). A basic specification formalism in the verification of reactive systems
is the strong fairness (aka Streett) objective, where given different types of
requests and corresponding grants, the requirement is that for each type, if the
request event happens infinitely often, then the corresponding grant event must
also happen infinitely often. All omega-regular objectives can be expressed as
Streett objectives and hence they are canonical in verification. Consider graphs/MDPs
with n vertices, m edges, and a Streett objectives with k pairs, and let b denote
the size of the description of the Streett objective for the sets of requests
and grants. The current best-known algorithm for the problem requires time O(min(n^2,
m sqrt{m log n}) + b log n). In this work we present randomized near-linear time
algorithms, with expected running time O~(m + b), where the O~ notation hides
poly-log factors. Our randomized algorithms are near-linear in the size of the
input, and hence optimal up to poly-log factors. '
alternative_title:
- LIPIcs
article_number: '7'
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: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Near-linear time algorithms
for Streett objectives in graphs and MDPs. In: Leibniz International Proceedings
in Informatics. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2019. doi:10.4230/LIPICS.CONCUR.2019.7'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2019). Near-linear
time algorithms for Streett objectives in graphs and MDPs. In Leibniz International
Proceedings in Informatics (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.7'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander
Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.”
In Leibniz International Proceedings in Informatics, Vol. 140. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.7.
ieee: K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Near-linear time
algorithms for Streett objectives in graphs and MDPs,” in Leibniz International
Proceedings in Informatics, Amsterdam, Netherlands, 2019, vol. 140.
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2019. Near-linear time algorithms
for Streett objectives in graphs and MDPs. Leibniz International Proceedings in
Informatics. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol.
140, 7.'
mla: Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives
in Graphs and MDPs.” Leibniz International Proceedings in Informatics,
vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.7.
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, Leibniz International
Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:07:58Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2022-08-12T10:54:34Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPICS.CONCUR.2019.7
ec_funded: 1
file:
- access_level: open_access
checksum: e1f0e4061212454574f34a1368d018ec
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T08:20:30Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6922'
file_name: 2019_LIPIcs_Chatterjee.pdf
file_size: 730112
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
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'
publication: Leibniz International Proceedings in Informatics
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near-linear time algorithms for Streett objectives in graphs and MDPs
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 140
year: '2019'
...
---
_id: '6888'
abstract:
- lang: eng
text: In this paper, we design novel liquid time-constant recurrent neural networks
for robotic control, inspired by the brain of the nematode, C. elegans. In the
worm's nervous system, neurons communicate through nonlinear time-varying synaptic
links established amongst them by their particular wiring structure. This property
enables neurons to express liquid time-constants dynamics and therefore allows
the network to originate complex behaviors with a small number of neurons. We
identify neuron-pair communication motifs as design operators and use them to
configure compact neuronal network structures to govern sequential robotic tasks.
The networks are systematically designed to map the environmental observations
to motor actions, by their hierarchical topology from sensory neurons, through
recurrently-wired interneurons, to motor neurons. The networks are then parametrized
in a supervised-learning scheme by a search-based algorithm. We demonstrate that
obtained networks realize interpretable dynamics. We evaluate their performance
in controlling mobile and arm robots, and compare their attributes to other artificial
neural network-based control agents. Finally, we experimentally show their superior
resilience to environmental noise, compared to the existing machine learning-based
methods.
alternative_title:
- ICRA
article_number: '8793840'
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Manuel
full_name: Zimmer, Manuel
last_name: Zimmer
- 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: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired
neural networks for interpretable robotic control. In: Proceedings - IEEE International
Conference on Robotics and Automation. Vol 2019-May. IEEE; 2019. doi:10.1109/icra.2019.8793840'
apa: 'Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., & Grosu, R. (2019).
Designing worm-inspired neural networks for interpretable robotic control. In
Proceedings - IEEE International Conference on Robotics and Automation
(Vol. 2019–May). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/icra.2019.8793840'
chicago: Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and
Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic
Control.” In Proceedings - IEEE International Conference on Robotics and Automation,
Vol. 2019–May. IEEE, 2019. https://doi.org/10.1109/icra.2019.8793840.
ieee: M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing
worm-inspired neural networks for interpretable robotic control,” in Proceedings
- IEEE International Conference on Robotics and Automation, Montreal, QC,
Canada, 2019, vol. 2019–May.
ista: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired
neural networks for interpretable robotic control. Proceedings - IEEE International
Conference on Robotics and Automation. ICRA: International Conference on Robotics
and Automation, ICRA, vol. 2019–May, 8793840.'
mla: Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable
Robotic Control.” Proceedings - IEEE International Conference on Robotics and
Automation, vol. 2019–May, 8793840, IEEE, 2019, doi:10.1109/icra.2019.8793840.
short: M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings
- IEEE International Conference on Robotics and Automation, IEEE, 2019.
conference:
end_date: 2019-05-24
location: Montreal, QC, Canada
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2019-05-20
date_created: 2019-09-18T08:09:51Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2021-01-12T08:09:28Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/icra.2019.8793840
file:
- access_level: open_access
checksum: f5545a6b60c3ffd01feb3613f81d03b6
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T17:30:38Z
date_updated: 2020-10-08T17:30:38Z
file_id: '8636'
file_name: 2019_ICRA_Lechner.pdf
file_size: 3265107
relation: main_file
success: 1
file_date_updated: 2020-10-08T17:30:38Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings - IEEE International Conference on Robotics and Automation
publication_identifier:
isbn:
- '9781538660270'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Designing worm-inspired neural networks for interpretable robotic control
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 2019-May
year: '2019'
...
---
_id: '6889'
abstract:
- lang: eng
text: 'We study Markov decision processes and turn-based stochastic games with parity
conditions. There are three qualitative winning criteria, namely, sure winning,
which requires all paths to satisfy the condition, almost-sure winning, which
requires the condition to be satisfied with probability 1, and limit-sure winning,
which requires the condition to be satisfied with probability arbitrarily close
to 1. We study the combination of two of these criteria for parity conditions,
e.g., there are two parity conditions one of which must be won surely, and the
other almost-surely. The problem has been studied recently by Berthon et al. for
MDPs with combination of sure and almost-sure winning, under infinite-memory strategies,
and the problem has been established to be in NP cap co-NP. Even in MDPs there
is a difference between finite-memory and infinite-memory strategies. Our main
results for combination of sure and almost-sure winning are as follows: (a) we
show that for MDPs with finite-memory strategies the problem is in NP cap co-NP;
(b) we show that for turn-based stochastic games the problem is co-NP-complete,
both for finite-memory and infinite-memory strategies; and (c) we present algorithmic
results for the finite-memory case, both for MDPs and turn-based stochastic games,
by reduction to non-stochastic parity games. In addition we show that all the
above complexity results also carry over to combination of sure and limit-sure
winning, and results for all other combinations can be derived from existing results
in the literature. Thus we present a complete picture for the study of combinations
of two qualitative winning criteria for parity conditions in MDPs and turn-based
stochastic games. '
alternative_title:
- LIPIcs
article_number: '6'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic
Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2019. doi:10.4230/LIPICS.CONCUR.2019.6'
apa: 'Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning
for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International
Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6'
chicago: Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative
Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6.
ieee: 'K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic
Parity Games,” presented at the CONCUR: International Conference on Concurrency
Theory, Amsterdam, Netherlands, 2019, vol. 140.'
ista: 'Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic
Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs,
vol. 140, 6.'
mla: Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning
for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6.
short: K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:11:43Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:09:28Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPICS.CONCUR.2019.6
file:
- access_level: open_access
checksum: 7b2ecfd4d9d02360308c0ca986fc10a7
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T08:49:45Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6923'
file_name: 2019_LIPIcs_Chatterjee.pdf
file_size: 509163
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Combinations of Qualitative Winning for Stochastic Parity 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2019'
...
---
_id: '6890'
abstract:
- lang: eng
text: Describing the protein interactions that form pleomorphic and asymmetric viruses
represents a considerable challenge to most structural biology techniques, including
X-ray crystallography and single particle cryo-electron microscopy. Obtaining
a detailed understanding of these interactions is nevertheless important, considering
the number of relevant human pathogens that do not follow strict icosahedral or
helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide
structural insights into complex biological environments and are well suited to
go beyond structures of perfectly symmetric viruses. This chapter discusses recent
developments showing that cryo-ET and subtomogram averaging can provide high-resolution
insights into hitherto unknown structural features of pleomorphic and asymmetric
virus particles. It also describes how these methods have significantly added
to our understanding of retrovirus capsid assemblies in immature and mature viruses.
Additional examples of irregular viruses and their associated proteins, whose
structures have been studied via cryo-ET and subtomogram averaging, further support
the versatility of these methods.
article_processing_charge: No
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary
Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus
Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008'
apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and
asymmetric viruses using cryo-electron tomography and subtomogram averaging. In
F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function
(Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008
chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic
and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
In Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008.
ieee: M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric
viruses using cryo-electron tomography and subtomogram averaging,” in Complementary
Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed.
Elsevier, 2019, pp. 117–159.
ista: 'Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies
to Study Virus Structure and Function. vol. 105, 117–159.'
mla: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and
Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.
short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study
Virus Structure and Function, Elsevier, 2019, pp. 117–159.
date_created: 2019-09-18T08:15:37Z
date_published: 2019-08-27T00:00:00Z
date_updated: 2023-08-30T06:56:00Z
day: '27'
department:
- _id: FlSc
doi: 10.1016/bs.aivir.2019.07.008
editor:
- first_name: Félix A.
full_name: Rey, Félix A.
last_name: Rey
external_id:
isi:
- '000501594500006'
pmid:
- ' 31522703'
intvolume: ' 105'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 117-159
pmid: 1
publication: Complementary Strategies to Study Virus Structure and Function
publication_identifier:
isbn:
- '9780128184561'
issn:
- 0065-3527
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
series_title: Advances in Virus Research
status: public
title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron
tomography and subtomogram averaging
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2019'
...
---
_id: '6891'
abstract:
- lang: eng
text: "While cells of mesenchymal or epithelial origin perform their effector functions
in a purely anchorage dependent manner, cells derived from the hematopoietic lineage
are not committed to operate only within a specific niche. Instead, these cells
are able to function autonomously of the molecular composition in a broad range
of tissue compartments. By this means, cells of the hematopoietic lineage retain
the capacity to disseminate into connective tissue and recirculate between organs,
building the foundation for essential processes such as tissue regeneration or
immune surveillance. \r\nCells of the immune system, specifically leukocytes,
are extraordinarily good at performing this task. These cells are able to flexibly
shift their mode of migration between an adhesion-mediated and an adhesion-independent
manner, instantaneously accommodating for any changes in molecular composition
of the external scaffold. The key component driving directed leukocyte migration
is the chemokine receptor 7, which guides the cell along gradients of chemokine
ligand. Therefore, the physical destination of migrating leukocytes is purely
deterministic, i.e. given by global directional cues such as chemokine gradients.
\r\nNevertheless, these cells typically reside in three-dimensional scaffolds
of inhomogeneous complexity, raising the question whether cells are able to locally
discriminate between multiple optional migration routes. Current literature provides
evidence that leukocytes, specifically dendritic cells, do indeed probe their
surrounding by virtue of multiple explorative protrusions. However, it remains
enigmatic how these cells decide which one is the more favorable route to follow
and what are the key players involved in performing this task. Due to the heterogeneous
environment of most tissues, and the vast adaptability of migrating leukocytes,
at this time it is not clear to what extent leukocytes are able to optimize their
migratory strategy by adapting their level of adhesiveness. And, given the fact
that leukocyte migration is characterized by branched cell shapes in combination
with high migration velocities, it is reasonable to assume that these cells require
fine tuned shape maintenance mechanisms that tightly coordinate protrusion and
adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed
to elucidate how rapidly migrating leukocytes opt for an ideal migratory path
while maintaining a continuous cell shape and balancing adhesive forces to efficiently
navigate through complex microenvironments. \r\nThe results of this study unraveled
a role for the microtubule cytoskeleton in promoting the decision making process
during path finding and for the first time point towards a microtubule-mediated
function in cell shape maintenance of highly ramified cells such as dendritic
cells. Furthermore, we found that migrating low-adhesive leukocytes are able to
instantaneously adapt to increased tensile load by engaging adhesion receptors.
This response was only occurring tangential to the substrate while adhesive properties
in the vertical direction were not increased. As leukocytes are primed for rapid
migration velocities, these results demonstrate that leukocyte integrins are able
to confer a high level of traction forces parallel to the cell membrane along
the direction of migration without wasting energy in gluing the cell to the substrate.
\r\nThus, the data in the here presented thesis provide new insights into the
pivotal role of cytoskeletal dynamics and the mechanisms of force transduction
during leukocyte migration. \r\nThereby the here presented results help to further
define fundamental principles underlying leukocyte migration and open up potential
therapeutic avenues of clinical relevance.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
citation:
ama: Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019.
doi:10.15479/AT:ISTA:6891
apa: Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891
chicago: Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.
ieee: A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,”
Institute of Science and Technology Austria, 2019.
ista: Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration.
Institute of Science and Technology Austria.
mla: Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.
short: A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration,
Institute of Science and Technology Austria, 2019.
date_created: 2019-09-19T08:19:44Z
date_published: 2019-07-24T00:00:00Z
date_updated: 2023-10-18T08:49:17Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:6891
file:
- access_level: closed
checksum: 00d100d6468e31e583051e0a006b640c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: akopf
date_created: 2019-10-15T05:28:42Z
date_updated: 2020-10-17T22:30:03Z
embargo_to: open_access
file_id: '6950'
file_name: Kopf_PhD_Thesis.docx
file_size: 74735267
relation: source_file
- access_level: open_access
checksum: 5d1baa899993ae6ca81aebebe1797000
content_type: application/pdf
creator: akopf
date_created: 2019-10-15T05:28:47Z
date_updated: 2020-10-17T22:30:03Z
embargo: 2020-10-16
file_id: '6951'
file_name: Kopf_PhD_Thesis1.pdf
file_size: 52787224
relation: main_file
file_date_updated: 2020-10-17T22:30:03Z
has_accepted_license: '1'
keyword:
- cell biology
- immunology
- leukocyte
- migration
- microfluidics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '171'
project:
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
publication_identifier:
eissn:
- 2663-337X
isbn:
- 978-3-99078-002-2
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/feeling-like-a-cell/
record:
- id: '6328'
relation: part_of_dissertation
status: public
- id: '15'
relation: part_of_dissertation
status: public
- id: '6877'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: The implication of cytoskeletal dynamics on leukocyte migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6894'
abstract:
- lang: eng
text: "Hybrid automata combine finite automata and dynamical systems, and model
the interaction of digital with physical systems. Formal analysis that can guarantee
the safety of all behaviors or rigorously witness failures, while unsolvable in
general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking,
assisted theorem proving.\r\nNevertheless, very few methods have addressed the
time-unbounded reachability analysis of hybrid automata and, for current sound
and automatic tools, scalability remains critical. We develop methods for the
polyhedral abstraction of hybrid automata, which construct coarse overapproximations
and tightens them incrementally, in a CEGAR fashion. We use template polyhedra,
i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile,
previously, directions were given by the user, we introduce (1) the first method\r\nfor
computing template directions from spurious counterexamples, so as to generalize
and\r\neliminate them. The method applies naturally to convex hybrid automata,
i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives
only, while for linear\r\nODE requires further abstraction. Specifically, we introduce
(2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate
(possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight
sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time
interpolation, which, combining interval arithmetic\r\nand template refinement,
computes appropriate (possibly non-uniform) time partitioning\r\nand template
directions along spurious trajectories, so as to eliminate them.\r\nWe obtain
sound and automatic methods for the reachability analysis over dense\r\nand unbounded
time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build
prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art
tools, on several benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
citation:
ama: Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems.
2019. doi:10.15479/AT:ISTA:6894
apa: Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid
systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894
chicago: Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid
Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.
ieee: M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,”
Institute of Science and Technology Austria, 2019.
ista: Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid
systems. Institute of Science and Technology Austria.
mla: Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid
Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.
short: M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems,
Institute of Science and Technology Austria, 2019.
date_created: 2019-09-22T14:08:44Z
date_published: 2019-09-30T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '30'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:6894
file:
- access_level: open_access
checksum: 773beaf4a85dc2acc2c12b578fbe1965
content_type: application/pdf
creator: mgiacobbe
date_created: 2019-09-27T14:15:05Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6916'
file_name: giacobbe_thesis.pdf
file_size: 4100685
relation: main_file
- access_level: closed
checksum: 97f1c3da71feefd27e6e625d32b4c75b
content_type: application/gzip
creator: mgiacobbe
date_created: 2019-09-27T14:22:04Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6917'
file_name: giacobbe_thesis_src.tar.gz
file_size: 7959732
relation: source_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '132'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '631'
relation: part_of_dissertation
status: public
- id: '647'
relation: part_of_dissertation
status: public
- id: '140'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic time-unbounded reachability analysis of hybrid systems
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6896'
abstract:
- lang: eng
text: "Until recently, a great amount of brain studies have been conducted in human
post mortem tissues, cell lines and model organisms. These researches provided
useful insights regarding cell-cell interactions occurring in the brain. However,
such approaches suffer from technical limitations and inaccurate modeling of the
tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background
essential for disease modeling. With the development of protocols to generate
human cerebral organoids, we are now closer to reproducing the early stages of
human brain development in vitro. As a result, more relevant cell-cell interaction
studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of
3D cultures over 2D in modulating brain cell-cell interactions during physiological
and pathological development, as well as the progress made in developing organoids
in which neurons, macroglia, microglia and vascularization are present. Finally,
we debate the limitations of those models and possible future directions."
article_number: '146458'
article_processing_charge: No
article_type: original
author:
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain
using cerebral organoids. Brain Research. 2019;1724. doi:10.1016/j.brainres.2019.146458
apa: Oliveira, B., Yahya, A. Ç., & Novarino, G. (2019). Modeling cell-cell interactions
in the brain using cerebral organoids. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2019.146458
chicago: Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell
Interactions in the Brain Using Cerebral Organoids.” Brain Research. Elsevier,
2019. https://doi.org/10.1016/j.brainres.2019.146458.
ieee: B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions
in the brain using cerebral organoids,” Brain Research, vol. 1724. Elsevier,
2019.
ista: Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in
the brain using cerebral organoids. Brain Research. 1724, 146458.
mla: Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using
Cerebral Organoids.” Brain Research, vol. 1724, 146458, Elsevier, 2019,
doi:10.1016/j.brainres.2019.146458.
short: B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019).
date_created: 2019-09-22T22:00:35Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T06:19:49Z
day: '01'
department:
- _id: GaNo
doi: 10.1016/j.brainres.2019.146458
external_id:
isi:
- '000491646600033'
pmid:
- '31521639'
intvolume: ' 1724'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
publication: Brain Research
publication_identifier:
eissn:
- '18726240'
issn:
- '00068993'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling cell-cell interactions in the brain using cerebral organoids
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 1724
year: '2019'
...