---
_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: '6328'
abstract:
- lang: eng
text: During metazoan development, immune surveillance and cancer dissemination,
cells migrate in complex three-dimensional microenvironments1,2,3. These spaces
are crowded by cells and extracellular matrix, generating mazes with differently
sized gaps that are typically smaller than the diameter of the migrating cell4,5.
Most mesenchymal and epithelial cells and some—but not all—cancer cells actively
generate their migratory path using pericellular tissue proteolysis6. By contrast,
amoeboid cells such as leukocytes use non-destructive strategies of locomotion7,
raising the question how these extremely fast cells navigate through dense tissues.
Here we reveal that leukocytes sample their immediate vicinity for large pore
sizes, and are thereby able to choose the path of least resistance. This allows
them to circumnavigate local obstacles while effectively following global directional
cues such as chemotactic gradients. Pore-size discrimination is facilitated by
frontward positioning of the nucleus, which enables the cells to use their bulkiest
compartment as a mechanical gauge. Once the nucleus and the closely associated
microtubule organizing centre pass the largest pore, cytoplasmic protrusions still
lingering in smaller pores are retracted. These retractions are coordinated by
dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence
and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning
in front of the microtubule organizing centre is a typical feature of amoeboid
migration, our findings link the fundamental organization of cellular polarity
to the strategy of locomotion.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Meghan K.
full_name: Driscoll, Meghan K.
last_name: Driscoll
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Erik S.
full_name: Welf, Erik S.
last_name: Welf
- first_name: Gaudenz
full_name: Danuser, Gaudenz
last_name: Danuser
- first_name: Reto
full_name: Fiolka, Reto
last_name: Fiolka
- 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: Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid
migration along the path of least resistance. Nature. 2019;568:546-550.
doi:10.1038/s41586-019-1087-5
apa: Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin,
J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along
the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5
chicago: Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K.
Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates
Amoeboid Migration along the Path of Least Resistance.” Nature. Springer
Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.
ieee: J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration
along the path of least resistance,” Nature, vol. 568. Springer Nature,
pp. 546–550, 2019.
ista: Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild
R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates
amoeboid migration along the path of least resistance. Nature. 568, 546–550.
mla: Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration
along the Path of Least Resistance.” Nature, vol. 568, Springer Nature,
2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.
short: J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin,
R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.
date_created: 2019-04-17T06:52:28Z
date_published: 2019-04-25T00:00:00Z
date_updated: 2024-03-28T23:30:40Z
day: '25'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
doi: 10.1038/s41586-019-1087-5
ec_funded: 1
external_id:
isi:
- '000465594200050'
pmid:
- '30944468'
intvolume: ' 568'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/
month: '04'
oa: 1
oa_version: Submitted Version
page: 546-550
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 265FAEBA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
publication: Nature
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/
record:
- id: '14697'
relation: dissertation_contains
status: public
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nuclear positioning facilitates amoeboid migration along the path of least
resistance
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6830'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron.
2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021
apa: Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell
grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021
chicago: Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial
Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021.
ieee: X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,”
Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.
ista: Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid.
Neuron. 103(5), 750–752.
mla: Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell
Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.
short: X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.
date_created: 2019-08-25T22:00:50Z
date_published: 2019-09-04T00:00:00Z
date_updated: 2024-03-28T23:30:42Z
day: '04'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2019.08.021
external_id:
isi:
- '000484400200002'
pmid:
- '31487522'
intvolume: ' 103'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.08.021
month: '09'
oa: 1
oa_version: Published Version
page: 750-752
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- '10974199'
issn:
- '08966273'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '7902'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Memo1 tiles the radial glial cell grid
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2019'
...
---
_id: '6627'
abstract:
- lang: eng
text: Cortical microtubule arrays in elongating epidermal cells in both the root
and stem of plants have the propensity of dynamic reorientations that are correlated
with the activation or inhibition of growth. Factors regulating plant growth,
among them the hormone auxin, have been recognized as regulators of microtubule
array orientations. Some previous work in the field has aimed at elucidating the
causal relationship between cell growth, the signaling of auxin or other growth-regulating
factors, and microtubule array reorientations, with various conclusions. Here,
we revisit this problem of causality with a comprehensive set of experiments in
Arabidopsis thaliana, using the now available pharmacological and genetic tools.
We use isolated, auxin-depleted hypocotyls, an experimental system allowing for
full control of both growth and auxin signaling. We demonstrate that reorientation
of microtubules is not directly triggered by an auxin signal during growth activation.
Instead, reorientation is triggered by the activation of the growth process itself
and is auxin-independent in its nature. We discuss these findings in the context
of previous relevant work, including that on the mechanical regulation of microtubule
array orientation.
article_number: '3337'
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in
the hypocotyl of arabidopsis thaliana is induced by the cell growth process and
independent of auxin signaling. International Journal of Molecular Sciences.
2019;20(13). doi:10.3390/ijms20133337
apa: Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule
arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth
process and independent of auxin signaling. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms20133337
chicago: Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical
Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the
Cell Growth Process and Independent of Auxin Signaling.” International Journal
of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.
ieee: M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule
arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth
process and independent of auxin signaling,” International Journal of Molecular
Sciences, vol. 20, no. 13. MDPI, 2019.
ista: Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays
in the hypocotyl of arabidopsis thaliana is induced by the cell growth process
and independent of auxin signaling. International Journal of Molecular Sciences.
20(13), 3337.
mla: Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in
the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and
Independent of Auxin Signaling.” International Journal of Molecular Sciences,
vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.
short: M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences
20 (2019).
date_created: 2019-07-11T12:00:32Z
date_published: 2019-07-07T00:00:00Z
date_updated: 2024-03-28T23:30:44Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/ijms20133337
ec_funded: 1
external_id:
isi:
- '000477041100221'
pmid:
- '31284661'
file:
- access_level: open_access
checksum: dd9d1cbb933a72ceb666c9667890ac51
content_type: application/pdf
creator: dernst
date_created: 2019-07-17T06:17:15Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6645'
file_name: 2019_JournalMolecularScience_Adamowski.pdf
file_size: 3330291
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '13'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis
thaliana is induced by the cell growth process and independent of auxin signaling
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: '7117'
abstract:
- lang: eng
text: We propose a novel generic shape optimization method for CAD models based
on the eXtended Finite Element Method (XFEM). Our method works directly on the
intersection between the model and a regular simulation grid, without the need
to mesh or remesh, thus removing a bottleneck of classical shape optimization
strategies. This is made possible by a novel hierarchical integration scheme that
accurately integrates finite element quantities with sub-element precision. For
optimization, we efficiently compute analytical shape derivatives of the entire
framework, from model intersection to integration rule generation and XFEM simulation.
Moreover, we describe a differentiable projection of shape parameters onto a constraint
manifold spanned by user-specified shape preservation, consistency, and manufacturability
constraints. We demonstrate the utility of our approach by optimizing mass distribution,
strength-to-weight ratio, and inverse elastic shape design objectives directly
on parameterized 3D CAD models.
article_number: '157'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Christian
full_name: Schumacher, Christian
last_name: Schumacher
- first_name: Espen
full_name: Knoop, Espen
last_name: Knoop
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Moritz
full_name: Bächer, Moritz
last_name: Bächer
citation:
ama: 'Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing
CAD Models with Extended Finite Elements. ACM Transactions on Graphics.
2019;38(6). doi:10.1145/3355089.3356576'
apa: 'Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer,
M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM
Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576'
chicago: 'Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger,
Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite
Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.'
ieee: 'C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer,
“X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions
on Graphics, vol. 38, no. 6. ACM, 2019.'
ista: 'Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD:
Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics.
38(6), 157.'
mla: 'Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite
Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019,
doi:10.1145/3355089.3356576.'
short: C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM
Transactions on Graphics 38 (2019).
date_created: 2019-11-26T14:22:09Z
date_published: 2019-11-06T00:00:00Z
date_updated: 2024-03-28T23:30:47Z
day: '06'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3355089.3356576
ec_funded: 1
external_id:
isi:
- '000498397300007'
file:
- access_level: open_access
checksum: 56a2fb019adcb556d2b022f5e5acb68c
content_type: application/pdf
creator: bbickel
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date_updated: 2020-07-14T12:47:49Z
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file_size: 1673176
relation: supplementary_material
title: X-CAD Supplemental Material
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content_type: application/pdf
creator: bbickel
date_created: 2019-11-26T14:24:27Z
date_updated: 2020-07-14T12:47:49Z
description: This is the author's version of the work.
file_id: '7120'
file_name: XCAD_authors_version.pdf
file_size: 14563618
relation: main_file
title: 'X-CAD: Optimizing CAD Models with Extended Finite Elements'
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checksum: 0d31e123286cbec9e28b2001c2bb0d55
content_type: video/mp4
creator: bbickel
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date_updated: 2020-07-14T12:47:49Z
file_id: '7121'
file_name: XCAD_video.mp4
file_size: 259979129
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file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '12897'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'X-CAD: Optimizing CAD Models with Extended Finite Elements'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2019'
...
---
_id: '6371'
abstract:
- lang: eng
text: "Decades of studies have revealed the mechanisms of gene regulation in molecular
detail. We make use of such well-described regulatory systems to explore how the
molecular mechanisms of protein-protein and protein-DNA interactions shape the
dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics
of protein-DNA binding determines the potential of regulatory networks to evolve
and adapt, which can be captured using a simple mathematical model. \r\nii) The
evolution of regulatory connections can lead to a significant amount of crosstalk
between binding proteins. We explore the effect of crosstalk on gene expression
from a target promoter, which seems to be modulated through binding competition
at non-specific DNA sites. \r\niii) We investigate how the very same biophysical
characteristics as in i) can generate significant fitness costs for cells through
global crosstalk, meaning non-specific DNA binding across the genomic background.
\r\niv) Binding competition between proteins at a target promoter is a prevailing
regulatory feature due to the prevalence of co-regulation at bacterial promoters.
However, the dynamics of these systems are not always straightforward to determine
even if the molecular mechanisms of regulation are known. A detailed model of
the biophysical interactions reveals that interference between the regulatory
proteins can constitute a new, generic form of system memory that records the
history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics
of protein-DNA binding can be harnessed to investigate the principles that shape
and ultimately limit cellular gene regulation. These results provide a basis for
studies of higher-level functionality, which arises from the underlying regulation.
\ \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
citation:
ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371
apa: Igler, C. (2019). On the nature of gene regulatory design - The biophysics
of transcription factor binding shapes gene regulation. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371
chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.
ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation,” Institute of Science and Technology Austria,
2019.
ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of
transcription factor binding shapes gene regulation. Institute of Science and
Technology Austria.
mla: Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.
short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription
Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria,
2019.
date_created: 2019-05-03T11:55:51Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2024-02-21T13:45:52Z
day: '03'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:6371
file:
- access_level: open_access
checksum: c0085d47c58c9cbcab1b0a783480f6da
content_type: application/pdf
creator: cigler
date_created: 2019-05-03T11:54:52Z
date_updated: 2021-02-11T11:17:13Z
embargo: 2020-05-02
file_id: '6373'
file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf
file_size: 12597663
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creator: cigler
date_created: 2019-05-03T11:54:54Z
date_updated: 2020-07-14T12:47:28Z
embargo_to: open_access
file_id: '6374'
file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx
file_size: 34644426
relation: source_file
file_date_updated: 2021-02-11T11:17:13Z
has_accepted_license: '1'
keyword:
- gene regulation
- biophysics
- transcription factor binding
- bacteria
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '152'
project:
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '67'
relation: part_of_dissertation
status: public
- id: '5585'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: On the nature of gene regulatory design - The biophysics of transcription factor
binding shapes gene regulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6189'
abstract:
- lang: eng
text: 'Suspended particles can alter the properties of fluids and in particular
also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset
al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic)
transition to turbulent puffs is affected by the addition of particles. Here weshow
that in addition to this known transition, with increasing concentration a supercritical
(i.e.,continuous) transition to a globally fluctuating state is found. At the
same time the Newtonian-typetransition to puffs is delayed to larger Reynolds
numbers. At even higher concentration only the globallyfluctuating state is found.
The dynamics of particle laden flows are hence determined by two competinginstabilities
that give rise to three flow regimes: Newtonian-type turbulence at low, a particle
inducedglobally fluctuating state at high, and a coexistence state at intermediate
concentrations.'
article_number: '114502'
article_processing_charge: No
author:
- first_name: Nishchal
full_name: Agrawal, Nishchal
id: 469E6004-F248-11E8-B48F-1D18A9856A87
last_name: Agrawal
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows.
Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502
apa: Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence
in particle laden flows. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.122.114502
chicago: Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence
in Particle Laden Flows.” Physical Review Letters. American Physical Society,
2019. https://doi.org/10.1103/PhysRevLett.122.114502.
ieee: N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle
laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical
Society, 2019.
ista: Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle
laden flows. Physical Review Letters. 122(11), 114502.
mla: Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.”
Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society,
2019, doi:10.1103/PhysRevLett.122.114502.
short: N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).
date_created: 2019-03-31T21:59:12Z
date_published: 2019-03-22T00:00:00Z
date_updated: 2024-03-28T23:30:48Z
day: '22'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.122.114502
external_id:
arxiv:
- '1809.06358'
isi:
- '000461922000006'
intvolume: ' 122'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.06358
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '9728'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Transition to turbulence in particle laden flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2019'
...
---
_id: '10286'
abstract:
- lang: eng
text: 'In this paper, we evaluate clock signals generated in ring oscillators and
self-timed rings and the way their jitter can be transformed into random numbers.
We show that counting the periods of the jittery clock signal produces random
numbers of significantly better quality than the methods in which the jittery
signal is simply sampled (the case in almost all current methods). Moreover, we
use the counter values to characterize and continuously monitor the source of
randomness. However, instead of using the widely used statistical variance, we
propose to use Allan variance to do so. There are two main advantages: Allan variance
is insensitive to low frequency noises such as flicker noise that are known to
be autocorrelated and significantly less circuitry is required for its computation
than that used to compute commonly used variance. We also show that it is essential
to use a differential principle of randomness extraction from the jitter based
on the use of two identical oscillators to avoid autocorrelations originating
from external and internal global jitter sources and that this fact is valid for
both kinds of rings. Last but not least, we propose a method of statistical testing
based on high order Markov model to show the reduced dependencies when the proposed
randomness extraction is applied.'
article_processing_charge: No
article_type: original
author:
- first_name: Elie Noumon
full_name: Allini, Elie Noumon
last_name: Allini
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
- first_name: Oto
full_name: Petura, Oto
last_name: Petura
- first_name: Florent
full_name: Bernard, Florent
last_name: Bernard
- first_name: Marek
full_name: Laban, Marek
last_name: Laban
- first_name: Viktor
full_name: Fischer, Viktor
last_name: Fischer
citation:
ama: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and
monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242.
doi:10.13154/tches.v2018.i3.214-242
apa: Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer,
V. (2018). Evaluation and monitoring of free running oscillators serving as source
of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems.
International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242
chicago: Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek
Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems. International Association for Cryptologic Research,
2018. https://doi.org/10.13154/tches.v2018.i3.214-242.
ieee: E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer,
“Evaluation and monitoring of free running oscillators serving as source of randomness,”
IACR Transactions on Cryptographic Hardware and Embedded Systems, vol.
2018, no. 3. International Association for Cryptologic Research, pp. 214–242,
2018.
ista: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation
and monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.
mla: Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic
Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.
short: E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR
Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.
date_created: 2021-11-14T23:01:25Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-11-15T10:48:49Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/tches.v2018.i3.214-242
file:
- access_level: open_access
checksum: b816b848f046c48a8357700d9305dce5
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T10:27:29Z
date_updated: 2021-11-15T10:27:29Z
file_id: '10289'
file_name: 2018_IACR_Allini.pdf
file_size: 955755
relation: main_file
success: 1
file_date_updated: 2021-11-15T10:27:29Z
has_accepted_license: '1'
intvolume: ' 2018'
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 214-242
publication: IACR Transactions on Cryptographic Hardware and Embedded Systems
publication_identifier:
eissn:
- 2569-2925
publication_status: published
publisher: International Association for Cryptologic Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evaluation and monitoring of free running oscillators serving as source of
randomness
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2018
year: '2018'
...
---
_id: '10883'
abstract:
- lang: eng
text: 'Solving parity games, which are equivalent to modal μ-calculus model checking,
is a central algorithmic problem in formal methods, with applications in reactive
synthesis, program repair, verification of branching-time properties, etc. Besides
the standard compu- tation model with the explicit representation of games, another
important theoretical model of computation is that of set-based symbolic algorithms.
Set-based symbolic algorithms use basic set operations and one-step predecessor
operations on the implicit description of games, rather than the explicit representation.
The significance of symbolic algorithms is that they provide scalable algorithms
for large finite-state systems, as well as for infinite-state systems with finite
quotient. Consider parity games on graphs with n vertices and parity conditions
with d priorities. While there is a rich literature of explicit algorithms for
parity games, the main results for set-based symbolic algorithms are as follows:
(a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic
space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations
and O(n) symbolic space. In this work, our contributions are as follows: (1) We
present a black-box set-based symbolic algorithm based on the explicit progress
measure algorithm. Two important consequences of our algorithm are as follows:
(a) a set-based symbolic algorithm for parity games that requires quasi-polynomially
many symbolic operations and O(n) symbolic space; and (b) any future improvement
in progress measure based explicit algorithms immediately imply an efficiency
improvement in our set-based symbolic algorithm for parity games. (2) We present
a set-based symbolic algorithm that requires quasi-polynomially many symbolic
operations and O(d · log n) symbolic space. Moreover, for the important special
case of d ≤ log n, our algorithm requires only polynomially many symbolic operations
and poly-logarithmic symbolic space.'
acknowledgement: 'A. S. is fully supported by the Vienna Science and Technology Fund
(WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund
(FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph
Games). For M.H the research leading to these results has received funding from
the European Research Council under the European Union’s Seventh Framework Programme
(FP/2007-2013) /ERC Grant Agreement no. 340506.'
alternative_title:
- EPiC Series in Computing
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: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based
symbolic algorithms for parity games. In: 22nd International Conference on
Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair;
2018:233-253. doi:10.29007/5z5k'
apa: 'Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial
set-based symbolic algorithms for parity games. In 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57,
pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k'
chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander
Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd
International Conference on Logic for Programming, Artificial Intelligence and
Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.
ieee: K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial
set-based symbolic algorithms for parity games,” in 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia,
2018, vol. 57, pp. 233–253.
ista: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based
symbolic algorithms for parity games. 22nd International Conference on Logic for
Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic
for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing,
vol. 57, 233–253.'
mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms
for Parity Games.” 22nd International Conference on Logic for Programming,
Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53,
doi:10.29007/5z5k.
short: K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International
Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair,
2018, pp. 233–253.
conference:
end_date: 2018-11-21
location: Awassa, Ethiopia
name: 'LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2018-11-17
date_created: 2022-03-18T12:46:32Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2022-07-29T09:24:31Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29007/5z5k
ec_funded: 1
external_id:
arxiv:
- '1909.04983'
file:
- access_level: open_access
checksum: 1229aa8640bd6db610c85decf2265480
content_type: application/pdf
creator: dernst
date_created: 2022-05-17T07:51:08Z
date_updated: 2022-05-17T07:51:08Z
file_id: '11392'
file_name: 2018_EPiCs_Chatterjee.pdf
file_size: 720893
relation: main_file
success: 1
file_date_updated: 2022-05-17T07:51:08Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 233-253
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: 22nd International Conference on Logic for Programming, Artificial Intelligence
and Reasoning
publication_identifier:
issn:
- 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quasipolynomial set-based symbolic algorithms for parity games
type: conference
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 57
year: '2018'
...
---
_id: '11'
abstract:
- lang: eng
text: We report on a novel strategy to derive mean-field limits of quantum mechanical
systems in which a large number of particles weakly couple to a second-quantized
radiation field. The technique combines the method of counting and the coherent
state approach to study the growth of the correlations among the particles and
in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon
system of equations from the Nelson model with ultraviolet cutoff and possibly
massless scalar field. In particular, we prove the convergence of the reduced
density matrices (of the nonrelativistic particles and the field bosons) associated
with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon
equations in trace norm. Furthermore, we derive explicit bounds on the rate of
convergence of the one-particle reduced density matrix of the nonrelativistic
particles in Sobolev norm.
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised
radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9'
apa: 'Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in
interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented
at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer.
https://doi.org/10.1007/978-3-030-01602-9_9'
chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.
ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction
with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits
of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.'
ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction
with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems
vol. 270, 185–214.'
mla: Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp.
185–214, doi:10.1007/978-3-030-01602-9_9.
short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.
conference:
end_date: 2017-04-01
location: Munich, Germany
name: 'MaLiQS: Macroscopic Limits of Quantum Systems'
start_date: 2017-03-30
date_created: 2018-12-11T11:44:08Z
date_published: 2018-10-27T00:00:00Z
date_updated: 2021-01-12T06:48:16Z
day: '27'
department:
- _id: RoSe
doi: 10.1007/978-3-030-01602-9_9
ec_funded: 1
external_id:
arxiv:
- '1806.10843'
intvolume: ' 270'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.10843
month: '10'
oa: 1
oa_version: Preprint
page: 185 - 214
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_status: published
publisher: Springer
publist_id: '8045'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mean-field limits of particles in interaction with quantised radiation fields
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2018'
...
---
_id: '1215'
abstract:
- lang: eng
text: "Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe
first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations
when they occur in examples and it is applied to the case of a group\r\ngenerator.
The second one, based on the previous one and a limit procedure, is an Itô\r\nformula
in a special class of Banach spaces having a product structure with the noise\r\nin
a Hilbert component; again the key point is the extension due to a cancellation.
This\r\nextension to Banach spaces and in particular the specific cancellation
are motivated\r\nby path-dependent Itô calculus."
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). The second named author benefited partially from the support of the
“FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H).
He is also grateful for the invitation to the Department of Mathematics of the University
of Pisa. The third named author is grateful for the invitation to ENSTA.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Franco
full_name: Flandoli, Franco
last_name: Flandoli
- first_name: Francesco
full_name: Russo, Francesco
last_name: Russo
- first_name: Giovanni A
full_name: Zanco, Giovanni A
id: 47491882-F248-11E8-B48F-1D18A9856A87
last_name: Zanco
citation:
ama: Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial
regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826.
doi:10.1007/s10959-016-0724-2
apa: Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus
under weak spatial regularity of the processes. Journal of Theoretical Probability.
Springer. https://doi.org/10.1007/s10959-016-0724-2
chicago: Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional
Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical
Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.
ieee: F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under
weak spatial regularity of the processes,” Journal of Theoretical Probability,
vol. 31, no. 2. Springer, pp. 789–826, 2018.
ista: Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak
spatial regularity of the processes. Journal of Theoretical Probability. 31(2),
789–826.
mla: Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial
Regularity of the Processes.” Journal of Theoretical Probability, vol.
31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.
short: F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31
(2018) 789–826.
date_created: 2018-12-11T11:50:45Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:09Z
day: '01'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1007/s10959-016-0724-2
file:
- access_level: open_access
checksum: 47686d58ec21c164540f1a980ff2163f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:13Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5266'
file_name: IST-2016-712-v1+1_s10959-016-0724-2.pdf
file_size: 671125
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 789-826
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Journal of Theoretical Probability
publication_status: published
publisher: Springer
publist_id: '6119'
pubrep_id: '712'
quality_controlled: '1'
scopus_import: 1
status: public
title: Infinite-dimensional calculus under weak spatial regularity of the processes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '185'
abstract:
- lang: eng
text: We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998),
and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the
setting of approximating maps of graphs on 2-dimensional surfaces by embeddings.
Our proof of this result is constructive and almost immediately implies an efficient
algorithm for testing whether a given piecewise linear map of a graph in a surface
is approximable by an embedding. More precisely, an instance of this problem consists
of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster
edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact
surface M given as the union of a set of pairwise disjoint discs corresponding
to the clusters and a set of pairwise disjoint "pipes" corresponding
to the bundles, connecting certain pairs of these discs. We are to decide whether
G can be embedded inside M so that the vertices in every cluster are drawn in
the corresponding disc, the edges in every bundle pass only through its corresponding
pipe, and every edge crosses the boundary of each disc at most once.
alternative_title:
- Leibniz International Proceedings in Information, LIPIcs
article_number: '39'
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: 'Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39'
apa: 'Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of
graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry,
Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39'
chicago: Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of
Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39.
ieee: 'R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented
at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol.
99.'
ista: 'Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG:
Symposium on Computational Geometry, Leibniz International Proceedings in Information,
LIPIcs, vol. 99, 39.'
mla: Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs.
Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.
short: R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:04Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:36Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2018.39
file:
- access_level: open_access
checksum: f1b94f1a75b37c414a1f61d59fb2cd4c
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:33:52Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5701'
file_name: 2018_LIPIcs_Fulek.pdf
file_size: 718857
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication_identifier:
isbn:
- 978-3-95977-066-8
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7735'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hanani-Tutte for approximating maps of graphs
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '188'
abstract:
- lang: eng
text: Smallest enclosing spheres of finite point sets are central to methods in
topological data analysis. Focusing on Bregman divergences to measure dissimilarity,
we prove bounds on the location of the center of a smallest enclosing sphere.
These bounds depend on the range of radii for which Bregman balls are convex.
acknowledgement: This research is partially supported by the Office of Naval Research,
through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR
109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of
the Austrian Science Fund
alternative_title:
- Leibniz International Proceedings in Information, LIPIcs
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ziga
full_name: Virk, Ziga
last_name: Virk
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff
points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35'
apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres
and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at
the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35'
chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing
Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.
ieee: 'H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and
Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational
Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.'
ista: 'Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff
points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz
International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.'
mla: Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points
in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.
short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018, p. 35:1-35:13.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:05Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2021-01-12T06:53:48Z
day: '11'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2018.35
file:
- access_level: open_access
checksum: 7509403803b3ac1aee94bbc2ad293d21
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:31:31Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5724'
file_name: 2018_LIPIcs_Edelsbrunner.pdf
file_size: 489080
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 35:1 - 35:13
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7733'
quality_controlled: '1'
scopus_import: 1
status: public
title: Smallest enclosing spheres and Chernoff points in Bregman geometry
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '306'
abstract:
- lang: eng
text: A cornerstone of statistical inference, the maximum entropy framework is being
increasingly applied to construct descriptive and predictive models of biological
systems, especially complex biological networks, from large experimental data
sets. Both its broad applicability and the success it obtained in different contexts
hinge upon its conceptual simplicity and mathematical soundness. Here we try to
concisely review the basic elements of the maximum entropy principle, starting
from the notion of ‘entropy’, and describe its usefulness for the analysis of
biological systems. As examples, we focus specifically on the problem of reconstructing
gene interaction networks from expression data and on recent work attempting to
expand our system-level understanding of bacterial metabolism. Finally, we highlight
some extensions and potential limitations of the maximum entropy approach, and
point to more recent developments that are likely to play a key role in the upcoming
challenges of extracting structures and information from increasingly rich, high-throughput
biological data.
article_number: e00596
author:
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino A, De Martino D. An introduction to the maximum entropy approach
and its application to inference problems in biology. Heliyon. 2018;4(4).
doi:10.1016/j.heliyon.2018.e00596
apa: De Martino, A., & De Martino, D. (2018). An introduction to the maximum
entropy approach and its application to inference problems in biology. Heliyon.
Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596
chicago: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum
Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon.
Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.
ieee: A. De Martino and D. De Martino, “An introduction to the maximum entropy approach
and its application to inference problems in biology,” Heliyon, vol. 4,
no. 4. Elsevier, 2018.
ista: De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach
and its application to inference problems in biology. Heliyon. 4(4), e00596.
mla: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum
Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon,
vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.
short: A. De Martino, D. De Martino, Heliyon 4 (2018).
date_created: 2018-12-11T11:45:44Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '01'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1016/j.heliyon.2018.e00596
ec_funded: 1
file:
- access_level: open_access
checksum: 67010cf5e3b3e0637c659371714a715a
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T07:36:24Z
date_updated: 2020-07-14T12:45:59Z
file_id: '5929'
file_name: 2018_Heliyon_DeMartino.pdf
file_size: 994490
relation: main_file
file_date_updated: 2020-07-14T12:45:59Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Heliyon
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: 1
status: public
title: An introduction to the maximum entropy approach and its application to inference
problems in biology
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: 4
year: '2018'
...
---
_id: '37'
abstract:
- lang: eng
text: Developmental processes are inherently dynamic and understanding them requires
quantitative measurements of gene and protein expression levels in space and time.
While live imaging is a powerful approach for obtaining such data, it is still
a challenge to apply it over long periods of time to large tissues, such as the
embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression
and signaling activity patterns in this organ can be studied by collecting tissue
sections at different developmental stages. In combination with immunohistochemistry,
this allows for measuring the levels of multiple developmental regulators in a
quantitative manner with high spatiotemporal resolution. The mean protein expression
levels over time, as well as embryo-to-embryo variability can be analyzed. A key
aspect of the approach is the ability to compare protein levels across different
samples. This requires a number of considerations in sample preparation, imaging
and data analysis. Here we present a protocol for obtaining time course data of
dorsoventral expression patterns from mouse and chick neural tube in the first
3 days of neural tube development. The described workflow starts from embryo dissection
and ends with a processed dataset. Software scripts for data analysis are included.
The protocol is adaptable and instructions that allow the user to modify different
steps are provided. Thus, the procedure can be altered for analysis of time-lapse
images and applied to systems other than the neural tube.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: 'Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling
profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863.
MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4'
apa: Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and
morphogen signaling profiles in the growing neural tube. In Morphogen Gradients
(Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4
chicago: Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and
Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients
, 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.
ieee: M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen
signaling profiles in the growing neural tube,” in Morphogen Gradients ,
vol. 1863, Springer Nature, 2018, pp. 47–63.
ista: 'Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen
signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods
in Molecular Biology, vol. 1863, 47–63.'
mla: Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and
Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients
, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.
short: M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018,
pp. 47–63.
date_created: 2018-12-11T11:44:17Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2021-01-12T07:49:03Z
day: '16'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1007/978-1-4939-8772-6_4
ec_funded: 1
file:
- access_level: open_access
checksum: 2a97d0649fdcfcf1bdca7c8ad1dce71b
content_type: application/pdf
creator: dernst
date_created: 2020-10-13T14:20:37Z
date_updated: 2020-10-13T14:20:37Z
file_id: '8656'
file_name: 2018_MIMB_Zagorski.pdf
file_size: 4906815
relation: main_file
success: 1
file_date_updated: 2020-10-13T14:20:37Z
has_accepted_license: '1'
intvolume: ' 1863'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 47 - 63
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: 'Morphogen Gradients '
publication_identifier:
isbn:
- 978-1-4939-8771-9
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
publist_id: '8018'
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Measuring dorsoventral pattern and morphogen signaling profiles in the growing
neural tube
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1863
year: '2018'
...
---
_id: '325'
abstract:
- lang: eng
text: Probabilistic programs extend classical imperative programs with real-valued
random variables and random branching. The most basic liveness property for such
programs is the termination property. The qualitative (aka almost-sure) termination
problem asks whether a given program program terminates with probability 1. While
ranking functions provide a sound and complete method for non-probabilistic programs,
the extension of them to probabilistic programs is achieved via ranking supermartingales
(RSMs). Although deep theoretical results have been established about RSMs, their
application to probabilistic programs with nondeterminism has been limited only
to programs of restricted control-flow structure. For non-probabilistic programs,
lexicographic ranking functions provide a compositional and practical approach
for termination analysis of real-world programs. In this work we introduce lexicographic
RSMs and show that they present a sound method for almost-sure termination of
probabilistic programs with nondeterminism. We show that lexicographic RSMs provide
a tool for compositional reasoning about almost-sure termination, and for probabilistic
programs with linear arithmetic they can be synthesized efficiently (in polynomial
time). We also show that with additional restrictions even asymptotic bounds on
expected termination time can be obtained through lexicographic RSMs. Finally,
we present experimental results on benchmarks adapted from previous work to demonstrate
the effectiveness of our approach.
article_number: '34'
author:
- first_name: Sheshansh
full_name: Agrawal, Sheshansh
last_name: Agrawal
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales:
an efficient approach to termination of probabilistic programs. In: Vol 2. ACM;
2018. doi:10.1145/3158122'
apa: 'Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking
supermartingales: an efficient approach to termination of probabilistic programs
(Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles,
CA, USA: ACM. https://doi.org/10.1145/3158122'
chicago: 'Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic
Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic
Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.'
ieee: 'S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales:
an efficient approach to termination of probabilistic programs,” presented at
the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol.
2, no. POPL.'
ista: 'Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales:
an efficient approach to termination of probabilistic programs. POPL: Principles
of Programming Languages vol. 2, 34.'
mla: 'Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient
Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM,
2018, doi:10.1145/3158122.'
short: S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.
conference:
end_date: 2018-01-13
location: Los Angeles, CA, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2018-01-07
date_created: 2018-12-11T11:45:50Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:07Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3158122
external_id:
arxiv:
- '1709.04037'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.04037
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: ACM
publist_id: '7540'
quality_controlled: '1'
status: public
title: 'Lexicographic ranking supermartingales: an efficient approach to termination
of probabilistic programs'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2018'
...
---
_id: '53'
abstract:
- lang: eng
text: In 2013, a publication repository was implemented at IST Austria and 2015
after a thorough preparation phase a data repository was implemented - both based
on the Open Source Software EPrints. In this text, designed as field report, we
will reflect on our experiences with Open Source Software in general and specifically
with EPrints regarding technical aspects but also regarding their characteristics
of the user community. The second part is a pleading for including the end users
in the process of implementation, adaption and evaluation.
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: 'Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories
at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993'
apa: 'Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional
repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993'
chicago: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The
Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.'
ieee: 'B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional
repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.'
ista: 'Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional
repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.'
mla: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional
Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.'
short: B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.
date_created: 2018-12-11T11:44:22Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2021-01-12T08:01:26Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v71i1.1993
file:
- access_level: open_access
checksum: 7ac61bade5f37db011ca435ebcf86797
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:40:27Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5702'
file_name: 2018_VOEB_Petritsch.pdf
file_size: 509434
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 71'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 199 - 206
publication: VÖB Mitteilungen
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publist_id: '8001'
scopus_import: 1
status: public
title: 'IST PubRep and IST DataRep: the institutional repositories at IST Austria'
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: 71
year: '2018'
...
---
_id: '536'
abstract:
- lang: eng
text: 'We consider the problem of consensus in the challenging classic model. In
this model, the adversary is adaptive; it can choose which processors crash at
any point during the course of the algorithm. Further, communication is via asynchronous
message passing: there is no known upper bound on the time to send a message from
one processor to another, and all messages and coin flips are seen by the adversary.
We describe a new randomized consensus protocol with expected message complexity
O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear
improvement over the best previously known protocol, and within logarithmic factors
of a known Ω(n2) message lower bound. The protocol further ensures that no process
sends more than O(nlog3n) messages in expectation, which is again within logarithmic
factors of optimal. We also present a generalization of the algorithm to an arbitrary
number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach
is to build a message-efficient, resilient mechanism for aggregating individual
processor votes, implementing the message-passing equivalent of a weak shared
coin. Roughly, in our protocol, a processor first announces its votes to small
groups, then propagates them to increasingly larger groups as it generates more
and more votes. To bound the number of messages that an individual process might
have to send or receive, the protocol progressively increases the weight of generated
votes. The main technical challenge is bounding the impact of votes that are still
“in flight” (generated, but not fully propagated) on the final outcome of the
shared coin, especially since such votes might have different weights. We achieve
this by leveraging the structure of the algorithm, and a technical argument based
on martingale concentration bounds. Overall, we show that it is possible to build
an efficient message-passing implementation of a shared coin, and in the process
(almost-optimally) solve the classic consensus problem in the asynchronous message-passing
model.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Valerie
full_name: King, Valerie
last_name: King
- first_name: Jared
full_name: Saia, Jared
last_name: Saia
citation:
ama: Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized
consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1
apa: Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient
randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1
chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient
Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1.
ieee: D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient
randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer,
pp. 489–501, 2018.
ista: Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized
consensus. Distributed Computing. 31(6), 489–501.
mla: Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.”
Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1.
short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018)
489–501.
date_created: 2018-12-11T11:47:01Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-02-23T12:23:25Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00446-017-0315-1
file:
- access_level: open_access
checksum: 69b46e537acdcac745237ddb853fcbb5
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T07:25:51Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5867'
file_name: 2017_DistribComp_Alistarh.pdf
file_size: 595707
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 489-501
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_identifier:
issn:
- '01782770'
publication_status: published
publisher: Springer
publist_id: '7281'
quality_controlled: '1'
scopus_import: 1
status: public
title: Communication-efficient randomized consensus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '554'
abstract:
- lang: eng
text: We analyse the canonical Bogoliubov free energy functional in three dimensions
at low temperatures in the dilute limit. We prove existence of a first-order phase
transition and, in the limit (Formula presented.), we determine the critical temperature
to be (Formula presented.) to leading order. Here, (Formula presented.) is the
critical temperature of the free Bose gas, ρ is the density of the gas and a is
the scattering length of the pair-interaction potential V. We also prove asymptotic
expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula
in the limit (Formula presented.).
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robin
full_name: Reuvers, Robin
last_name: Reuvers
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: 'Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional
II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403.
doi:10.1007/s00220-017-3064-x'
apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov
free energy functional II: The dilute Limit. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x'
chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov
Free Energy Functional II: The Dilute Limit.” Communications in Mathematical
Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.'
ieee: 'M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy
functional II: The dilute Limit,” Communications in Mathematical Physics,
vol. 360, no. 1. Springer, pp. 347–403, 2018.'
ista: 'Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional
II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.'
mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II:
The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no.
1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.'
short: M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical
Physics 360 (2018) 347–403.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:02:35Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-017-3064-x
external_id:
arxiv:
- '1511.05953'
intvolume: ' 360'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.05953
month: '05'
oa: 1
oa_version: Submitted Version
page: 347-403
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- '00103616'
publication_status: published
publisher: Springer
publist_id: '7260'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The Bogoliubov free energy functional II: The dilute Limit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 360
year: '2018'
...
---
_id: '562'
abstract:
- lang: eng
text: Primary neuronal cell culture preparations are widely used to investigate
synaptic functions. This chapter describes a detailed protocol for the preparation
of a neuronal cell culture in which giant calyx-type synaptic terminals are formed.
This chapter also presents detailed protocols for utilizing the main technical
advantages provided by such a preparation, namely, labeling and imaging of synaptic
organelles and electrophysiological recordings directly from presynaptic terminals.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Dimitar
full_name: Dimitrov, Dimitar
last_name: Dimitrov
- first_name: Laurent
full_name: Guillaud, Laurent
last_name: Guillaud
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central
nervous system synapses and application for imaging and electrophysiological analyses.
In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215.
doi:10.1007/978-1-4939-7571-6_15'
apa: Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture
of mouse giant central nervous system synapses and application for imaging and
electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors
(Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15
chicago: Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi.
“Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging
and Electrophysiological Analyses.” In Neurotrophic Factors, edited by
Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.
ieee: D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant
central nervous system synapses and application for imaging and electrophysiological
analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer,
2018, pp. 201–215.
ista: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant
central nervous system synapses and application for imaging and electrophysiological
analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.'
mla: Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses
and Application for Imaging and Electrophysiological Analyses.” Neurotrophic
Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15,
doi:10.1007/978-1-4939-7571-6_15.
short: D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.),
Neurotrophic Factors, Springer, 2018, pp. 201–215.
date_created: 2018-12-11T11:47:11Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:05Z
day: '01'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1007/978-1-4939-7571-6_15
editor:
- first_name: Stephen D.
full_name: Skaper, Stephen D.
last_name: Skaper
external_id:
pmid:
- '29222783'
file:
- access_level: open_access
checksum: 8aa174ca65a56fbb19e9f88cff3ac3fd
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T07:47:43Z
date_updated: 2020-07-14T12:47:09Z
file_id: '7046'
file_name: 2018_NeurotrophicFactors_Dimitrov.pdf
file_size: 787407
relation: main_file
file_date_updated: 2020-07-14T12:47:09Z
has_accepted_license: '1'
intvolume: ' 1727'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 201 - 215
pmid: 1
publication: Neurotrophic Factors
publication_status: published
publisher: Springer
publist_id: '7252'
quality_controlled: '1'
scopus_import: 1
status: public
title: Culture of mouse giant central nervous system synapses and application for
imaging and electrophysiological analyses
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1727
year: '2018'
...
---
_id: '6354'
abstract:
- lang: eng
text: Blood platelets are critical for hemostasis and thrombosis, but also play
diverse roles during immune responses. We have recently reported that platelets
migrate at sites of infection in vitro and in vivo. Importantly, platelets use
their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing
efficient intravascular bacterial trapping. Here, we describe a method that allows
analyzing platelet migration in vitro, focusing on their ability to collect bacteria
and trap bacteria under flow.
acknowledgement: ' FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project
41/16 (F.G.)'
article_number: e3018
author:
- first_name: Shuxia
full_name: Fan, Shuxia
last_name: Fan
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
citation:
ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping
assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018
apa: Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration
and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018
chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet
Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol,
2018. https://doi.org/10.21769/bioprotoc.3018.
ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and
bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol,
2018.
ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial
trapping assay under flow. Bio-Protocol. 8(18), e3018.
mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under
Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.
short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).
date_created: 2019-04-29T09:40:33Z
date_published: 2018-09-20T00:00:00Z
date_updated: 2021-01-12T08:07:12Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.21769/bioprotoc.3018
ec_funded: 1
file:
- access_level: open_access
checksum: d4588377e789da7f360b553ae02c5119
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T08:04:33Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6360'
file_name: 2018_BioProtocol_Fan.pdf
file_size: 2928337
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '18'
keyword:
- Platelets
- Cell migration
- Bacteria
- Shear flow
- Fibrinogen
- E. coli
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Bio-Protocol
publication_identifier:
issn:
- 2331-8325
publication_status: published
publisher: Bio-Protocol
quality_controlled: '1'
status: public
title: Platelet migration and bacterial trapping assay under 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2018'
...
---
_id: '6459'
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018.
doi:10.5281/zenodo.1410279
apa: 'Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented
at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279'
chicago: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria,
2018. https://doi.org/10.5281/zenodo.1410279.
ieee: B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.
ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.
mla: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria,
2018, doi:10.5281/zenodo.1410279.
short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.
conference:
end_date: 2018-09-26
location: Graz, Austria
name: Open-Access-Tage
start_date: 2018-09-24
date_created: 2019-05-16T07:27:14Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2020-07-14T23:06:21Z
day: '24'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.1410279
file:
- access_level: open_access
checksum: 9063ab4d10ea93353c3a03bbf53fbcf1
content_type: application/pdf
creator: dernst
date_created: 2019-05-16T07:26:25Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6460'
file_name: Poster_Beitrag_125_Petritsch.pdf
file_size: 1967778
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
keyword:
- Open Access
- Publication Analysis
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
status: public
title: Open Access at IST Austria 2009-2017
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_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '690'
abstract:
- lang: eng
text: We consider spectral properties and the edge universality of sparse random
matrices, the class of random matrices that includes the adjacency matrices of
the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density
up to the spectral edges. Under a suitable condition on the sparsity, we also
prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations
if a deterministic shift of the spectral edge due to the sparsity is included.
For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom
fluctuations of the second largest eigenvalue when p is much larger than N−2/3
with a deterministic shift of order (Np)−1.
article_number: 543-616
author:
- first_name: Jii
full_name: Lee, Jii
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices.
Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8
apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse
random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8
chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse
Random Matrices.” Probability Theory and Related Fields. Springer, 2018.
https://doi.org/10.1007/s00440-017-0787-8.
ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random
matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer,
2018.
ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random
matrices. Probability Theory and Related Fields. 171(1–2), 543–616.
mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random
Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616,
Springer, 2018, doi:10.1007/s00440-017-0787-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).
date_created: 2018-12-11T11:47:56Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2021-01-12T08:09:33Z
day: '14'
department:
- _id: LaEr
doi: 10.1007/s00440-017-0787-8
ec_funded: 1
external_id:
arxiv:
- '1605.08767'
intvolume: ' 171'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.08767
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '7017'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local law and Tracy–Widom limit for sparse random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2018'
...
---
_id: '703'
abstract:
- lang: eng
text: We consider the NP-hard problem of MAP-inference for undirected discrete graphical
models. We propose a polynomial time and practically efficient algorithm for finding
a part of its optimal solution. Specifically, our algorithm marks some labels
of the considered graphical model either as (i) optimal, meaning that they belong
to all optimal solutions of the inference problem; (ii) non-optimal if they provably
do not belong to any solution. With access to an exact solver of a linear programming
relaxation to the MAP-inference problem, our algorithm marks the maximal possible
(in a specified sense) number of labels. We also present a version of the algorithm,
which has access to a suboptimal dual solver only and still can ensure the (non-)optimality
for the marked labels, although the overall number of the marked labels may decrease.
We propose an efficient implementation, which runs in time comparable to a single
run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art
results on computational benchmarks from machine learning and computer vision.
author:
- first_name: Alexander
full_name: Shekhovtsov, Alexander
last_name: Shekhovtsov
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative
relaxed inference with graphical models. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884
apa: Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency
via iterative relaxed inference with graphical models. IEEE Transactions on
Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884
chicago: Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum
Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions
on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.
ieee: A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative
relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis
and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.
ista: Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative
relaxed inference with graphical models. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 40(7), 1668–1682.
mla: Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference
with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.
short: A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern
Analysis and Machine Intelligence 40 (2018) 1668–1682.
date_created: 2018-12-11T11:48:01Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2021-01-12T08:11:32Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/TPAMI.2017.2730884
external_id:
arxiv:
- '1508.07902'
intvolume: ' 40'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.07902
month: '07'
oa: 1
oa_version: Preprint
page: 1668-1682
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_identifier:
issn:
- '01628828'
publication_status: published
publisher: IEEE
publist_id: '6992'
quality_controlled: '1'
scopus_import: 1
status: public
title: Maximum persistency via iterative relaxed inference with graphical models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2018'
...
---
_id: '7116'
abstract:
- lang: eng
text: 'Training deep learning models has received tremendous research interest recently.
In particular, there has been intensive research on reducing the communication
cost of training when using multiple computational devices, through reducing the
precision of the underlying data representation. Naturally, such methods induce
system trade-offs—lowering communication precision could de-crease communication
overheads and improve scalability; but, on the other hand, it can also reduce
the accuracy of training. In this paper, we study this trade-off space, and ask:Can
low-precision communication consistently improve the end-to-end performance of
training modern neural networks, with no accuracy loss?From the performance point
of view, the answer to this question may appear deceptively easy: compressing
communication through low precision should help when the ratio between communication
and computation is high. However, this answer is less straightforward when we
try to generalize this principle across various neural network architectures (e.g.,
AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g.,
EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL),
and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is
not clear how a realistic realization of all these factors maps to the speed up
provided by low-precision communication. In this paper, we conduct an empirical
study to answer this question and report the insights.'
article_processing_charge: No
author:
- first_name: Demjan
full_name: Grubic, Demjan
last_name: Grubic
- first_name: Leo
full_name: Tam, Leo
last_name: Tam
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for
deep learning with low-precision communications: An empirical study. In: Proceedings
of the 21st International Conference on Extending Database Technology. OpenProceedings;
2018:145-156. doi:10.5441/002/EDBT.2018.14'
apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous
multi-GPU training for deep learning with low-precision communications: An empirical
study. In Proceedings of the 21st International Conference on Extending Database
Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14'
chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous
Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical
Study.” In Proceedings of the 21st International Conference on Extending Database
Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.'
ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study,” in Proceedings
of the 21st International Conference on Extending Database Technology, Vienna,
Austria, 2018, pp. 145–156.'
ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study. Proceedings
of the 21st International Conference on Extending Database Technology. EDBT: Conference
on Extending Database Technology, 145–156.'
mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with
Low-Precision Communications: An Empirical Study.” Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings,
2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.'
short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings, 2018,
pp. 145–156.
conference:
end_date: 2018-03-29
location: Vienna, Austria
name: 'EDBT: Conference on Extending Database Technology'
start_date: 2018-03-26
date_created: 2019-11-26T14:19:11Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2023-02-23T12:59:17Z
day: '26'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.5441/002/EDBT.2018.14
file:
- access_level: open_access
checksum: ec979b56abc71016d6e6adfdadbb4afe
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T14:23:04Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7118'
file_name: 2018_OpenProceedings_Grubic.pdf
file_size: 1603204
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 145-156
publication: Proceedings of the 21st International Conference on Extending Database
Technology
publication_identifier:
isbn:
- '9783893180783'
issn:
- 2367-2005
publication_status: published
publisher: OpenProceedings
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Synchronous multi-GPU training for deep learning with low-precision communications:
An empirical study'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7407'
abstract:
- lang: eng
text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems
where a prover can convince a verifier that he "wastes" disk space. PoS were introduced
as a more ecological and economical replacement for proofs of work which are currently
used to secure blockchains like Bitcoin. In this work we investigate extensions
of PoS which allow the prover to embed useful data into the dedicated space, which
later can be recovered. Our first contribution is a security proof for the original
PoS from CRYPTO''15 in the random oracle model (the original proof only applied
to a restricted class of adversaries which can store a subset of the data an honest
prover would store). When this PoS is instantiated with recent constructions of
maximally depth robust graphs, our proof implies basically optimal security. As
a second contribution we show three different extensions of this PoS where useful
data can be embedded into the space required by the prover. Our security proof
for the PoS extends (non-trivially) to these constructions. We discuss how some
of these variants can be used as proofs of catalytic space (PoCS), a notion we
put forward in this work, and which basically is a PoS where most of the space
required by the prover can be used to backup useful data. Finally we discuss how
one of the extensions is a candidate construction for a proof of replication (PoR),
a proof system recently suggested in the Filecoin whitepaper. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical
Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59'
apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations
in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25).
San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ITCS.2019.59'
chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations
in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.
ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical
Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018,
vol. 124, p. 59:1-59:25.
ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical
Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer
Science Conference, LIPIcs, vol. 124, 59:1-59:25.'
mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in
Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.
short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference
(ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.
conference:
end_date: 2019-01-12
location: San Diego, CA, United States
name: 'ITCS: Innovations in theoretical Computer Science Conference'
start_date: 2019-01-10
date_created: 2020-01-30T09:16:05Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2021-01-12T08:13:26Z
day: '31'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.4230/LIPICS.ITCS.2019.59
ec_funded: 1
file:
- access_level: open_access
checksum: 5cebb7f7849a3beda898f697d755dd96
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T08:17:52Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7443'
file_name: 2018_LIPIcs_Pietrzak.pdf
file_size: 822884
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 124'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/194
month: '12'
oa: 1
oa_version: Published Version
page: 59:1-59:25
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019)
publication_identifier:
isbn:
- 978-3-95977-095-8
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Proofs of catalytic space
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2018'
...
---
_id: '7812'
abstract:
- lang: eng
text: Deep neural networks (DNNs) continue to make significant advances, solving
tasks from image classification to translation or reinforcement learning. One
aspect of the field receiving considerable attention is efficiently executing
deep models in resource-constrained environments, such as mobile or embedded devices.
This paper focuses on this problem, and proposes two new compression methods,
which jointly leverage weight quantization and distillation of larger teacher
networks into smaller student networks. The first method we propose is called
quantized distillation and leverages distillation during the training process,
by incorporating distillation loss, expressed with respect to the teacher, into
the training of a student network whose weights are quantized to a limited set
of levels. The second method, differentiable quantization, optimizes the location
of quantization points through stochastic gradient descent, to better fit the
behavior of the teacher model. We validate both methods through experiments on
convolutional and recurrent architectures. We show that quantized shallow students
can reach similar accuracy levels to full-precision teacher models, while providing
order of magnitude compression, and inference speedup that is linear in the depth
reduction. In sum, our results enable DNNs for resource-constrained environments
to leverage architecture and accuracy advances developed on more powerful devices.
article_processing_charge: No
author:
- first_name: Antonio
full_name: Polino, Antonio
last_name: Polino
- first_name: Razvan
full_name: Pascanu, Razvan
last_name: Pascanu
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and
quantization. In: 6th International Conference on Learning Representations.
; 2018.'
apa: Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via
distillation and quantization. In 6th International Conference on Learning
Representations. Vancouver, Canada.
chicago: Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression
via Distillation and Quantization.” In 6th International Conference on Learning
Representations, 2018.
ieee: A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation
and quantization,” in 6th International Conference on Learning Representations,
Vancouver, Canada, 2018.
ista: 'Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation
and quantization. 6th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Polino, Antonio, et al. “Model Compression via Distillation and Quantization.”
6th International Conference on Learning Representations, 2018.
short: A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference
on Learning Representations, 2018.
conference:
end_date: 2018-05-03
location: Vancouver, Canada
name: 'ICLR: International Conference on Learning Representations'
start_date: 2018-04-30
date_created: 2020-05-10T22:00:51Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-23T13:18:41Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '1802.05668'
file:
- access_level: open_access
checksum: a4336c167978e81891970e4e4517a8c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T13:02:00Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7894'
file_name: 2018_ICLR_Polino.pdf
file_size: 308339
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: 6th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: 1
status: public
title: Model compression via distillation and quantization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '8547'
abstract:
- lang: eng
text: The cerebral cortex contains multiple hierarchically organized areas with
distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying
the emergence of this diversity remain unclear. Here, we have quantitatively investigated
the neuronal output of individual progenitor cells in the ventricular zone of
the developing mouse neocortex using a combination of methods that together circumvent
the biases and limitations of individual approaches. We found that individual
cortical progenitor cells show a high degree of stochasticity and generate pyramidal
cell lineages that adopt a wide range of laminar configurations. Mathematical
modelling these lineage data suggests that a small number of progenitor cell populations,
each generating pyramidal cells following different stochastic developmental programs,
suffice to generate the heterogenous complement of pyramidal cell lineages that
collectively build the complex cytoarchitecture of the neocortex.
acknowledgement: We thank I. Andrew and S.E. Bae for excellent technical assistance,
F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members
of the Marín and Rico laboratories for stimulating discussions and ideas. Our research
on this topic is supported by grants from the European Research Council (ERC-2017-AdG
787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M.
L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received
support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO
postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the
European Commission under the H2020 Programme.
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Llorca, Alfredo
last_name: Llorca
- first_name: Gabriele
full_name: Ciceri, Gabriele
last_name: Ciceri
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Fong K.
full_name: Wong, Fong K.
last_name: Wong
- first_name: Giovanni
full_name: Diana, Giovanni
last_name: Diana
- first_name: Eleni
full_name: Serafeimidou, Eleni
last_name: Serafeimidou
- first_name: Marian
full_name: Fernández-Otero, Marian
last_name: Fernández-Otero
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Sebastian J.
full_name: Arnold, Sebastian J.
last_name: Arnold
- first_name: Martin
full_name: Meyer, Martin
last_name: Meyer
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Miguel
full_name: Maravall, Miguel
last_name: Maravall
- first_name: Oscar
full_name: Marín, Oscar
last_name: Marín
citation:
ama: Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors
underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088
apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou,
E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly
of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/494088
chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni
Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor
Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv.
Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.
ieee: A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie
the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor
Laboratory.
ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero
M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous
progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture.
bioRxiv, 10.1101/494088.
mla: Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the
Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/494088.
short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou,
M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
O. Marín, BioRxiv (n.d.).
date_created: 2020-09-21T12:01:50Z
date_published: 2018-12-13T00:00:00Z
date_updated: 2021-01-12T08:20:00Z
day: '13'
department:
- _id: SiHi
doi: 10.1101/494088
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/494088
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Heterogeneous progenitor cell behaviors underlie the assembly of neocortical
cytoarchitecture
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '86'
abstract:
- lang: eng
text: Responsiveness—the requirement that every request to a system be eventually
handled—is one of the fundamental liveness properties of a reactive system. Average
response time is a quantitative measure for the responsiveness requirement used
commonly in performance evaluation. We show how average response time can be computed
on state-transition graphs, on Markov chains, and on game graphs. In all three
cases, we give polynomial-time algorithms.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein
Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
(WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland
under grant 2014/15/D/ST6/04543.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh
M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer;
2018:143-161. doi:10.1007/978-3-319-95246-8_9'
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average
response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles
of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average
Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia
Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,”
in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani,
Eds. Springer, 2018, pp. 143–161.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time.
In: Principles of Modeling. LNCS, vol. 10760, 143–161.'
mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles
of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018,
pp. 143–61, doi:10.1007/978-3-319-95246-8_9.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani
(Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-95246-8_9
ec_funded: 1
editor:
- first_name: Marten
full_name: Lohstroh, Marten
last_name: Lohstroh
- first_name: Patricia
full_name: Derler, Patricia
last_name: Derler
- first_name: Marjan
full_name: Sirjani, Marjan
last_name: Sirjani
file:
- access_level: open_access
checksum: 9995c6ce6957333baf616fc4f20be597
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:22:18Z
date_updated: 2020-07-14T12:48:14Z
file_id: '7053'
file_name: 2018_PrinciplesModeling_Chatterjee.pdf
file_size: 516307
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 10760'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 143 - 161
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Principles of Modeling
publication_status: published
publisher: Springer
publist_id: '7968'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing average response time
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10760
year: '2018'
...
---
_id: '9229'
alternative_title:
- Molecular and cellular neuroscience
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera
Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001
apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod.
https://doi.org/10.20388/omp2018.00s1.001
chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod,
2018. https://doi.org/10.20388/omp2018.00s1.001.
ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,”
Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University
of Nizhny Novgorod, p. 11, 2018.
ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. 4(S1), 11.
mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University
of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.
short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.
date_created: 2021-03-07T23:01:25Z
date_published: 2018-06-30T00:00:00Z
date_updated: 2021-12-03T07:31:05Z
day: '30'
department:
- _id: JoDa
doi: 10.20388/omp2018.00s1.001
intvolume: ' 4'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://operamedphys.org/content/molecular-and-cellular-neuroscience
month: '06'
oa: 1
oa_version: Published Version
page: '11'
publication: Opera Medica et Physiologica
publication_identifier:
eissn:
- 2500-2295
issn:
- 2500-2287
publication_status: published
publisher: Lobachevsky State University of Nizhny Novgorod
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diffraction-unlimited optical imaging for synaptic physiology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 4
year: '2018'
...
---
_id: '6005'
abstract:
- lang: eng
text: Network games are widely used as a model for selfish resource-allocation problems.
In the classicalmodel, each player selects a path connecting her source and target
vertices. The cost of traversingan edge depends on theload; namely, number of
players that traverse it. Thus, it abstracts the factthat different users may
use a resource at different times and for different durations, which playsan important
role in determining the costs of the users in reality. For example, when transmittingpackets
in a communication network, routing traffic in a road network, or processing a
task in aproduction system, actual sharing and congestion of resources crucially
depends on time.In [13], we introducedtimed network games, which add a time component
to network games.Each vertexvin the network is associated with a cost function,
mapping the load onvto theprice that a player pays for staying invfor one time
unit with this load. Each edge in thenetwork is guarded by the time intervals
in which it can be traversed, which forces the players tospend time in the vertices.
In this work we significantly extend the way time can be referred toin timed network
games. In the model we study, the network is equipped withclocks, and, as intimed
automata, edges are guarded by constraints on the values of the clocks, and their
traversalmay involve a reset of some clocks. We argue that the stronger model
captures many realisticnetworks. The addition of clocks breaks the techniques
we developed in [13] and we developnew techniques in order to show that positive
results on classic network games carry over to thestronger timed setting.
alternative_title:
- LIPIcs
article_number: '23'
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks
(Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science,
Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.MFCS.2018.23'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom,
2018, vol. 117.'
ista: 'Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2018.
conference:
end_date: 2018-08-31
location: Liverpool, United Kingdom
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2018-08-27
date_created: 2019-02-14T14:12:09Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-02-23T14:02:58Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPICS.MFCS.2018.23
file:
- access_level: open_access
checksum: 41ab2ae9b63f5eb49fa995250c0ba128
content_type: application/pdf
creator: dernst
date_created: 2019-02-14T14:22:04Z
date_updated: 2020-07-14T12:47:15Z
file_id: '6007'
file_name: 2018_LIPIcs_Avni.pdf
file_size: 542889
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 117'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '963'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Timed network games with clocks
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2018'
...
---
_id: '315'
abstract:
- lang: eng
text: 'More than 100 years after Grigg’s influential analysis of species’ borders,
the causes of limits to species’ ranges still represent a puzzle that has never
been understood with clarity. The topic has become especially important recently
as many scientists have become interested in the potential for species’ ranges
to shift in response to climate change—and yet nearly all of those studies fail
to recognise or incorporate evolutionary genetics in a way that relates to theoretical
developments. I show that range margins can be understood based on just two measurable
parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and
(ii) the strength of genetic drift, which reduces genetic diversity. Together,
these two parameters define an ‘expansion threshold’: adaptation fails when genetic
drift reduces genetic diversity below that required for adaptation to a heterogeneous
environment. When the key parameters drop below this expansion threshold locally,
a sharp range margin forms. When they drop below this threshold throughout the
species’ range, adaptation collapses everywhere, resulting in either extinction
or formation of a fragmented metapopulation. Because the effects of dispersal
differ fundamentally with dimension, the second parameter—the strength of genetic
drift—is qualitatively different compared to a linear habitat. In two-dimensional
habitats, genetic drift becomes effectively independent of selection. It decreases
with ‘neighbourhood size’—the number of individuals accessible by dispersal within
one generation. Moreover, in contrast to earlier predictions, which neglected
evolution of genetic variance and/or stochasticity in two dimensions, dispersal
into small marginal populations aids adaptation. This is because the reduction
of both genetic and demographic stochasticity has a stronger effect than the cost
of dispersal through increased maladaptation. The expansion threshold thus provides
a novel, theoretically justified, and testable prediction for formation of the
range margin and collapse of the species’ range.'
article_number: e2005372
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: Polechova J. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372
apa: Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a
species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372
chicago: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of
a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.
ieee: J. Polechova, “Is the sky the limit? On the expansion threshold of a species’
range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.
ista: Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 16(6), e2005372.
mla: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’
Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science,
2018, doi:10.1371/journal.pbio.2005372.
short: J. Polechova, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:45:46Z
date_published: 2018-06-15T00:00:00Z
date_updated: 2023-02-23T14:10:16Z
day: '15'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005372
file:
- access_level: open_access
checksum: 908c52751bba30c55ed36789e5e4c84d
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:30:03Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5870'
file_name: 2017_PLOS_Polechova.pdf
file_size: 6968201
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- '15449173'
publication_status: published
publisher: Public Library of Science
publist_id: '7550'
quality_controlled: '1'
related_material:
record:
- id: '9839'
relation: research_data
status: public
scopus_import: 1
status: public
title: Is the sky the limit? On the expansion threshold of a species’ range
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: 16
year: '2018'
...
---
_id: '186'
abstract:
- lang: eng
text: 'A drawing of a graph on a surface is independently even if every pair of
nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus
of a graph G is the minimum g such that G has an independently even drawing on
the orientable surface of genus g. An unpublished result by Robertson and Seymour
implies that for every t, every graph of sufficiently large genus contains as
a minor a projective t × t grid or one of the following so-called t-Kuratowski
graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We
show that the ℤ2-genus of graphs in these families is unbounded in t; in fact,
equal to their genus. Together, this implies that the genus of a graph is bounded
from above by a function of its ℤ2-genus, solving a problem posed by Schaefer
and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem
on orientable surfaces.'
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: 'Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40'
apa: 'Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol.
99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry,
Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40'
chicago: Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40.
ieee: 'R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at
the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99,
p. 40.1-40.14.'
ista: 'Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium
on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.'
mla: Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol.
99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.
short: R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018, p. 40.1-40.14.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:05Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2023-08-14T12:43:51Z
day: '11'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2018.40
external_id:
arxiv:
- '1803.05085'
intvolume: ' 99'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.05085
month: '06'
oa: 1
oa_version: Submitted Version
page: 40.1 - 40.14
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7734'
quality_controlled: '1'
related_material:
record:
- id: '11593'
relation: later_version
status: public
scopus_import: '1'
status: public
title: The ℤ2-Genus of Kuratowski minors
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '433'
abstract:
- lang: eng
text: 'A thrackle is a graph drawn in the plane so that every pair of its edges
meet exactly once: either at a common end vertex or in a proper crossing. We prove
that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are
defined similarly, except that every pair of edges that do not share a vertex
are allowed to cross an odd number of times. It is also shown that the maximum
number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound
is best possible for infinitely many values of n.'
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: János
full_name: Pach, János
last_name: Pach
citation:
ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer;
2018:160-166. doi:10.1007/978-3-319-73915-1_14'
apa: 'Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol.
10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization,
Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14'
chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,”
10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.'
ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at
the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States,
2018, vol. 10692, pp. 160–166.'
ista: 'Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph
Drawing and Network Visualization, LNCS, vol. 10692, 160–166.'
mla: 'Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound.
Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.'
short: R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.
conference:
end_date: 2017-09-27
location: Boston, MA, United States
name: 'GD 2017: Graph Drawing and Network Visualization'
start_date: 201-09-25
date_created: 2018-12-11T11:46:27Z
date_published: 2018-01-21T00:00:00Z
date_updated: 2023-08-24T14:39:32Z
day: '21'
department:
- _id: UlWa
doi: 10.1007/978-3-319-73915-1_14
external_id:
arxiv:
- '1708.08037'
intvolume: ' 10692'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08037
month: '01'
oa: 1
oa_version: Submitted Version
page: 160 - 166
publication_status: published
publisher: Springer
publist_id: '7390'
quality_controlled: '1'
related_material:
record:
- id: '5857'
relation: later_version
status: public
scopus_import: 1
status: public
title: 'Thrackles: An improved upper bound'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10692
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113'
apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113'
chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.'
ieee: 'R. Faria et al., “Data from: Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes, Dryad, 10.5061/dryad.72cg113.'
mla: 'Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a
Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.'
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
(2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6095'
relation: used_in_publication
status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '5457'
abstract:
- lang: eng
text: "We consider the problem of expected cost analysis over nondeterministic probabilistic
programs, which aims at automated methods for analyzing the resource-usage of
such programs. Previous approaches for this problem could only handle nonnegative
bounded costs. However, in many scenarios, such as queuing networks or analysis
of cryptocurrency protocols, both positive and negative costs are necessary and
the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient
approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic
probabilistic programs. Our approach can handle (a) general positive and negative
costs with bounded updates in variables; and (b) nonnegative costs with general
updates to variables. We show that several natural examples which could not be
handled by previous approaches are captured in our framework.\r\n\r\nMoreover,
our approach leads to an efficient polynomial-time algorithm, while no previous
approach for cost analysis of probabilistic programs could guarantee polynomial
runtime. Finally, we show the effectiveness of our approach by presenting experimental
results on a variety of programs, motivated by real-world applications, for which
we efficiently synthesize tight resource-usage bounds."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
- first_name: '5'
full_name: Anonymous, 5
last_name: Anonymous
- first_name: '6'
full_name: Anonymous, 6
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous
6. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria;
2018.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, &
Anonymous, 6. (2018). Cost analysis of nondeterministic probabilistic programs.
IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6
Anonymous. Cost Analysis of Nondeterministic Probabilistic Programs. IST
Austria, 2018.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous,
Cost analysis of nondeterministic probabilistic programs. IST Austria,
2018.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous
6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria,
27p.
mla: Anonymous, 1, et al. Cost Analysis of Nondeterministic Probabilistic Programs.
IST Austria, 2018.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous,
Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.
date_created: 2018-12-12T11:39:26Z
date_published: 2018-11-11T00:00:00Z
date_updated: 2023-08-25T08:07:48Z
day: '11'
ddc:
- '000'
file:
- access_level: open_access
checksum: ba3adafd36fe200385ccda583063b9eb
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:32Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5493'
file_name: IST-2018-1066-v1+1_techreport.pdf
file_size: 4202966
relation: main_file
- access_level: closed
checksum: 6cf3a19164bb8e5048a9c8c84dfd9fa3
content_type: text/plain
creator: dernst
date_created: 2019-05-10T13:22:12Z
date_updated: 2020-07-14T12:47:00Z
file_id: '6402'
file_name: authors-names.txt
file_size: 322
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '1066'
related_material:
record:
- id: '6175'
relation: later_version
status: public
scopus_import: 1
status: public
title: Cost analysis of nondeterministic probabilistic programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '10864'
abstract:
- lang: eng
text: We prove that every congruence distributive variety has directed Jónsson terms,
and every congruence modular variety has directed Gumm terms. The directed terms
we construct witness every case of absorption witnessed by the original Jónsson
or Gumm terms. This result is equivalent to a pair of claims about absorption
for admissible preorders in congruence distributive and congruence modular varieties,
respectively. For finite algebras, these absorption theorems have already seen
significant applications, but until now, it was not clear if the theorems hold
for general algebras as well. Our method also yields a novel proof of a result
by P. Lipparini about the existence of a chain of terms (which we call Pixley
terms) in varieties that are at the same time congruence distributive and k-permutable
for some k.
acknowledgement: The second author was supported by National Science Center grant
DEC-2011-/01/B/ST6/01006.
article_processing_charge: No
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- first_name: Marcin
full_name: Kozik, Marcin
last_name: Kozik
- first_name: Ralph
full_name: McKenzie, Ralph
last_name: McKenzie
- first_name: Matthew
full_name: Moore, Matthew
last_name: Moore
citation:
ama: 'Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms.
In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra,
and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7'
apa: 'Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and
directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic
Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham:
Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7'
chicago: 'Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption
and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal
Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham:
Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.'
ieee: 'A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson
terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and
Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018,
pp. 203–220.'
ista: 'Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson
terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer
Science. vol. 16, 203–220.'
mla: Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi
on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited
by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.
short: A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don
Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science,
Springer Nature, Cham, 2018, pp. 203–220.
date_created: 2022-03-18T10:30:32Z
date_published: 2018-03-21T00:00:00Z
date_updated: 2023-09-05T15:37:18Z
day: '21'
department:
- _id: VlKo
doi: 10.1007/978-3-319-74772-9_7
editor:
- first_name: J
full_name: Czelakowski, J
last_name: Czelakowski
external_id:
arxiv:
- '1502.01072'
intvolume: ' 16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.01072
month: '03'
oa: 1
oa_version: Preprint
page: 203-220
place: Cham
publication: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer
Science
publication_identifier:
eisbn:
- '9783319747729'
eissn:
- 2211-2766
isbn:
- '9783319747712'
issn:
- 2211-2758
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: OCTR
status: public
title: Absorption and directed Jónsson terms
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_id: '184'
abstract:
- lang: eng
text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial
complex is shellable is NP-hard, hence NP-complete. This resolves a question raised,
e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d
≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable
is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible
pure d-dimensional complexes.
acknowledgement: 'Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR:
38087RM) of Czech-French collaboration.'
alternative_title:
- Leibniz International Proceedings in Information, LIPIcs
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete.
In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16.
doi:10.4230/LIPIcs.SoCG.2018.41'
apa: 'Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability
is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational
Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SoCG.2018.41'
chicago: Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.
ieee: 'X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability
is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest,
Hungary, 2018, vol. 99, p. 41:1-41:16.'
ista: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete.
SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in
Information, LIPIcs, vol. 99, 41:1-41:16.'
mla: Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.
short: X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:04Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2023-09-06T11:10:57Z
day: '11'
ddc:
- '516'
- '000'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2018.41
file:
- access_level: open_access
checksum: d12bdd60f04a57307867704b5f930afd
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:35:02Z
date_updated: 2020-07-14T12:45:18Z
file_id: '5725'
file_name: 2018_LIPIcs_Goaoc.pdf
file_size: 718414
relation: main_file
file_date_updated: 2020-07-14T12:45:18Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 41:1 - 41:16
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7736'
quality_controlled: '1'
related_material:
record:
- id: '7108'
relation: later_version
status: public
scopus_import: 1
status: public
title: Shellability is NP-complete
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '285'
abstract:
- lang: eng
text: In graph theory, as well as in 3-manifold topology, there exist several width-type
parameters to describe how "simple" or "thin" a given graph
or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs,
or the concept of thin position for 3-manifolds, play an important role when studying
algorithmic problems; in particular, there is a variety of problems in computational
3-manifold topology - some of them known to be computationally hard in general
- that become solvable in polynomial time as soon as the dual graph of the input
triangulation has bounded treewidth. In view of these algorithmic results, it
is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth.
We show that this is not the case, i.e., that there exists an infinite family
of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth
(the latter implies the former, but we present two separate proofs). We derive
these results from work of Agol and of Scharlemann and Thompson, by exhibiting
explicit connections between the topology of a 3-manifold M on the one hand and
width-type parameters of the dual graphs of triangulations of M on the other hand,
answering a question that had been raised repeatedly by researchers in computational
3-manifold topology. In particular, we show that if a closed, orientable, irreducible,
non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then
the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).
acknowledgement: Research of the second author was supported by the Einstein Foundation
(project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons
Visiting Professors” program).
alternative_title:
- LIPIcs
article_number: '46'
article_processing_charge: No
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Jonathan
full_name: Spreer, Jonathan
last_name: Spreer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds.
In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46'
apa: 'Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated
3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry,
Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46'
chicago: Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of
Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46.
ieee: 'K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,”
presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary,
2018, vol. 99.'
ista: 'Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.'
mla: Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds.
Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.
short: K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:37Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-06T11:13:41Z
day: '01'
ddc:
- '516'
- '000'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2018.46
external_id:
arxiv:
- '1712.00434'
file:
- access_level: open_access
checksum: 530d084116778135d5bffaa317479cac
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:32:38Z
date_updated: 2020-07-14T12:45:51Z
file_id: '5713'
file_name: 2018_LIPIcs_Huszar.pdf
file_size: 642522
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7614'
quality_controlled: '1'
related_material:
record:
- id: '7093'
relation: later_version
status: public
scopus_import: 1
status: public
title: On the treewidth of triangulated 3-manifolds
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '13059'
abstract:
- lang: eng
text: "This dataset contains a GitHub repository containing all the data, analysis,
Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast
and accurate large multiple sequence alignments with a root-to-leaf regressive
method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated
and well as the main figures and tables from the manuscript.\r\nThe repository
is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor
details on how to use the regressive alignment algorithm, see the T-Coffee software
suite (https://github.com/cbcrg/tcoffee)."
article_processing_charge: No
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: di Tommaso, Paolo
last_name: di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence
alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846
apa: Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2018). Fast and accurate large multiple sequence alignments with
a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846
chicago: Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.
ieee: E. Garriga et al., “Fast and accurate large multiple sequence alignments
with a root-to-leaf regressive method.” Zenodo, 2018.
ista: Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence
alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.
mla: Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments
with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.
short: E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).
date_created: 2023-05-23T16:08:20Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2023-09-06T14:32:51Z
day: '07'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.5281/ZENODO.2025846
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.3271452
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '7181'
relation: used_in_publication
status: public
status: public
title: Fast and accurate large multiple sequence alignments with a root-to-leaf regressive
method
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '49'
abstract:
- lang: eng
text: Nowadays, quantum computation is receiving more and more attention as an alternative
to the classical way of computing. For realizing a quantum computer, different
devices are investigated as potential quantum bits. In this thesis, the focus
is on Ge hut wires, which turned out to be promising candidates for implementing
hole spin quantum bits. The advantages of Ge as a material system are the low
hyperfine interaction for holes and the strong spin orbit coupling, as well as
the compatibility with the highly developed CMOS processes in industry. In addition,
Ge can also be isotopically purified which is expected to boost the spin coherence
times. The strong spin orbit interaction for holes in Ge on the one hand enables
the full electrical control of the quantum bit and on the other hand should allow
short spin manipulation times. Starting with a bare Si wafer, this work covers
the entire process reaching from growth over the fabrication and characterization
of hut wire devices up to the demonstration of hole spin resonance. From experiments
with single quantum dots, a large g-factor anisotropy between the in-plane and
the out-of-plane direction was found. A comparison to a theoretical model unveiled
the heavy-hole character of the lowest energy states. The second part of the thesis
addresses double quantum dot devices, which were realized by adding two gate electrodes
to a hut wire. In such devices, Pauli spin blockade was observed, which can serve
as a read-out mechanism for spin quantum bits. Applying oscillating electric fields
in spin blockade allowed the demonstration of continuous spin rotations and the
extraction of a lower bound for the spin dephasing time. Despite the strong spin
orbit coupling in Ge, the obtained value for the dephasing time is comparable
to what has been recently reported for holes in Si. All in all, the presented
results point out the high potential of Ge hut wires as a platform for long-lived,
fast and fully electrically tunable hole spin quantum bits.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
citation:
ama: Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033
apa: Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033
chicago: Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033.
ieee: H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute
of Science and Technology Austria, 2018.
ista: Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute
of Science and Technology Austria.
mla: Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033.
short: H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:21Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-07T12:27:43Z
day: '30'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:th_1033
file:
- access_level: open_access
checksum: b653b5216251f938ddbeafd1de88667c
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T07:13:28Z
date_updated: 2020-07-14T12:46:35Z
file_id: '6249'
file_name: 2018_Thesis_Watzinger.pdf
file_size: 85539748
relation: main_file
- access_level: closed
checksum: 39bcf8de7ac5b1bb516b11ce2f966785
content_type: application/zip
creator: dernst
date_created: 2019-04-09T07:13:27Z
date_updated: 2020-07-14T12:46:35Z
file_id: '6250'
file_name: 2018_Thesis_Watzinger_source.zip
file_size: 21830697
relation: source_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '77'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8005'
pubrep_id: '1033'
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Ge hut wires - from growth to hole spin resonance
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: '2018'
...
---
_id: '201'
abstract:
- lang: eng
text: 'We describe arrangements of three-dimensional spheres from a geometrical
and topological point of view. Real data (fitting this setup) often consist of
soft spheres which show certain degree of deformation while strongly packing against
each other. In this context, we answer the following questions: If we model a
soft packing of spheres by hard spheres that are allowed to overlap, can we measure
the volume in the overlapped areas? Can we be more specific about the overlap
volume, i.e. quantify how much volume is there covered exactly twice, three times,
or k times? What would be a good optimization criteria that rule the arrangement
of soft spheres while making a good use of the available space? Fixing a particular
criterion, what would be the optimal sphere configuration? The first result of
this thesis are short formulas for the computation of volumes covered by at least
k of the balls. The formulas exploit information contained in the order-k Voronoi
diagrams and its closely related Level-k complex. The used complexes lead to a
natural generalization into poset diagrams, a theoretical formalism that contains
the order-k and degree-k diagrams as special cases. In parallel, we define different
criteria to determine what could be considered an optimal arrangement from a geometrical
point of view. Fixing a criterion, we find optimal soft packing configurations
in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools
from computational topology on real physical data, to show the potentials of higher-order
diagrams in the description of melting crystals. The results of the experiments
leaves us with an open window to apply the theories developed in this thesis in
real applications.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026
apa: Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026
chicago: Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.
ieee: M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology
Austria, 2018.
ista: Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and
Technology Austria.
mla: Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.
short: M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology
Austria, 2018.
date_created: 2018-12-11T11:45:10Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2023-09-07T12:25:32Z
day: '11'
ddc:
- '514'
- '516'
degree_awarded: PhD
department:
- _id: HeEd
doi: 10.15479/AT:ISTA:th_1026
file:
- access_level: closed
checksum: dd699303623e96d1478a6ae07210dd05
content_type: application/zip
creator: kschuh
date_created: 2019-02-05T07:43:31Z
date_updated: 2020-07-14T12:45:24Z
file_id: '5918'
file_name: IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip
file_size: 11827713
relation: source_file
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checksum: ba163849a190d2b41d66fef0e4983294
content_type: application/pdf
creator: kschuh
date_created: 2019-02-05T07:43:45Z
date_updated: 2020-07-14T12:45:24Z
file_id: '5919'
file_name: IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf
file_size: 4783846
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '171'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7712'
pubrep_id: '1026'
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Multiple covers with balls
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '68'
abstract:
- lang: eng
text: The most common assumption made in statistical learning theory is the assumption
of the independent and identically distributed (i.i.d.) data. While being very
convenient mathematically, it is often very clearly violated in practice. This
disparity between the machine learning theory and applications underlies a growing
demand in the development of algorithms that learn from dependent data and theory
that can provide generalization guarantees similar to the independent situations.
This thesis is dedicated to two variants of dependencies that can arise in practice.
One is a dependence on the level of samples in a single learning task. Another
dependency type arises in the multi-task setting when the tasks are dependent
on each other even though the data for them can be i.i.d. In both cases we model
the data (samples or tasks) as stochastic processes and introduce new algorithms
for both settings that take into account and exploit the resulting dependencies.
We prove the theoretical guarantees on the performance of the introduced algorithms
under different evaluation criteria and, in addition, we compliment the theoretical
study by the empirical one, where we evaluate some of the algorithms on two real
world datasets to highlight their practical applicability.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexander
full_name: Zimin, Alexander
id: 37099E9C-F248-11E8-B48F-1D18A9856A87
last_name: Zimin
citation:
ama: Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048
apa: Zimin, A. (2018). Learning from dependent data. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048
chicago: Zimin, Alexander. “Learning from Dependent Data.” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.
ieee: A. Zimin, “Learning from dependent data,” Institute of Science and Technology
Austria, 2018.
ista: Zimin A. 2018. Learning from dependent data. Institute of Science and Technology
Austria.
mla: Zimin, Alexander. Learning from Dependent Data. Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.
short: A. Zimin, Learning from Dependent Data, Institute of Science and Technology
Austria, 2018.
date_created: 2018-12-11T11:44:27Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-07T12:29:07Z
day: '01'
ddc:
- '004'
- '519'
degree_awarded: PhD
department:
- _id: ChLa
doi: 10.15479/AT:ISTA:TH1048
ec_funded: 1
file:
- access_level: open_access
checksum: e849dd40a915e4d6c5572b51b517f098
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T07:32:47Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6253'
file_name: 2018_Thesis_Zimin.pdf
file_size: 1036137
relation: main_file
- access_level: closed
checksum: da092153cec55c97461bd53c45c5d139
content_type: application/zip
creator: dernst
date_created: 2019-04-09T07:32:47Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6254'
file_name: 2018_Thesis_Zimin_Source.zip
file_size: 637490
relation: source_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '92'
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7986'
pubrep_id: '1048'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Learning from dependent data
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '83'
abstract:
- lang: eng
text: "A proof system is a protocol between a prover and a verifier over a common
input in which an honest prover convinces the verifier of the validity of true
statements. Motivated by the success of decentralized cryptocurrencies, exemplified
by Bitcoin, the focus of this thesis will be on proof systems which found applications
in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies.
In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs
of space (PoSpace) were suggested as more ecological, economical, and egalitarian
alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the
state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling
lower bounds, and are therefore complex. Moreover, when these PoSpace are used
in cryptocurrencies like Spacemint, miners can only start mining after ensuring
that a commitment to their space is already added in a special transaction to
the blockchain. Proofs of sequential work (PoSW) are proof systems in which a
prover, upon receiving a statement x and a time parameter T, computes a proof
which convinces the verifier that T time units had passed since x was received.
Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics,
Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come
up with more than one accepting proof for any true statement. In this thesis we
construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace
in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and
unlike current constructions of PoSW, which either achieve efficient verification
of sequential work, or faster-than-recomputing verification of correctness of
proofs, but not both at the same time, ours achieve the best of these two worlds."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
citation:
ama: Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies.
2018. doi:10.15479/AT:ISTA:TH_1046
apa: Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046
chicago: Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046.
ieee: H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,”
Institute of Science and Technology Austria, 2018.
ista: Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies.
Institute of Science and Technology Austria.
mla: Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.
short: H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies,
Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:32Z
date_published: 2018-09-05T00:00:00Z
date_updated: 2023-09-07T12:30:23Z
day: '05'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:TH_1046
ec_funded: 1
file:
- access_level: open_access
checksum: c4b5f7d111755d1396787f41886fc674
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T06:43:41Z
date_updated: 2020-07-14T12:48:11Z
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creator: dernst
date_created: 2019-04-09T06:43:41Z
date_updated: 2020-07-14T12:48:11Z
file_id: '6246'
file_name: 2018_Thesis_Abusalah_source.tar.gz
file_size: 2029190
relation: source_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '59'
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7971'
pubrep_id: '1046'
related_material:
record:
- id: '1229'
relation: part_of_dissertation
status: public
- id: '1235'
relation: part_of_dissertation
status: public
- id: '1236'
relation: part_of_dissertation
status: public
- id: '559'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Proof systems for sustainable decentralized cryptocurrencies
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '197'
abstract:
- lang: eng
text: Modern computer vision systems heavily rely on statistical machine learning
models, which typically require large amounts of labeled data to be learned reliably.
Moreover, very recently computer vision research widely adopted techniques for
representation learning, which further increase the demand for labeled data. However,
for many important practical problems there is relatively small amount of labeled
data available, so it is problematic to leverage full potential of the representation
learning methods. One way to overcome this obstacle is to invest substantial resources
into producing large labelled datasets. Unfortunately, this can be prohibitively
expensive in practice. In this thesis we focus on the alternative way of tackling
the aforementioned issue. We concentrate on methods, which make use of weakly-labeled
or even unlabeled data. Specifically, the first half of the thesis is dedicated
to the semantic image segmentation task. We develop a technique, which achieves
competitive segmentation performance and only requires annotations in a form of
global image-level labels instead of dense segmentation masks. Subsequently, we
present a new methodology, which further improves segmentation performance by
leveraging tiny additional feedback from a human annotator. By using our methods
practitioners can greatly reduce the amount of data annotation effort, which is
required to learn modern image segmentation models. In the second half of the
thesis we focus on methods for learning from unlabeled visual data. We study a
family of autoregressive models for modeling structure of natural images and discuss
potential applications of these models. Moreover, we conduct in-depth study of
one of these applications, where we develop the state-of-the-art model for the
probabilistic image colorization task.
acknowledgement: I also gratefully acknowledge the support of NVIDIA Corporation with
the donation of the GPUs used for this research.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
citation:
ama: Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural
Images. 2018. doi:10.15479/AT:ISTA:th_1021
apa: Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling
of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021
chicago: Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised
Modeling of Natural Images.” Institute of Science and Technology Austria, 2018.
https://doi.org/10.15479/AT:ISTA:th_1021.
ieee: A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of
Natural Images,” Institute of Science and Technology Austria, 2018.
ista: Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling
of Natural Images. Institute of Science and Technology Austria.
mla: Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling
of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021.
short: A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of
Natural Images, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:45:09Z
date_published: 2018-05-25T00:00:00Z
date_updated: 2023-09-07T12:51:46Z
day: '25'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: ChLa
doi: 10.15479/AT:ISTA:th_1021
ec_funded: 1
file:
- access_level: open_access
checksum: bc678e02468d8ebc39dc7267dfb0a1c4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:57Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5113'
file_name: IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf
file_size: 12918758
relation: main_file
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checksum: bc66973b086da5a043f1162dcfb1fde4
content_type: application/zip
creator: dernst
date_created: 2019-04-05T09:34:49Z
date_updated: 2020-07-14T12:45:22Z
file_id: '6225'
file_name: 2018_Thesis_Kolesnikov_source.zip
file_size: 55973760
relation: source_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '113'
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7718'
pubrep_id: '1021'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '6774'
abstract:
- lang: eng
text: "A central problem of algebraic topology is to understand the homotopy groups
\ \U0001D70B\U0001D451(\U0001D44B) of a topological space X. For the computational
version of the problem, it is well known that there is no algorithm to decide
whether the fundamental group \U0001D70B1(\U0001D44B) of a given finite simplicial
complex X is trivial. On the other hand, there are several algorithms that, given
a finite simplicial complex X that is simply connected (i.e., with \U0001D70B1(\U0001D44B)
\ trivial), compute the higher homotopy group \U0001D70B\U0001D451(\U0001D44B)
\ for any given \U0001D451≥2 . However, these algorithms come with a caveat:
They compute the isomorphism type of \U0001D70B\U0001D451(\U0001D44B) , \U0001D451≥2
\ as an abstract finitely generated abelian group given by generators and relations,
but they work with very implicit representations of the elements of \U0001D70B\U0001D451(\U0001D44B)
. Converting elements of this abstract group into explicit geometric maps from
the d-dimensional sphere \U0001D446\U0001D451 to X has been one of the main
unsolved problems in the emerging field of computational homotopy theory. Here
we present an algorithm that, given a simply connected space X, computes \U0001D70B\U0001D451(\U0001D44B)
\ and represents its elements as simplicial maps from a suitable triangulation
of the d-sphere \U0001D446\U0001D451 to X. For fixed d, the algorithm runs
in time exponential in size(\U0001D44B) , the number of simplices of X. Moreover,
we prove that this is optimal: For every fixed \U0001D451≥2 , we construct a
family of simply connected spaces X such that for any simplicial map representing
a generator of \U0001D70B\U0001D451(\U0001D44B) , the size of the triangulation
of \U0001D446\U0001D451 on which the map is defined, is exponential in size(\U0001D44B)
."
article_type: original
author:
- first_name: Marek
full_name: Filakovský, Marek
id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
last_name: Filakovský
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
orcid: 0000-0001-8878-8397
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Stephan Y
full_name: Zhechev, Stephan Y
id: 3AA52972-F248-11E8-B48F-1D18A9856A87
last_name: Zhechev
citation:
ama: Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives
of homotopy group elements. Journal of Applied and Computational Topology.
2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5
apa: Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing
simplicial representatives of homotopy group elements. Journal of Applied and
Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5
chicago: Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing
Simplicial Representatives of Homotopy Group Elements.” Journal of Applied
and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5.
ieee: M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial
representatives of homotopy group elements,” Journal of Applied and Computational
Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.
ista: Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives
of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4),
177–231.
mla: Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy
Group Elements.” Journal of Applied and Computational Topology, vol. 2,
no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5.
short: M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and
Computational Topology 2 (2018) 177–231.
date_created: 2019-08-08T06:47:40Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-07T13:10:36Z
day: '01'
ddc:
- '514'
department:
- _id: UlWa
doi: 10.1007/s41468-018-0021-5
file:
- access_level: open_access
checksum: cf9e7fcd2a113dd4828774fc75cdb7e8
content_type: application/pdf
creator: dernst
date_created: 2019-08-08T06:55:21Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6775'
file_name: 2018_JourAppliedComputTopology_Filakovsky.pdf
file_size: 1056278
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 2'
issue: 3-4
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 177-231
project:
- _id: 25F8B9BC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M01980
name: Robust invariants of Nonlinear Systems
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
record:
- id: '6681'
relation: dissertation_contains
status: public
status: public
title: Computing simplicial representatives of homotopy group elements
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: 2
year: '2018'
...
---
_id: '133'
abstract:
- lang: eng
text: Synchronous programs are easy to specify because the side effects of an operation
are finished by the time the invocation of the operation returns to the caller.
Asynchronous programs, on the other hand, are difficult to specify because there
are side effects due to pending computation scheduled as a result of the invocation
of an operation. They are also difficult to verify because of the large number
of possible interleavings of concurrent computation threads. We present synchronization,
a new proof rule that simplifies the verification of asynchronous programs by
introducing the fiction, for proof purposes, that asynchronous operations complete
synchronously. Synchronization summarizes an asynchronous computation as immediate
atomic effect. Modular verification is enabled via pending asynchronous calls
in atomic summaries, and a complementary proof rule that eliminates pending asynchronous
calls when components and their specifications are composed. We evaluate synchronization
in the context of a multi-layer refinement verification methodology on a collection
of benchmark programs.
alternative_title:
- LIPIcs
article_number: '21'
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
- 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: 'Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21'
apa: 'Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous
(Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory,
Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21'
chicago: Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the
Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
https://doi.org/10.4230/LIPIcs.CONCUR.2018.21.
ieee: 'B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,”
presented at the CONCUR: International Conference on Concurrency Theory, Beijing,
China, 2018, vol. 118.'
ista: 'Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR:
International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.'
mla: Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21.
short: B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018.
conference:
end_date: 2018-09-07
location: Beijing, China
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:48Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2023-09-07T13:18:00Z
day: '13'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2018.21
file:
- access_level: open_access
checksum: c90895f4c5fafc18ddc54d1c8848077e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:46Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5368'
file_name: IST-2018-853-v2+2_concur2018.pdf
file_size: 745438
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 118'
language:
- iso: eng
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: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7790'
pubrep_id: '1039'
quality_controlled: '1'
related_material:
record:
- id: '6426'
relation: earlier_version
status: public
- id: '8332'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Synchronizing the asynchronous
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2018'
...
---
_id: '187'
abstract:
- lang: eng
text: 'Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and
r consists of all points in ℝd that have k or more points of X within distance
r. We consider two filtrations - one in scale obtained by fixing k and increasing
r, and the other in depth obtained by fixing r and decreasing k - and we compute
the persistence diagrams of both. While standard methods suffice for the filtration
in scale, we need novel geometric and topological concepts for the filtration
in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal
integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module
from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. '
acknowledgement: This work is partially supported by the DFG Collaborative Research
Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35
of the Austrian Science Fund (FWF).
alternative_title:
- LIPIcs
article_number: '34'
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: 'Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls.
In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34'
apa: 'Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of
Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry,
Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34'
chicago: Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence
of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34.
ieee: 'H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean
balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest,
Hungary, 2018, vol. 99.'
ista: 'Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean
balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.'
mla: Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of
Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018, doi:10.4230/LIPIcs.SoCG.2018.34.
short: H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2018.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:05Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2023-09-07T13:29:00Z
day: '11'
ddc:
- '516'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2018.34
file:
- access_level: open_access
checksum: d8c0533ad0018eb4ed1077475eb8fc18
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:27:22Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5738'
file_name: 2018_LIPIcs_Edelsbrunner_Osang.pdf
file_size: 528018
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7732'
quality_controlled: '1'
related_material:
record:
- id: '9317'
relation: later_version
status: public
- id: '9056'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The multi-cover persistence of Euclidean balls
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '692'
abstract:
- lang: eng
text: We consider families of confocal conics and two pencils of Apollonian circles
having the same foci. We will show that these families of curves generate trivial
3-webs and find the exact formulas describing them.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
citation:
ama: Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata.
2018;194(1):55-64. doi:10.1007/s10711-017-0265-6
apa: Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae
Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6
chicago: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae
Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.
ieee: A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae
Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.
ista: Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae
Dedicata. 194(1), 55–64.
mla: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae
Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6.
short: A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-08T11:40:29Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s10711-017-0265-6
ec_funded: 1
external_id:
isi:
- '000431418800004'
file:
- access_level: open_access
checksum: 1febcfc1266486053a069e3425ea3713
content_type: application/pdf
creator: kschuh
date_created: 2020-01-03T11:35:08Z
date_updated: 2020-07-14T12:47:44Z
file_id: '7222'
file_name: 2018_Springer_Akopyan.pdf
file_size: 1140860
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 194'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 55 - 64
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '7014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3-Webs generated by confocal conics and circles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 194
year: '2018'
...
---
_id: '77'
abstract:
- lang: eng
text: Holes confined in quantum dots have gained considerable interest in the past
few years due to their potential as spin qubits. Here we demonstrate two-axis
control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double
quantum dot device. The Pauli spin blockade principle allowed us to demonstrate
electric dipole spin resonance by applying a radio frequency electric field to
one of the electrodes defining the double quantum dot. Coherent hole spin oscillations
with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of
130 ns are measured. The reported results emphasize the potential of Ge as a platform
for fast and electrically tunable hole spin qubit devices.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
article_processing_charge: Yes
article_type: original
author:
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Fei
full_name: Gao, Fei
last_name: Gao
- first_name: Ting
full_name: Wang, Ting
last_name: Wang
- first_name: Friedrich
full_name: Schäffler, Friedrich
last_name: Schäffler
- first_name: Jian
full_name: Zhang, Jian
last_name: Zhang
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature
Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4
apa: Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F.,
… Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4
chicago: Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich
Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature
Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4.
ieee: H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications,
vol. 9, no. 3902. Nature Publishing Group, 2018.
ista: Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros
G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).
mla: Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications,
vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.
short: H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang,
G. Katsaros, Nature Communications 9 (2018).
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-25T00:00:00Z
date_updated: 2023-09-08T11:44:02Z
day: '25'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41467-018-06418-4
ec_funded: 1
external_id:
isi:
- '000445560800010'
file:
- access_level: open_access
checksum: e7148c10a64497e279c4de570b6cc544
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:28:30Z
date_updated: 2020-07-14T12:48:02Z
file_id: '5687'
file_name: 2018_NatureComm_Watzinger.pdf
file_size: 1063469
relation: main_file
file_date_updated: 2020-07-14T12:48:02Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3902 '
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
- _id: 2552F888-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y00715
name: Loch Spin-Qubits und Majorana-Fermionen in Germanium
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A germanium hole spin qubit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '401'
abstract:
- lang: eng
text: The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells,
oscillates spontaneously in a wide variety of systems. Although much of the signal
cascade regulating myosin activity has been characterized, the origin of such
oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation
in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension,
but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase.
Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial
actomyosin cortex, and dynamically maintained by a self-activation loop reliant
on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin
phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling
Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic
biochemical oscillator at the core of myosin II regulatory network, shedding light
on the spatio-temporal dynamics of force generation.
article_number: '1210'
article_processing_charge: No
author:
- first_name: Xiang
full_name: Qin, Xiang
last_name: Qin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Thomas
full_name: Mangeat, Thomas
last_name: Mangeat
- first_name: Chang
full_name: Liu, Chang
last_name: Liu
- first_name: Pralay
full_name: Majumder, Pralay
last_name: Majumder
- first_name: Jjiaying
full_name: Liu, Jjiaying
last_name: Liu
- first_name: Valerie
full_name: Choesmel Cadamuro, Valerie
last_name: Choesmel Cadamuro
- first_name: Jocelyn
full_name: Mcdonald, Jocelyn
last_name: Mcdonald
- first_name: Yinyao
full_name: Liu, Yinyao
last_name: Liu
- first_name: Bin
full_name: Yi, Bin
last_name: Yi
- first_name: Xiaobo
full_name: Wang, Xiaobo
last_name: Wang
citation:
ama: Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal
myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5
apa: Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang,
X. (2018). A biochemical network controlling basal myosin oscillation. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5
chicago: Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder,
Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling
Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group,
2018. https://doi.org/10.1038/s41467-018-03574-5.
ieee: X. Qin et al., “A biochemical network controlling basal myosin oscillation,”
Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.
ista: Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro
V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal
myosin oscillation. Nature Communications. 9(1), 1210.
mla: Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.”
Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018,
doi:10.1038/s41467-018-03574-5.
short: X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel
Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).
date_created: 2018-12-11T11:46:16Z
date_published: 2018-03-23T00:00:00Z
date_updated: 2023-09-08T11:41:45Z
day: '23'
ddc:
- '539'
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-018-03574-5
external_id:
isi:
- '000428165400009'
file:
- access_level: open_access
checksum: 87a427bc2e8724be3dd22a4efdd21a33
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:45Z
date_updated: 2020-07-14T12:46:22Z
file_id: '4902'
file_name: IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf
file_size: 3780491
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '7427'
pubrep_id: '996'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A biochemical network controlling basal myosin oscillation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '318'
abstract:
- lang: eng
text: The insect’s fat body combines metabolic and immunological functions. In this
issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells
of the fat body are not static, but can actively “swim” toward sites of epithelial
injury, where they physically clog the wound and locally secrete antimicrobial
peptides.
acknowledgement: Short Survey
article_processing_charge: No
author:
- first_name: Alessandra M
full_name: Casano, Alessandra M
id: 3DBA3F4E-F248-11E8-B48F-1D18A9856A87
last_name: Casano
orcid: 0000-0002-6009-6804
- 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: Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell.
2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009
apa: Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing.
Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009
chicago: Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound
Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009.
ieee: A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental
Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.
ista: Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental
Cell. 44(4), 405–406.
mla: Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.”
Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009.
short: A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.
date_created: 2018-12-11T11:45:47Z
date_published: 2018-02-26T00:00:00Z
date_updated: 2023-09-08T11:42:28Z
day: '26'
department:
- _id: MiSi
doi: 10.1016/j.devcel.2018.02.009
external_id:
isi:
- '000426150700002'
pmid:
- '29486189'
intvolume: ' 44'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29486189
month: '02'
oa: 1
oa_version: Published Version
page: 405 - 406
pmid: 1
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '7547'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A fat lot of good for wound healing
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2018'
...
---
_id: '410'
abstract:
- lang: eng
text: Lesion verification and quantification is traditionally done via histological
examination of sectioned brains, a time-consuming process that relies heavily
on manual estimation. Such methods are particularly problematic in posterior cortical
regions (e.g. visual cortex), where sectioning leads to significant damage and
distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes,
which relies on the same techniques, suffers from similar drawbacks and requires
even higher precision. Here, we propose a new, simple method for quantitative
lesion characterization and electrode localization that is less labor-intensive
and yields more detailed results than conventional methods. We leverage staining
techniques standard in electron microscopy with the use of commodity micro-CT
imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed
these in resin and scan entire brains in a micro-CT machine. The scans result
in 3D reconstructions of the brains with section thickness dependent on sample
size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be
segmented manually or automatically. Because the method captures the entire intact
brain volume, comparisons within and across studies are more tractable, and the
extent of lesions and electrodes may be studied with higher accuracy than with
current methods.
article_number: '5184'
article_processing_charge: No
author:
- first_name: Javier
full_name: Masís, Javier
last_name: Masís
- first_name: David
full_name: Mankus, David
last_name: Mankus
- first_name: Steffen
full_name: Wolff, Steffen
last_name: Wolff
- first_name: Grigori
full_name: Guitchounts, Grigori
last_name: Guitchounts
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: David
full_name: Cox, David
last_name: Cox
citation:
ama: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based
method for quantitative brain lesion characterization and electrode localization.
Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z
apa: Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox,
D. (2018). A micro-CT-based method for quantitative brain lesion characterization
and electrode localization. Scientific Reports. Nature Publishing Group.
https://doi.org/10.1038/s41598-018-23247-z
chicago: Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian
A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion
Characterization and Electrode Localization.” Scientific Reports. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z.
ieee: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A
micro-CT-based method for quantitative brain lesion characterization and electrode
localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group,
2018.
ista: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based
method for quantitative brain lesion characterization and electrode localization.
Scientific Reports. 8(1), 5184.
mla: Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion
Characterization and Electrode Localization.” Scientific Reports, vol.
8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z.
short: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific
Reports 8 (2018).
date_created: 2018-12-11T11:46:19Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2023-09-08T11:48:39Z
day: '26'
ddc:
- '571'
- '572'
department:
- _id: MaJö
doi: 10.1038/s41598-018-23247-z
external_id:
isi:
- '000428234100005'
file:
- access_level: open_access
checksum: 653fcb852f899c75b00ceee2a670d738
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:42Z
date_updated: 2020-07-14T12:46:23Z
file_id: '4831'
file_name: IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf
file_size: 2359430
relation: main_file
file_date_updated: 2020-07-14T12:46:23Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7419'
pubrep_id: '994'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A micro-CT-based method for quantitative brain lesion characterization and
electrode localization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '277'
abstract:
- lang: eng
text: 'Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA
levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant
suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2.
Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions.
We previously identified interaction of the C-terminal domain of Arabidopsis telomerase
reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing
protein. Here we explore protein–protein interactions of the ARM protein, AtTERT
domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling
protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid
(Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both
the N- and C-terminal domains of AtTERT in different cellular compartments. ARM
interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly
or through interaction with POT1a. The putative human ARM homolog co-precipitates
telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis
arm mutants shows no obvious changes in telomere length or telomerase activity,
suggesting that ARM is not essential for telomere maintenance. The observed interactions
with telomerase and Myb-like domain proteins (TRF-like family I) may therefore
reflect possible non-telomeric functions. Transcript levels of several DNA repair
and ribosomal genes are affected in arm mutants, and ARM, likely in association
with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs
in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric
functions of telomerase, and can also perform its own telomerase-independent functions.'
article_processing_charge: No
article_type: original
author:
- first_name: Ladislav
full_name: Dokládal, Ladislav
last_name: Dokládal
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: David
full_name: Honys, David
last_name: Honys
- first_name: Nikoleta
full_name: Dupláková, Nikoleta
last_name: Dupláková
- first_name: Lan
full_name: Lee, Lan
last_name: Lee
- first_name: Stanton
full_name: Gelvin, Stanton
last_name: Gelvin
- first_name: Eva
full_name: Sýkorová, Eva
last_name: Sýkorová
citation:
ama: Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates
in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420.
doi:10.1007/s11103-018-0747-4
apa: Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &
Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase
interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4
chicago: Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee,
Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in
a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018.
https://doi.org/10.1007/s11103-018-0747-4.
ieee: L. Dokládal et al., “An armadillo-domain protein participates in a
telomerase interaction network,” Plant Molecular Biology, vol. 97, no.
5. Springer, pp. 407–420, 2018.
ista: Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E.
2018. An armadillo-domain protein participates in a telomerase interaction network.
Plant Molecular Biology. 97(5), 407–420.
mla: Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase
Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer,
2018, pp. 407–20, doi:10.1007/s11103-018-0747-4.
short: L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová,
Plant Molecular Biology 97 (2018) 407–420.
date_created: 2018-12-11T11:45:34Z
date_published: 2018-06-12T00:00:00Z
date_updated: 2023-09-08T13:21:05Z
day: '12'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1007/s11103-018-0747-4
external_id:
isi:
- '000438981700009'
file:
- access_level: open_access
checksum: 451ae47616e6af2533099f596b2a47fb
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:23:08Z
date_updated: 2020-07-14T12:45:45Z
file_id: '7834'
file_name: 2018_PlantMolecBio_Dokladal.pdf
file_size: 1150679
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 97'
isi: 1
issue: '5'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 407 - 420
publication: Plant Molecular Biology
publication_status: published
publisher: Springer
publist_id: '7625'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An armadillo-domain protein participates in a telomerase interaction network
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '299'
abstract:
- lang: eng
text: We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative
analysis of hybrid continuous and Boolean signals that combine numerical values
and discrete events. The evaluation of the signals is based on rich temporal specifications
expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular
Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative
monitoring (property satisfaction checking), trace diagnostics for explaining
and justifying property violations and specification-driven measurement of quantitative
features of the signal.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Olivier
full_name: Lebeltel, Olivier
last_name: Lebeltel
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Dogan
full_name: Ulus, Dogan
last_name: Ulus
citation:
ama: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and
quantitative trace analysis with extended signal temporal logic. In: Beyer D,
Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18'
apa: 'Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018).
AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal
logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18'
chicago: 'Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan
Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal
Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer,
2018. https://doi.org/10.1007/978-3-319-89963-3_18.'
ieee: 'D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative
and quantitative trace analysis with extended signal temporal logic,” presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.'
ista: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative
and quantitative trace analysis with extended signal temporal logic. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806,
303–319.'
mla: 'Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis
with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman,
vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18.'
short: D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M.
Huisman (Eds.), Springer, 2018, pp. 303–319.
conference:
end_date: 2018-04-20
location: Thessaloniki, Greece
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2018-04-14
date_created: 2018-12-11T11:45:41Z
date_published: 2018-04-14T00:00:00Z
date_updated: 2023-09-08T11:52:02Z
day: '14'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-89963-3_18
editor:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Marieke
full_name: Huisman, Marieke
last_name: Huisman
external_id:
isi:
- '00445822600018'
file:
- access_level: open_access
checksum: e11db3b9c8e27a1c7d1c738cc5e4d25a
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T07:33:05Z
date_updated: 2020-07-14T12:45:58Z
file_id: '5928'
file_name: 2018_LNCS_Nickovic.pdf
file_size: 3267209
relation: main_file
file_date_updated: 2020-07-14T12:45:58Z
has_accepted_license: '1'
intvolume: ' 10806'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 303 - 319
publication_status: published
publisher: Springer
publist_id: '7582'
quality_controlled: '1'
related_material:
record:
- id: '10861'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'AMT 2.0: Qualitative and quantitative trace analysis with extended signal
temporal logic'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10806
year: '2018'
...
---
_id: '413'
abstract:
- lang: eng
text: Being cared for when sick is a benefit of sociality that can reduce disease
and improve survival of group members. However, individuals providing care risk
contracting infectious diseases themselves. If they contract a low pathogen dose,
they may develop low-level infections that do not cause disease but still affect
host immunity by either decreasing or increasing the host’s vulnerability to subsequent
infections. Caring for contagious individuals can thus significantly alter the
future disease susceptibility of caregivers. Using ants and their fungal pathogens
as a model system, we tested if the altered disease susceptibility of experienced
caregivers, in turn, affects their expression of sanitary care behavior. We found
that low-level infections contracted during sanitary care had protective or neutral
effects on secondary exposure to the same (homologous) pathogen but consistently
caused high mortality on superinfection with a different (heterologous) pathogen.
In response to this risk, the ants selectively adjusted the expression of their
sanitary care. Specifically, the ants performed less grooming and more antimicrobial
disinfection when caring for nestmates contaminated with heterologous pathogens
compared with homologous ones. By modulating the components of sanitary care in
this way the ants acquired less infectious particles of the heterologous pathogens,
resulting in reduced superinfection. The performance of risk-adjusted sanitary
care reveals the remarkable capacity of ants to react to changes in their disease
susceptibility, according to their own infection history and to flexibly adjust
collective care to individual risk.
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Katharina
full_name: Seif, Katharina
id: 90F7894A-02CF-11E9-976E-E38CFE5CBC1D
last_name: Seif
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
id: 31757262-F248-11E8-B48F-1D18A9856A87
last_name: Naderlinger
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing
risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115
apa: Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V.,
& Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted
sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115
chicago: Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth
Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by
Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1713501115.
ieee: M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted
sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp.
2782–2787, 2018.
ista: Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018.
Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11),
2782–2787.
mla: Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted
Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018,
pp. 2782–87, doi:10.1073/pnas.1713501115.
short: M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S.
Cremer, PNAS 115 (2018) 2782–2787.
date_created: 2018-12-11T11:46:20Z
date_published: 2018-03-13T00:00:00Z
date_updated: 2023-09-08T13:22:21Z
day: '13'
department:
- _id: SyCr
doi: 10.1073/pnas.1713501115
ec_funded: 1
external_id:
isi:
- '000427245400069'
pmid:
- '29463746'
intvolume: ' 115'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29463746
month: '03'
oa: 1
oa_version: Published Version
page: 2782 - 2787
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7416'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/
scopus_import: '1'
status: public
title: Ants avoid superinfections by performing risk-adjusted sanitary care
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '195'
abstract:
- lang: eng
text: We demonstrate that identical impurities immersed in a two-dimensional many-particle
bath can be viewed as flux-tube-charged-particle composites described by fractional
statistics. In particular, we find that the bath manifests itself as an external
magnetic flux tube with respect to the impurities, and hence the time-reversal
symmetry is broken for the effective Hamiltonian describing the impurities. The
emerging flux tube acts as a statistical gauge field after a certain critical
coupling. This critical coupling corresponds to the intersection point between
the quasiparticle state and the phonon wing, where the angular momentum is transferred
from the impurity to the bath. This amounts to a novel configuration with emerging
anyons. The proposed setup paves the way to realizing anyons using electrons interacting
with superfluid helium or lattice phonons, as well as using atomic impurities
in ultracold gases.
article_number: '045402'
article_processing_charge: No
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions.
Physical Review B - Condensed Matter and Materials Physics. 2018;98(4).
doi:10.1103/PhysRevB.98.045402
apa: Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities
in two dimensions. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402
chicago: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum
Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402.
ieee: E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in
two dimensions,” Physical Review B - Condensed Matter and Materials Physics,
vol. 98, no. 4. American Physical Society, 2018.
ista: Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in
two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4),
045402.
mla: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities
in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics,
vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.
short: E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials
Physics 98 (2018).
date_created: 2018-12-11T11:45:08Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2023-09-08T13:22:57Z
day: '15'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.98.045402
ec_funded: 1
external_id:
arxiv:
- '1712.00308'
isi:
- '000436939100007'
intvolume: ' 98'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.00308
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anyonic statistics of quantum impurities in two dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '203'
abstract:
- lang: eng
text: Asymmetric auxin distribution is instrumental for the differential growth
that causes organ bending on tropic stimuli and curvatures during plant development.
Local differences in auxin concentrations are achieved mainly by polarized cellular
distribution of PIN auxin transporters, but whether other mechanisms involving
auxin homeostasis are also relevant for the formation of auxin gradients is not
clear. Here we show that auxin methylation is required for asymmetric auxin distribution
across the hypocotyl, particularly during its response to gravity. We found that
loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1)
prematurely unfold the apical hook, and that their hypocotyls are impaired in
gravitropic reorientation. This defect is linked to an auxin-dependent increase
in PIN gene expression, leading to an increased polar auxin transport and lack
of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation
in the iamt1 mutant could be restored with either endodermis-specific expression
of IAMT1 or partial inhibition of polar auxin transport, which also results in
normal PIN gene expression levels. We propose that IAA methylation is necessary
in gravity-sensing cells to restrict polar auxin transport within the range of
auxin levels that allow for differential responses.
article_processing_charge: No
author:
- first_name: Mohamad
full_name: Abbas, Mohamad
id: 47E8FC1C-F248-11E8-B48F-1D18A9856A87
last_name: Abbas
- first_name: García J
full_name: Hernández, García J
last_name: Hernández
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Sophia L
full_name: Samodelov, Sophia L
last_name: Samodelov
- first_name: Martina
full_name: Kolb, Martina
last_name: Kolb
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ulrich Z
full_name: Hammes, Ulrich Z
last_name: Hammes
- first_name: Matias D
full_name: Zurbriggen, Matias D
last_name: Zurbriggen
- first_name: Miguel
full_name: Blázquez, Miguel
last_name: Blázquez
- first_name: David
full_name: Alabadí, David
last_name: Alabadí
citation:
ama: Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for
differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115
apa: Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml,
J., … Alabadí, D. (2018). Auxin methylation is required for differential growth
in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115
chicago: Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov,
Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez,
and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.”
PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.
ieee: M. Abbas et al., “Auxin methylation is required for differential growth
in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences,
pp. 6864–6869, 2018.
ista: Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ,
Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for
differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.
mla: Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth
in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences,
2018, pp. 6864–69, doi:10.1073/pnas.1806565115.
short: M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml,
U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.
date_created: 2018-12-11T11:45:11Z
date_published: 2018-06-26T00:00:00Z
date_updated: 2023-09-08T13:24:40Z
day: '26'
department:
- _id: JiFr
doi: 10.1073/pnas.1806565115
ec_funded: 1
external_id:
isi:
- '000436245000096'
intvolume: ' 115'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.nottingham.ac.uk/52388/
month: '06'
oa: 1
oa_version: None
page: 6864-6869
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7710'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin methylation is required for differential growth in Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '399'
abstract:
- lang: eng
text: Following an earlier calculation in 3D, we calculate the 2D critical temperature
of a dilute, translation-invariant Bose gas using a variational formulation of
the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This
provides the first analytical calculation of the Kosterlitz-Thouless transition
temperature that includes the constant in the logarithm.
acknowledgement: We thank Robert Seiringer and Daniel Ueltschi for bringing the issue
of the change in critical temperature to our attention. We also thank the Erwin
Schrödinger Institute (all authors) and the Department of Mathematics, University
of Copenhagen (MN) for the hospitality during the period this work was carried out.
We gratefully acknowledge the financial support by the European Unions Seventh Framework
Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR)
as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant
No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430
and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).
article_number: '10007'
article_processing_charge: No
article_type: original
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robin
full_name: Reuvers, Robin
last_name: Reuvers
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature
of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1).
doi:10.1209/0295-5075/121/10007
apa: Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of
the critical temperature of a dilute Bose gas in the Bogoliubov approximation.
EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007
chicago: Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of
the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.”
EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.
ieee: M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical
temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL,
vol. 121, no. 1. IOP Publishing Ltd., 2018.
ista: Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature
of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.
mla: Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of
a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no.
1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.
short: M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).
date_created: 2018-12-11T11:46:15Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-08T13:30:51Z
day: '01'
department:
- _id: RoSe
doi: 10.1209/0295-5075/121/10007
external_id:
arxiv:
- '1706.01822'
isi:
- '000460003000003'
intvolume: ' 121'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.01822
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: EPL
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '7432'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov
approximation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 121
year: '2018'
...
---
_id: '5830'
abstract:
- lang: eng
text: CLE peptides have been implicated in various developmental processes of plants
and mediate their responses to environmental stimuli. However, the biological
relevance of most CLE genes remains to be functionally characterized. Here, we
report that CLE9, which is expressed in stomata, acts as an essential regulator
in the induction of stomatal closure. Exogenous application of CLE9 peptides or
overexpression of CLE9 effectively led to stomatal closure and enhanced drought
tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress.
CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants,
indicating that ABA is required for CLE9-medaited guard cell signalling. We further
deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were
responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by
the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants.
In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2)
and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished
in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively.
Collectively, our results reveal a novel ABA-dependent function of CLE9 in the
regulation of stomatal apertures, thereby suggesting a potential role of CLE9
in the stress acclimatization of plants.
article_processing_charge: No
author:
- first_name: Luosha
full_name: Zhang, Luosha
last_name: Zhang
- first_name: Xiong
full_name: Shi, Xiong
last_name: Shi
- first_name: Yutao
full_name: Zhang, Yutao
last_name: Zhang
- first_name: Jiajing
full_name: Wang, Jiajing
last_name: Wang
- first_name: Jingwei
full_name: Yang, Jingwei
last_name: Yang
- first_name: Takashi
full_name: Ishida, Takashi
last_name: Ishida
- first_name: Wenqian
full_name: Jiang, Wenqian
last_name: Jiang
- first_name: Xiangyu
full_name: Han, Xiangyu
last_name: Han
- first_name: Jingke
full_name: Kang, Jingke
last_name: Kang
- first_name: Xuening
full_name: Wang, Xuening
last_name: Wang
- first_name: Lixia
full_name: Pan, Lixia
last_name: Pan
- first_name: Shuo
full_name: Lv, Shuo
last_name: Lv
- first_name: Bing
full_name: Cao, Bing
last_name: Cao
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Jinbin
full_name: Wu, Jinbin
last_name: Wu
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Zhubing
full_name: Hu, Zhubing
last_name: Hu
- first_name: Langjun
full_name: Cui, Langjun
last_name: Cui
- first_name: Shinichiro
full_name: Sawa, Shinichiro
last_name: Sawa
- first_name: Junmin
full_name: He, Junmin
last_name: He
- first_name: Guodong
full_name: Wang, Guodong
last_name: Wang
citation:
ama: Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated
by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana.
Plant Cell and Environment. 2018. doi:10.1111/pce.13475
apa: Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018).
CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide,
and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley.
https://doi.org/10.1111/pce.13475
chicago: Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi
Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated
by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.”
Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.
ieee: L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated
by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,”
Plant Cell and Environment. Wiley, 2018.
ista: Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J,
Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang
G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen
peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.
mla: Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by
Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant
Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.
short: L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han,
J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui,
S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).
date_created: 2019-01-13T22:59:11Z
date_published: 2018-10-31T00:00:00Z
date_updated: 2023-09-11T12:43:31Z
day: '31'
department:
- _id: JiFr
doi: 10.1111/pce.13475
external_id:
isi:
- '000459014800021'
pmid:
- '30378140'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30378140
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Cell and Environment
publication_identifier:
issn:
- '01407791'
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen
peroxide, and nitric oxide in arabidopsis thaliana
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '288'
abstract:
- lang: eng
text: Recent lineage tracing studies have revealed that mammary gland homeostasis
relies on unipotent stem cells. However, whether and when lineage restriction
occurs during embryonic mammary development, and which signals orchestrate cell
fate specification, remain unknown. Using a combination of in vivo clonal analysis
with whole mount immunofluorescence and mathematical modelling of clonal dynamics,
we found that embryonic multipotent mammary cells become lineage-restricted surprisingly
early in development, with evidence for unipotency as early as E12.5 and no statistically
discernable bipotency after E15.5. To gain insights into the mechanisms governing
the switch from multipotency to unipotency, we used gain-of-function Notch1 mice
and demonstrated that Notch activation cell autonomously dictates luminal cell
fate specification to both embryonic and basally committed mammary cells. These
functional studies have important implications for understanding the signals underlying
cell plasticity and serve to clarify how reactivation of embryonic programs in
adult cells can lead to cancer.
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Lilja, Anna
last_name: Lilja
- first_name: Veronica
full_name: Rodilla, Veronica
last_name: Rodilla
- first_name: Mathilde
full_name: Huyghe, Mathilde
last_name: Huyghe
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Camille
full_name: Landragin, Camille
last_name: Landragin
- first_name: Olivier
full_name: Renaud, Olivier
last_name: Renaud
- first_name: Olivier
full_name: Leroy, Olivier
last_name: Leroy
- first_name: Steffen
full_name: Rulands, Steffen
last_name: Rulands
- first_name: Benjamin
full_name: Simons, Benjamin
last_name: Simons
- first_name: Silvia
full_name: Fré, Silvia
last_name: Fré
citation:
ama: Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells
reveals the existence of unipotent stem cells that retain long-term plasticity
in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687.
doi:10.1038/s41556-018-0108-1
apa: Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud,
O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence
of unipotent stem cells that retain long-term plasticity in the embryonic mammary
gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1
chicago: Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille
Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and
Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence
of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary
Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1.
ieee: A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals
the existence of unipotent stem cells that retain long-term plasticity in the
embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing
Group, pp. 677–687, 2018.
ista: Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O,
Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals
the existence of unipotent stem cells that retain long-term plasticity in the
embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.
mla: Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the
Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic
Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing
Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.
short: A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O.
Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.
date_created: 2018-12-11T11:45:38Z
date_published: 2018-05-21T00:00:00Z
date_updated: 2023-09-11T12:44:08Z
day: '21'
department:
- _id: EdHa
doi: 10.1038/s41556-018-0108-1
external_id:
isi:
- '000433237300003'
pmid:
- '29784917'
intvolume: ' 20'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964
month: '05'
oa: 1
oa_version: Submitted Version
page: 677 - 687
pmid: 1
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7594'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clonal analysis of Notch1-expressing cells reveals the existence of unipotent
stem cells that retain long-term plasticity in the embryonic mammary gland
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2018'
...
---
_id: '304'
abstract:
- lang: eng
text: "Additive manufacturing has recently seen drastic improvements in resolution,
making it now possible to fabricate features at scales of hundreds or even dozens
of nanometers, which previously required very expensive lithographic methods.\r\nAs
a result, additive manufacturing now seems poised for optical applications, including
those relevant to computer graphics, such as material design, as well as display
and imaging applications.\r\n \r\nIn this work, we explore the use of additive
manufacturing for generating structural colors, where the structures are designed
using a fabrication-aware optimization process.\r\nThis requires a combination
of full-wave simulation, a feasible parameterization of the design space, and
a tailored optimization procedure.\r\nMany of these components should be re-usable
for the design of other optical structures at this scale.\r\n \r\nWe show initial
results of material samples fabricated based on our designs.\r\nWhile these suffer
from the prototype character of state-of-the-art fabrication hardware, we believe
they clearly demonstrate the potential of additive nanofabrication for structural
colors and other graphics applications."
acknowledgement: This work was in part supported by King Abdullah University of Science
and Technology Baseline Funding.
alternative_title:
- ACM Transactions on Graphics
article_number: '159'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Wolfgang
full_name: Heidrich, Wolfgang
last_name: Heidrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color
for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376
apa: Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of
nanostructural color for additive manufacturing. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3197517.3201376
chicago: Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design
of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics.
ACM, 2018. https://doi.org/10.1145/3197517.3201376.
ieee: T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural
color for additive manufacturing,” ACM Transactions on Graphics, vol. 37,
no. 4. ACM, 2018.
ista: Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural
color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.
mla: Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for
Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4,
159, ACM, 2018, doi:10.1145/3197517.3201376.
short: T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).
date_created: 2018-12-11T11:45:43Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-11T12:46:13Z
day: '01'
ddc:
- '000'
- '535'
- '680'
department:
- _id: BeBi
doi: 10.1145/3197517.3201376
ec_funded: 1
external_id:
isi:
- '000448185000120'
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has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
pubrep_id: '1028'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/
scopus_import: '1'
status: public
title: Computational design of nanostructural color for additive manufacturing
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '12'
abstract:
- lang: eng
text: Molding is a popular mass production method, in which the initial expenses
for the mold are offset by the low per-unit production cost. However, the physical
fabrication constraints of the molding technique commonly restrict the shape of
moldable objects. For a complex shape, a decomposition of the object into moldable
parts is a common strategy to address these constraints, with plastic model kits
being a popular and illustrative example. However, conducting such a decomposition
requires considerable expertise, and it depends on the technical aspects of the
fabrication technique, as well as aesthetic considerations. We present an interactive
technique to create such decompositions for two-piece molding, in which each part
of the object is cast between two rigid mold pieces. Given the surface description
of an object, we decompose its thin-shell equivalent into moldable parts by first
performing a coarse decomposition and then utilizing an active contour model for
the boundaries between individual parts. Formulated as an optimization problem,
the movement of the contours is guided by an energy reflecting fabrication constraints
to ensure the moldability of each part. Simultaneously, the user is provided with
editing capabilities to enforce aesthetic guidelines. Our interactive interface
provides control of the contour positions by allowing, for example, the alignment
of part boundaries with object features. Our technique enables a novel workflow,
as it empowers novice users to explore the design space, and it generates fabrication-ready
two-piece molds that can be used either for casting or industrial injection molding
of free-form objects.
article_number: '135'
article_processing_charge: No
author:
- first_name: Kazutaka
full_name: Nakashima, Kazutaka
last_name: Nakashima
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Emmanuel
full_name: Iarussi, Emmanuel
id: 33F19F16-F248-11E8-B48F-1D18A9856A87
last_name: Iarussi
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Takeo
full_name: Igarashi, Takeo
last_name: Igarashi
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity:
Interactive shell decomposition for fabrication with two-piece rigid molds. ACM
Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341'
apa: 'Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel,
B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece
rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341'
chicago: 'Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo
Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication
with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.'
ieee: 'K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel,
“CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid
molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.'
ista: 'Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018.
CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid
molds. ACM Transaction on Graphics. 37(4), 135.'
mla: 'Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for
Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol.
37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341.'
short: K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel,
ACM Transaction on Graphics 37 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-11T12:48:09Z
day: '04'
ddc:
- '004'
- '516'
- '670'
department:
- _id: BeBi
doi: 10.1145/3197517.3201341
ec_funded: 1
external_id:
isi:
- '000448185000096'
file:
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checksum: 6a5368bc86c4e1a9fcfe588fd1f14ee8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:38Z
date_updated: 2020-07-14T12:44:38Z
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creator: system
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date_updated: 2020-07-14T12:44:38Z
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creator: system
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date_updated: 2020-07-14T12:44:38Z
file_id: '5363'
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file_size: 527972
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: ACM Transaction on Graphics
publication_status: published
publisher: ACM
publist_id: '8044'
pubrep_id: '1037'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/
scopus_import: '1'
status: public
title: 'CoreCavity: Interactive shell decomposition for fabrication with two-piece
rigid molds'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '454'
abstract:
- lang: eng
text: Direct reciprocity is a mechanism for cooperation among humans. Many of our
daily interactions are repeated. We interact repeatedly with our family, friends,
colleagues, members of the local and even global community. In the theory of repeated
games, it is a tacit assumption that the various games that a person plays simultaneously
have no effect on each other. Here we introduce a general framework that allows
us to analyze “crosstalk” between a player’s concurrent games. In the presence
of crosstalk, the action a person experiences in one game can alter the person’s
decision in another. We find that crosstalk impedes the maintenance of cooperation
and requires stronger levels of forgiveness. The magnitude of the effect depends
on the population structure. In more densely connected social groups, crosstalk
has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract
crosstalk. The crosstalk framework provides a unified interpretation of direct
and upstream reciprocity in the context of repeated games.
acknowledgement: "This work was supported by the European Research Council (ERC) start
grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23
(C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research
grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.)
and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger
fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support
from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported
in part by\r\na gift from B Wu and Eric Larson."
article_number: '555'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: David
full_name: Rand, David
last_name: Rand
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated
games impedes direct reciprocity and requires stronger levels of forgiveness.
Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8
apa: Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk
in concurrent repeated games impedes direct reciprocity and requires stronger
levels of forgiveness. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/s41467-017-02721-8
chicago: Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and
Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity
and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.
ieee: J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent
repeated games impedes direct reciprocity and requires stronger levels of forgiveness,”
Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.
ista: Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent
repeated games impedes direct reciprocity and requires stronger levels of forgiveness.
Nature Communications. 9(1), 555.
mla: Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct
Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications,
vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8.
short: J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications
9 (2018).
date_created: 2018-12-11T11:46:34Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2023-09-11T12:51:03Z
day: '07'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1038/s41467-017-02721-8
ec_funded: 1
external_id:
isi:
- '000424318200001'
file:
- access_level: open_access
checksum: b6b90367545b4c615891c960ab0567f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:18Z
date_updated: 2020-07-14T12:46:31Z
file_id: '4741'
file_name: IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf
file_size: 843646
relation: main_file
file_date_updated: 2020-07-14T12:46:31Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '7368'
pubrep_id: '964'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crosstalk in concurrent repeated games impedes direct reciprocity and requires
stronger levels of forgiveness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '320'
abstract:
- lang: eng
text: 'Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express
a complex machinery of rapid signaling mechanisms, including specialized voltage-gated
ion channels to generate brief action potentials (APs). However, short APs are
associated with overlapping Na+ and K+ fluxes and are therefore energetically
expensive. How the potentially vicious combination of high AP frequency and inefficient
spike generation can be reconciled with limited energy supply is presently unclear.
To address this question, we performed direct recordings from the PV+-BC axon,
the subcellular structure where active conductances for AP initiation and propagation
are located. Surprisingly, the energy required for the AP was, on average, only
∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination
of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels,
which minimized ion flux overlap during APs. Thus, the complementary tuning of
axonal Na+ and K+ channel gating optimizes both fast signaling properties and
metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing
GABAergic interneuron axons are energetically efficient, which is highly unexpected
given their brief duration. High energy efficiency emerges from the combination
of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3
channels in the axon. '
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Hua
full_name: Hu, Hua
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Fabian
full_name: Roth, Fabian
last_name: Roth
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel
gating underlies fast and energy-efficient action potentials in GABAergic interneuron
axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024
apa: Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary
tuning of Na+ and K+ channel gating underlies fast and energy-efficient action
potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024
chicago: Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary
Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action
Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024.
ieee: H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+
and K+ channel gating underlies fast and energy-efficient action potentials in
GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165,
2018.
ista: Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and
K+ channel gating underlies fast and energy-efficient action potentials in GABAergic
interneuron axons. Neuron. 98(1), 156–165.
mla: Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies
Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron,
vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024.
short: H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.
date_created: 2018-12-11T11:45:48Z
date_published: 2018-04-04T00:00:00Z
date_updated: 2023-09-11T12:45:10Z
day: '04'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2018.02.024
ec_funded: 1
external_id:
isi:
- '000429192100016'
file:
- access_level: open_access
checksum: 76070f3729f9c603e1080d0151aa2b11
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:37:50Z
date_updated: 2020-07-14T12:46:03Z
file_id: '5690'
file_name: 2018_Neuron_Hu.pdf
file_size: 3180444
relation: main_file
file_date_updated: 2020-07-14T12:46:03Z
has_accepted_license: '1'
intvolume: ' 98'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 156 - 165
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '7545'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/
scopus_import: '1'
status: public
title: Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient
action potentials in GABAergic interneuron 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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '423'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
acknowledgement: "We are grateful to Remy Chait for his help and assistance with establishing
our experimental setups and to Tobias Bergmiller for valuable insights into some
specific experimental details. We thank Luciano Marraffini for donating us the pCas9
plasmid used in this study. We also want to express our gratitude to Seth Barribeau,
Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable
discussions on the manuscript. Finally, we would like to thank the \r\neditors and
reviewers for their helpful comments and suggestions."
article_number: e32035
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can
limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035
apa: Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based
herd immunity can limit phage epidemics in bacterial populations. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.32035
chicago: Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.”
ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.
ieee: P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd
immunity can limit phage epidemics in bacterial populations,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity
can limit phage epidemics in bacterial populations. eLife. 7, e32035.
mla: Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics
in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications,
2018, doi:10.7554/eLife.32035.
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).
date_created: 2018-12-11T11:46:23Z
date_published: 2018-03-09T00:00:00Z
date_updated: 2023-09-11T12:49:17Z
day: '09'
ddc:
- '576'
department:
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.32035
ec_funded: 1
external_id:
isi:
- '000431035800001'
file:
- access_level: open_access
checksum: 447cf6e680bdc3c01062a8737d876569
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:36:07Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5689'
file_name: 2018_eLife_Payne.pdf
file_size: 3533881
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7400'
quality_controlled: '1'
related_material:
record:
- id: '9840'
relation: research_data
status: public
scopus_import: '1'
status: public
title: CRISPR-based herd immunity can limit phage epidemics in bacterial populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '5791'
abstract:
- lang: eng
text: Due to data compression or low resolution, nearby vertices and edges of a
graph drawing may be bundled to a common node or arc. We model such a “compromised”
drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily
small ε>0 into a proper drawing (in which the vertices are distinct points, any
two edges intersect in finitely many points, and no three edges have a common
interior point) that minimizes the number of crossings. An ε-perturbation, for
every ε>0, is given by a piecewise linear map (Formula Presented), where with
||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution
for this optimization problem when G is a cycle and the map φ has no spurs (i.e.,
no two adjacent edges are mapped to overlapping arcs). We also show that the problem
becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii)
when φ may have spurs and G is a cycle or a union of disjoint paths.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Csaba D.
full_name: Tóth, Csaba D.
last_name: Tóth
citation:
ama: 'Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282.
Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16'
apa: 'Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings
(Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization,
Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16'
chicago: Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed
Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.
ieee: R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented
at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282,
pp. 229–241.
ista: Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph
Drawing and Network Visualization, LNCS, vol. 11282, 229–241.
mla: Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings.
Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.
short: R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.
conference:
end_date: 2018-09-28
location: Barcelona, Spain
name: Graph Drawing and Network Visualization
start_date: 2018-09-26
date_created: 2018-12-30T22:59:15Z
date_published: 2018-12-18T00:00:00Z
date_updated: 2023-09-11T12:49:55Z
day: '18'
department:
- _id: UlWa
doi: 10.1007/978-3-030-04414-5_16
external_id:
arxiv:
- '1808.07608'
isi:
- '000672802500016'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.07608
month: '12'
oa: 1
oa_version: Preprint
page: 229-241
publication_identifier:
isbn:
- '9783030044138'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crossing minimization in perturbed drawings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: '11282 '
year: '2018'
...
---
_id: '291'
abstract:
- lang: eng
text: Over the past decade, the edge of chaos has proven to be a fruitful starting
point for investigations of shear flows when the laminar base flow is linearly
stable. Numerous computational studies of shear flows demonstrated the existence
of states that separate laminar and turbulent regions of the state space. In addition,
some studies determined invariant solutions that reside on this edge. In this
paper, we study the unstable manifold of one such solution with the aid of continuous
symmetry reduction, which we formulate here for the simultaneous quotiening of
axial and azimuthal symmetries. Upon our investigation of the unstable manifold,
we discover a previously unknown traveling-wave solution on the laminar-turbulent
boundary with a relatively complex structure. By means of low-dimensional projections,
we visualize different dynamical paths that connect these solutions to the turbulence.
Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits
qualitatively different regions whose properties are influenced by the nearby
invariant solutions.
article_number: '054401'
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow.
Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401
apa: Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary
in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401
chicago: Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary
in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018.
https://doi.org/10.1103/PhysRevFluids.3.054401.
ieee: N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in
pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society,
2018.
ista: Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe
flow. Physical Review Fluids. 3(5), 054401.
mla: Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary
in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American
Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.
short: N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:45:39Z
date_published: 2018-05-30T00:00:00Z
date_updated: 2023-09-11T12:45:44Z
day: '30'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.054401
external_id:
arxiv:
- '1802.01918'
isi:
- '000433426200001'
intvolume: ' 3'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.01918
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '7590'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complexity of the laminar-turbulent boundary in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '58'
abstract:
- lang: eng
text: 'Inside a two-dimensional region (``cake""), there are m nonoverlapping
tiles of a certain kind (``toppings""). We want to expand the toppings
while keeping them nonoverlapping, and possibly add some blank pieces of the same
``certain kind,"" such that the entire cake is covered. How many blanks
must we add? We study this question in several cases: (1) The cake and toppings
are general polygons. (2) The cake and toppings are convex figures. (3) The cake
and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear
polygon and the toppings are axis-parallel rectangles. In all four cases, we provide
tight bounds on the number of blanks.'
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Erel
full_name: Segal Halevi, Erel
last_name: Segal Halevi
citation:
ama: Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM
Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X
apa: Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements.
SIAM Journal on Discrete Mathematics. Society for Industrial and Applied
Mathematics . https://doi.org/10.1137/16M110407X
chicago: Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal
Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial
and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.
ieee: A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,”
SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial
and Applied Mathematics , pp. 2242–2257, 2018.
ista: Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements.
SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.
mla: Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.”
SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial
and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.
short: A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018)
2242–2257.
date_created: 2018-12-11T11:44:24Z
date_published: 2018-09-06T00:00:00Z
date_updated: 2023-09-11T12:48:39Z
day: '06'
department:
- _id: HeEd
doi: 10.1137/16M110407X
ec_funded: 1
external_id:
arxiv:
- '1604.00960'
isi:
- '000450810500036'
intvolume: ' 32'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.00960
month: '09'
oa: 1
oa_version: Preprint
page: 2242 - 2257
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: SIAM Journal on Discrete Mathematics
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7996'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting blanks in polygonal arrangements
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '9840'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44'
apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data
from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
Dryad. https://doi.org/10.5061/dryad.42n44'
chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
Dryad, 2018. https://doi.org/10.5061/dryad.42n44.'
ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.'
mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage
Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.'
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2023-09-11T12:49:17Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.42n44
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '423'
relation: used_in_publication
status: public
status: public
title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
populations'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '616'
abstract:
- lang: eng
text: Social insects protect their colonies from infectious disease through collective
defences that result in social immunity. In ants, workers first try to prevent
infection of colony members. Here, we show that if this fails and a pathogen establishes
an infection, ants employ an efficient multicomponent behaviour − "destructive
disinfection" − to prevent further spread of disease through the colony.
Ants specifically target infected pupae during the pathogen's non-contagious incubation
period, relying on chemical 'sickness cues' emitted by pupae. They then remove
the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which
enters the body and prevents pathogen replication from the inside out. Like the
immune system of a body that specifically targets and eliminates infected cells,
this social immunity measure sacrifices infected brood to stop the pathogen completing
its lifecycle, thus protecting the rest of the colony. Hence, the same principles
of disease defence apply at different levels of biological organisation.
article_number: e32073
article_processing_charge: Yes
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected
brood prevents systemic disease spread in ant colonies. eLife. 2018;7.
doi:10.7554/eLife.32073
apa: Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt,
T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic
disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073
chicago: Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse,
Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection
of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife.
eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.
ieee: C. Pull et al., “Destructive disinfection of infected brood prevents
systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences
Publications, 2018.
ista: Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown
M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic
disease spread in ant colonies. eLife. 7, e32073.
mla: Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents
Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife
Sciences Publications, 2018, doi:10.7554/eLife.32073.
short: C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt,
M. Brown, S. Cremer, ELife 7 (2018).
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-09T00:00:00Z
date_updated: 2023-09-11T12:54:26Z
day: '09'
ddc:
- '570'
- '590'
department:
- _id: SyCr
doi: 10.7554/eLife.32073
ec_funded: 1
external_id:
isi:
- '000419601300001'
file:
- access_level: open_access
checksum: 540f941e8d3530a9441e4affd94f07d7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:43Z
date_updated: 2020-07-14T12:47:20Z
file_id: '4832'
file_name: IST-2018-978-v1+1_elife-32073-v1.pdf
file_size: 1435585
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DDF0F0-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '302004'
name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities
in ant societies: a chemo-neuro-immunological approach'
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7188'
pubrep_id: '978'
quality_controlled: '1'
related_material:
record:
- id: '819'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Destructive disinfection of infected brood prevents systemic disease spread
in ant colonies
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '132'
abstract:
- lang: eng
text: Pancreas development involves a coordinated process in which an early phase
of cell segregation is followed by a longer phase of lineage restriction, expansion,
and tissue remodeling. By combining clonal tracing and whole-mount reconstruction
with proliferation kinetics and single-cell transcriptional profiling, we define
the functional basis of pancreas morphogenesis. We show that the large-scale organization
of mouse pancreas can be traced to the activity of self-renewing precursors positioned
at the termini of growing ducts, which act collectively to drive serial rounds
of stochastic ductal bifurcation balanced by termination. During this phase of
branching morphogenesis, multipotent precursors become progressively fate-restricted,
giving rise to self-renewing acinar-committed precursors that are conveyed with
growing ducts, as well as ductal progenitors that expand the trailing ducts and
give rise to delaminating endocrine cells. These findings define quantitatively
how the functional behavior and lineage progression of precursor pools determine
the large-scale patterning of pancreatic sub-compartments.
acknowledgement: E.H. is funded by a Junior Research Fellowship from Trinity College,
Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller
Young Researcher Prize for support.
article_processing_charge: No
article_type: original
author:
- first_name: Magdalena
full_name: Sznurkowska, Magdalena
last_name: Sznurkowska
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Roberta
full_name: Azzarelli, Roberta
last_name: Azzarelli
- first_name: Steffen
full_name: Rulands, Steffen
last_name: Rulands
- first_name: Sonia
full_name: Nestorowa, Sonia
last_name: Nestorowa
- first_name: Christopher
full_name: Hindley, Christopher
last_name: Hindley
- first_name: Jennifer
full_name: Nichols, Jennifer
last_name: Nichols
- first_name: Berthold
full_name: Göttgens, Berthold
last_name: Göttgens
- first_name: Meritxell
full_name: Huch, Meritxell
last_name: Huch
- first_name: Anna
full_name: Philpott, Anna
last_name: Philpott
- first_name: Benjamin
full_name: Simons, Benjamin
last_name: Simons
citation:
ama: Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and
fate behavior of precursors during pancreas development. Developmental Cell.
2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028
apa: Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S.,
Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior
of precursors during pancreas development. Developmental Cell. Cell Press.
https://doi.org/10.1016/j.devcel.2018.06.028
chicago: Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands,
Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage
Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental
Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028.
ieee: M. Sznurkowska et al., “Defining lineage potential and fate behavior
of precursors during pancreas development,” Developmental Cell, vol. 46,
no. 3. Cell Press, pp. 360–375, 2018.
ista: Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C,
Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential
and fate behavior of precursors during pancreas development. Developmental Cell.
46(3), 360–375.
mla: Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior
of Precursors during Pancreas Development.” Developmental Cell, vol. 46,
no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.
short: M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C.
Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental
Cell 46 (2018) 360–375.
date_created: 2018-12-11T11:44:48Z
date_published: 2018-08-06T00:00:00Z
date_updated: 2023-09-11T12:52:41Z
day: '06'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.devcel.2018.06.028
external_id:
isi:
- '000441327300012'
file:
- access_level: open_access
checksum: 78d2062b9e3c3b90fe71545aeb6d2f65
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:49:49Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5694'
file_name: 2018_DevelopmentalCell_Sznurkowska.pdf
file_size: 8948384
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 360 - 375
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '7791'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Defining lineage potential and fate behavior of precursors during pancreas
development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2018'
...
---
_id: '42'
abstract:
- lang: eng
text: Seeds derive from ovules upon fertilization and therefore the total number
of ovules determines the final seed yield, a fundamental trait in crop plants.
Among the factors that co-ordinate the process of ovule formation, the transcription
factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK)
have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2
causes a severe reduction in ovule number, a phenotype that can be rescued by
CK treatment. In this study, we combined CK quantification with an integrative
genome-wide target identification approach to select Arabidopsis genes regulated
by CUCs that are also involved in CK metabolism. We focused our attention on the
functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1,
which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able
to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role
for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance
of CUCs and CKs in the determination of seed yield.
acknowledgement: This work was funded by the Ministry of Education, Youth and Sports
of the Czech Republic through the National Program of Sustainability (grant no.
LO1204).
article_processing_charge: No
author:
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Silvia
full_name: Manrique, Silvia
last_name: Manrique
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped
Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number
in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176.
doi:10.1093/jxb/ery281
apa: Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo,
L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis
to determine ovule number in arabidopsis. Journal of Experimental Botany.
Oxford University Press. https://doi.org/10.1093/jxb/ery281
chicago: Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák,
and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis
to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany.
Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.
ieee: M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo,
“Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine
ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69,
no. 21. Oxford University Press, pp. 5169–5176, 2018.
ista: Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped
Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number
in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.
mla: Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin
Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental
Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.
short: M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal
of Experimental Botany 69 (2018) 5169–5176.
date_created: 2018-12-11T11:44:19Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-09-11T12:52:03Z
day: '26'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1093/jxb/ery281
external_id:
isi:
- '000448163900015'
file:
- access_level: open_access
checksum: ca3b6711040b1662488aeb3d1f961f13
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:44:16Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5691'
file_name: 2018_JournalExperimBotany_Cucinotta.pdf
file_size: 1292128
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
issue: '21'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 5169 - 5176
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '8012'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine
ovule number in arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 69
year: '2018'
...
---
_id: '46'
abstract:
- lang: eng
text: We analyze a disordered central spin model, where a central spin interacts
equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg
chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase,
we find that the coupling to the central spin suffices to delocalize the chain
for a substantial range of coupling strengths. We calculate the phase diagram
of the model and identify the phase boundary between the MBL and ergodic phase.
Within the localized phase, the central spin significantly enhances the rate of
the logarithmic entanglement growth and its saturation value. We attribute the
increase in entanglement entropy to a nonextensive enhancement of magnetization
fluctuations induced by the central spin. Finally, we demonstrate that correlation
functions of the central spin can be utilized to distinguish between MBL and ergodic
phases of the 1D chain. Hence, we propose the use of a central spin as a possible
experimental probe to identify the MBL phase.
acknowledgement: F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807
through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich
(NIM) by the German Excellence Initiative, and the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation programme (Grant
Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the
ARO STIR program, and a Google research award.
article_number: '161122'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Hetterich, Daniel
last_name: Hetterich
- first_name: Norman
full_name: Yao, Norman
last_name: Yao
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Frank
full_name: Pollmann, Frank
last_name: Pollmann
- first_name: Björn
full_name: Trauzettel, Björn
last_name: Trauzettel
citation:
ama: Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization
of many-body localization in central spin models. Physical Review B. 2018;98(16).
doi:10.1103/PhysRevB.98.161122
apa: Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018).
Detection and characterization of many-body localization in central spin models.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122
chicago: Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn
Trauzettel. “Detection and Characterization of Many-Body Localization in Central
Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122.
ieee: D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection
and characterization of many-body localization in central spin models,” Physical
Review B, vol. 98, no. 16. American Physical Society, 2018.
ista: Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and
characterization of many-body localization in central spin models. Physical Review
B. 98(16), 161122.
mla: Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization
in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American
Physical Society, 2018, doi:10.1103/PhysRevB.98.161122.
short: D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review
B 98 (2018).
date_created: 2018-12-11T11:44:20Z
date_published: 2018-10-15T00:00:00Z
date_updated: 2023-09-11T12:55:03Z
day: '15'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.98.161122
external_id:
arxiv:
- '1806.08316'
isi:
- '000448596500002'
intvolume: ' 98'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.08316
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '8008'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Detection and characterization of many-body localization in central spin models
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '308'
abstract:
- lang: eng
text: Migrating cells penetrate tissue barriers during development, inflammatory
responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally
confined environments requires changes in the mechanical properties of the surrounding
cells using embryonic Drosophila melanogaster hemocytes, also called macrophages,
as a model. We find that macrophage invasion into the germband through transient
separation of the apposing ectoderm and mesoderm requires cell deformations and
reductions in apical tension in the ectoderm. Interestingly, the genetic pathway
governing these mechanical shifts acts downstream of the only known tumor necrosis
factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald.
Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal
cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated
tight junction protein). We therefore elucidate a distinct molecular pathway that
controls tissue tension and demonstrate the importance of such regulation for
invasive migration in vivo.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
article_type: original
author:
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Julia
full_name: Biebl, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Biebl
- first_name: Michael
full_name: Smutny, Michael
last_name: Smutny
- first_name: Jana
full_name: Veselá, Jana
id: 433253EE-F248-11E8-B48F-1D18A9856A87
last_name: Veselá
- first_name: Ekaterina
full_name: Papusheva, Ekaterina
id: 41DB591E-F248-11E8-B48F-1D18A9856A87
last_name: Papusheva
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Alessandra M
full_name: Casano, Alessandra M
id: 3DBA3F4E-F248-11E8-B48F-1D18A9856A87
last_name: Casano
orcid: 0000-0002-6009-6804
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension
in the embryo to facilitate macrophage invasive migration. Developmental Cell.
2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002
apa: Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G.,
… Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo
to facilitate macrophage invasive migration. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2018.04.002
chicago: Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina
Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano,
and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to
Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier,
2018. https://doi.org/10.1016/j.devcel.2018.04.002.
ieee: A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the
embryo to facilitate macrophage invasive migration,” Developmental Cell,
vol. 45, no. 3. Elsevier, pp. 331–346, 2018.
ista: Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W,
György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension
in the embryo to facilitate macrophage invasive migration. Developmental Cell.
45(3), 331–346.
mla: Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo
to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol.
45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.
short: A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W.
Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018)
331–346.
date_created: 2018-12-11T11:45:44Z
date_published: 2018-05-07T00:00:00Z
date_updated: 2023-09-11T13:22:13Z
day: '07'
department:
- _id: DaSi
- _id: CaHe
- _id: Bio
- _id: EM-Fac
- _id: MiSi
doi: 10.1016/j.devcel.2018.04.002
ec_funded: 1
external_id:
isi:
- '000432461400009'
pmid:
- '29738712'
intvolume: ' 45'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2018.04.002
month: '05'
oa: 1
oa_version: Published Version
page: 331 - 346
pmid: 1
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: Drosophila TNFa´s Funktion in Immunzellen
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: Developmental Cell
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/
scopus_import: '1'
status: public
title: Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage
invasive migration
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2018'
...
---
_id: '17'
abstract:
- lang: eng
text: Creeping flow of polymeric fluid without inertia exhibits elastic instabilities
and elastic turbulence accompanied by drag enhancement due to elastic stress produced
by flow-stretched polymers. However, in inertia-dominated flow at high Re and
low fluid elasticity El, a reduction in turbulent frictional drag is caused by
an intricate competition between inertial and elastic stresses. Here we explore
the effect of inertia on the stability of viscoelastic flow in a broad range of
control parameters El and (Re,Wi). We present the stability diagram of observed
flow regimes in Wi-Re coordinates and find that the instabilities' onsets show
an unexpectedly nonmonotonic dependence on El. Further, three distinct regions
in the diagram are identified based on El. Strikingly, for high-elasticity fluids
we discover a complete relaminarization of flow at Reynolds number in the range
of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive
effects may be explained by a finite polymer extensibility and a suppression of
vorticity at high Wi. Our results call for further theoretical and numerical development
to uncover the role of inertial effect on elastic turbulence in a viscoelastic
flow.
article_number: '103302 '
article_processing_charge: No
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic
flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302
apa: Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction
in viscoelastic flow. Physical Review Fluids. American Physical Society.
https://doi.org/10.1103/PhysRevFluids.3.103302
chicago: Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction
in Viscoelastic Flow.” Physical Review Fluids. American Physical Society,
2018. https://doi.org/10.1103/PhysRevFluids.3.103302.
ieee: A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic
flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society,
2018.
ista: Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic
flow. Physical Review Fluids. 3(10), 103302.
mla: Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction
in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302,
American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302.
short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:11Z
date_published: 2018-10-15T00:00:00Z
date_updated: 2023-09-11T12:59:28Z
day: '15'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103302
ec_funded: 1
external_id:
isi:
- '000447311500001'
file:
- access_level: open_access
checksum: e1445be33e8165114e96246275600750
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:14Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4800'
file_name: IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf
file_size: 1409040
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8038'
pubrep_id: '1061'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Drag enhancement and drag reduction in viscoelastic flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '281'
abstract:
- lang: eng
text: 'Although cells respond specifically to environments, how environmental identity
is encoded intracellularly is not understood. Here, we study this organization
of information in budding yeast by estimating the mutual information between environmental
transitions and the dynamics of nuclear translocation for 10 transcription factors.
Our method of estimation is general, scalable, and based on decoding from single
cells. The dynamics of the transcription factors are necessary to encode the highest
amounts of extracellular information, and we show that information is transduced
through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can
encode the nature of multiple stresses, but only if stress is high; specialists
(Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly
and for a wider range of magnitudes. In particular, Dot6 encodes almost as much
information as Msn2, the master regulator of the environmental stress response.
Each transcription factor reports differently, and it is only their collective
behavior that distinguishes between multiple environmental states. Changes in
the dynamics of the localization of transcription factors thus constitute a precise,
distributed internal representation of extracellular change. We predict that such
multidimensional representations are common in cellular decision-making.'
acknowledgement: This work was supported by the Biotechnology and Biological Sciences
Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences
Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to
G.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Alejandro
full_name: Granados, Alejandro
last_name: Granados
- first_name: Julian
full_name: Pietsch, Julian
last_name: Pietsch
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Isebail
full_name: Farquhar, Isebail
last_name: Farquhar
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Peter
full_name: Swain, Peter
last_name: Swain
citation:
ama: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed
and dynamic intracellular organization of extracellular information. PNAS.
2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
apa: Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G.,
& Swain, P. (2018). Distributed and dynamic intracellular organization of
extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115
chicago: Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar,
Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization
of Extracellular Information.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1716659115.
ieee: A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and
P. Swain, “Distributed and dynamic intracellular organization of extracellular
information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp.
6088–6093, 2018.
ista: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018.
Distributed and dynamic intracellular organization of extracellular information.
PNAS. 115(23), 6088–6093.
mla: Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization
of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy
of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
short: A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P.
Swain, PNAS 115 (2018) 6088–6093.
date_created: 2018-12-11T11:45:35Z
date_published: 2018-06-05T00:00:00Z
date_updated: 2023-09-11T12:58:24Z
day: '05'
department:
- _id: GaTk
doi: 10.1073/pnas.1716659115
external_id:
isi:
- '000434114900071'
pmid:
- '29784812'
intvolume: ' 115'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/09/21/192039
month: '06'
oa: 1
oa_version: Preprint
page: 6088 - 6093
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7618'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Distributed and dynamic intracellular organization of extracellular information
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '620'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis requires the coordinated assembly of various
endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates
a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis,
but specific roles for PtdIns(4)P other than as the biosynthetic precursor of
PtdIns(4,5)P2 have not been clarified. In this study we investigated the role
of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction
of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and
the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that
both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic
internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts)
and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment
of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2
is required for membrane internalization. We also found that the localization
to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p
and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant,
but not in the mss4(ts) mutant. These results suggest distinct roles in successive
steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.
article_number: jcs207696
article_processing_charge: No
author:
- first_name: Wataru
full_name: Yamamoto, Wataru
last_name: Yamamoto
- first_name: Suguru
full_name: Wada, Suguru
last_name: Wada
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns
4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of
Cell Science. 2018;131(1). doi:10.1242/jcs.207696
apa: Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima,
J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and
PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.207696
chicago: Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus,
Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4
P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of
Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.
ieee: W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P
and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell
Science, vol. 131, no. 1. Company of Biologists, 2018.
ista: Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J.
2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast
receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.
mla: Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and
PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell
Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.
short: W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J.
Toshima, Journal of Cell Science 131 (2018).
date_created: 2018-12-11T11:47:32Z
date_published: 2018-01-04T00:00:00Z
date_updated: 2023-09-11T12:57:13Z
day: '04'
department:
- _id: DaSi
doi: 10.1242/jcs.207696
external_id:
isi:
- '000424786900012'
pmid:
- '29192062'
intvolume: ' 131'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29192062
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '7184'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast
receptor mediated endocytosis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 131
year: '2018'
...
---
_id: '182'
abstract:
- lang: eng
text: We describe a new algorithm for the parametric identification problem for
signal temporal logic (STL), stated as follows. Given a densetime real-valued
signal w and a parameterized temporal logic formula φ, compute the subset of the
parameter space that renders the formula satisfied by the signal. Unlike previous
solutions, which were based on search in the parameter space or quantifier elimination,
our procedure works recursively on φ and computes the evolution over time of the
set of valid parameter assignments. This procedure is similar to that of monitoring
or computing the robustness of φ relative to w. Our implementation and experiments
demonstrate that this approach can work well in practice.
alternative_title:
- HSCC Proceedings
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
citation:
ama: 'Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL.
In: Proceedings of the 21st International Conference on Hybrid Systems.
ACM; 2018:177-186. doi:10.1145/3178126.3178132'
apa: 'Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification
for STL. In Proceedings of the 21st International Conference on Hybrid Systems
(pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132'
chicago: Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric
Identification for STL.” In Proceedings of the 21st International Conference
on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132.
ieee: A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification
for STL,” in Proceedings of the 21st International Conference on Hybrid Systems,
Porto, Portugal, 2018, pp. 177–186.
ista: 'Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification
for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC:
Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.'
mla: Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings
of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86,
doi:10.1145/3178126.3178132.
short: A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International
Conference on Hybrid Systems, ACM, 2018, pp. 177–186.
conference:
end_date: 2018-04-13
location: Porto, Portugal
name: 'HSCC: Hybrid Systems: Computation and Control'
start_date: 2018-04-11
date_created: 2018-12-11T11:45:04Z
date_published: 2018-04-11T00:00:00Z
date_updated: 2023-09-11T13:30:51Z
day: '11'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3178126.3178132
external_id:
isi:
- '000474781600020'
file:
- access_level: open_access
checksum: 81eabc96430e84336ea88310ac0a1ad0
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:18:29Z
date_updated: 2020-07-14T12:45:17Z
file_id: '7833'
file_name: 2018_HSCC_Bakhirkin.pdf
file_size: 5900421
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 177 - 186
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the 21st International Conference on Hybrid Systems
publication_identifier:
isbn:
- '978-1-4503-5642-8 '
publication_status: published
publisher: ACM
publist_id: '7739'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient parametric identification for STL
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '143'
abstract:
- lang: eng
text: 'Vector Addition Systems with States (VASS) provide a well-known and fundamental
model for the analysis of concurrent processes, parameterized systems, and are
also used as abstract models of programs in resource bound analysis. In this paper
we study the problem of obtaining asymptotic bounds on the termination time of
a given VASS. In particular, we focus on the practically important case of obtaining
polynomial bounds on termination time. Our main contributions are as follows:
First, we present a polynomial-time algorithm for deciding whether a given VASS
has a linear asymptotic complexity. We also show that if the complexity of a VASS
is not linear, it is at least quadratic. Second, we classify VASS according to
quantitative properties of their cycles. We show that certain singularities in
these properties are the key reason for non-polynomial asymptotic complexity of
VASS. In absence of singularities, we show that the asymptotic complexity is always
polynomial and of the form Θ(nk), for some integer k d, where d is the dimension
of the VASS. We present a polynomial-time algorithm computing the optimal k. For
general VASS, the same algorithm, which is based on a complete technique for the
construction of ranking functions in VASS, produces a valid lower bound, i.e.,
a k such that the termination complexity is (nk). Our results are based on new
insights into the geometry of VASS dynamics, which hold the potential for further
applicability to VASS analysis.'
alternative_title:
- ACM/IEEE Symposium on Logic in Computer Science
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Dominik
full_name: Velan, Dominik
last_name: Velan
- first_name: Florian
full_name: Zuleger, Florian
last_name: Zuleger
citation:
ama: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient
algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033.
IEEE; 2018:185-194. doi:10.1145/3209108.3209191'
apa: 'Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger,
F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS
(Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science,
Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik
Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination
Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.
ieee: 'T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger,
“Efficient algorithms for asymptotic bounds on termination time in VASS,” presented
at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033,
pp. 185–194.'
ista: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient
algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer
Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.'
mla: Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination
Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.
short: T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:,
IEEE, 2018, pp. 185–194.
conference:
end_date: 2018-07-12
location: Oxford, United Kingdom
name: 'LICS: Logic in Computer Science'
start_date: 2018-07-09
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-09T00:00:00Z
date_updated: 2023-09-11T13:23:42Z
day: '09'
department:
- _id: KrCh
doi: 10.1145/3209108.3209191
ec_funded: 1
external_id:
isi:
- '000545262800020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.10985
month: '07'
oa: 1
oa_version: Preprint
page: 185 - 194
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_identifier:
isbn:
- 978-1-4503-5583-4
publication_status: published
publisher: IEEE
publist_id: '7780'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient algorithms for asymptotic bounds on termination time in VASS
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: F138033
year: '2018'
...
---
_id: '273'
abstract:
- lang: eng
text: The accuracy of information retrieval systems is often measured using complex
loss functions such as the average precision (AP) or the normalized discounted
cumulative gain (NDCG). Given a set of positive and negative samples, the parameters
of a retrieval system can be estimated by minimizing these loss functions. However,
the non-differentiability and non-decomposability of these loss functions does
not allow for simple gradient based optimization algorithms. This issue is generally
circumvented by either optimizing a structured hinge-loss upper bound to the loss
function or by using asymptotic methods like the direct-loss minimization framework.
Yet, the high computational complexity of loss-augmented inference, which is necessary
for both the frameworks, prohibits its use in large training data sets. To alleviate
this deficiency, we present a novel quicksort flavored algorithm for a large class
of non-decomposable loss functions. We provide a complete characterization of
the loss functions that are amenable to our algorithm, and show that it includes
both AP and NDCG based loss functions. Furthermore, we prove that no comparison
based algorithm can improve upon the computational complexity of our approach
asymptotically. We demonstrate the effectiveness of our approach in the context
of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning
models for a variety of vision tasks. We show that our approach provides significantly
better results than simpler decomposable loss functions, while requiring a comparable
training time.
article_processing_charge: No
author:
- first_name: Pritish
full_name: Mohapatra, Pritish
last_name: Mohapatra
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: C V
full_name: Jawahar, C V
last_name: Jawahar
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
citation:
ama: 'Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization
for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389'
apa: 'Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M.
P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF
Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt
Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389'
chicago: Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and
M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018
IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701.
IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389.
ieee: P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient
optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on
Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp.
3693–3701.
ista: 'Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient
optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer
Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern
Recognition, 3693–3701.'
mla: Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.”
2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE,
2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389.
short: P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018
IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp.
3693–3701.
conference:
end_date: 2018-06-22
location: Salt Lake City, UT, USA
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2018-06-18
date_created: 2018-12-11T11:45:33Z
date_published: 2018-06-28T00:00:00Z
date_updated: 2023-09-11T13:24:43Z
day: '28'
department:
- _id: VlKo
doi: 10.1109/cvpr.2018.00389
ec_funded: 1
external_id:
arxiv:
- '1604.08269'
isi:
- '000457843603087'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.08269
month: '06'
oa: 1
oa_version: Preprint
page: 3693-3701
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
isbn:
- '9781538664209'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient optimization for rank-based loss functions
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '289'
abstract:
- lang: eng
text: We report on quantum capacitance measurements of high quality, graphite- and
hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices.
At zero applied magnetic field, we observe a number of electron density- and electrical
displacement-tuned features in the electronic compressibility associated with
changes in Fermi surface topology. At high displacement field and low density,
strong trigonal warping gives rise to emergent Dirac gullies centered near the
corners of the hexagonal Brillouin and related by three fold rotation symmetry.
At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy
of the Landau levels from two to three. Weak incompressible states are also observed
at integer filling within these triplets Landau levels, which a Hartree-Fock analysis
indicates are associated with Coulomb-driven nematic phases that spontaneously
break rotation symmetry.
acknowledgement: The experimental work at UCSB was funded by the National Science
Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National
Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support
from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture,
Sports, Science and Technology, Japan, and the Japan Society for the Promotion of
Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings
Fellowship from the California Nanosystems Institute at the University of California,
Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard
foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator
funded through the Major Research Instrumentation program of the U.S. National Science
Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities,
which are supported by the MRSEC Program of the U.S. National Science Foundation
under Grant No. DMR- 1720256.
article_number: '167601'
article_processing_charge: No
article_type: original
author:
- first_name: Alexander
full_name: Zibrov, Alexander
last_name: Zibrov
- first_name: Rao
full_name: Peng, Rao
id: 47C23AC6-02D0-11E9-BD0E-99399A5D3DEB
last_name: Peng
orcid: 0000-0003-1250-0021
- first_name: Carlos
full_name: Kometter, Carlos
last_name: Kometter
- first_name: Jia
full_name: Li, Jia
last_name: Li
- first_name: Cory
full_name: Dean, Cory
last_name: Dean
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Kenji
full_name: Watanabe, Kenji
last_name: Watanabe
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Andrea
full_name: Young, Andrea
last_name: Young
citation:
ama: Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking
quantum hall states in ABA trilayer graphene. Physical Review Letters.
2018;121(16). doi:10.1103/PhysRevLett.121.167601
apa: Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young,
A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states
in ABA trilayer graphene. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.121.167601
chicago: Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi
Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies
and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical
Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601.
ieee: A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking
quantum hall states in ABA trilayer graphene,” Physical Review Letters,
vol. 121, no. 16. American Physical Society, 2018.
ista: Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn
M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall
states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.
mla: Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking
Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters,
vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601.
short: A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe,
M. Serbyn, A. Young, Physical Review Letters 121 (2018).
date_created: 2018-12-11T11:45:38Z
date_published: 2018-10-19T00:00:00Z
date_updated: 2023-09-11T13:39:50Z
day: '19'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.121.167601
external_id:
arxiv:
- '1805.01038'
isi:
- '000447307500007'
intvolume: ' 121'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.01038
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA
trilayer graphene
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 121
year: '2018'
...
---
_id: '287'
abstract:
- lang: eng
text: In this paper, we discuss biological effects of electromagnetic (EM) fields
in the context of cancer biology. In particular, we review the nanomechanical
properties of microtubules (MTs), the latter being one of the most successful
targets for cancer therapy. We propose an investigation on the coupling of electromagnetic
radiation to mechanical vibrations of MTs as an important basis for biological
and medical applications. In our opinion, optomechanical methods can accurately
monitor and control the mechanical properties of isolated MTs in a liquid environment.
Consequently, studying nanomechanical properties of MTs may give useful information
for future applications to diagnostic and therapeutic technologies involving non-invasive
externally applied physical fields. For example, electromagnetic fields or high
intensity ultrasound can be used therapeutically avoiding harmful side effects
of chemotherapeutic agents or classical radiation therapy.
acknowledgement: The work of SB has been supported by the European Unions Horizon
2020 research and innovation program under the Marie Sklodowska Curie grant agreement
No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC
(Canada) for his research. MC acknowledges support from the Czech Science Foundation,
projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211
and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.
article_processing_charge: No
author:
- first_name: Vahid
full_name: Salari, Vahid
last_name: Salari
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Michal
full_name: Cifra, Michal
last_name: Cifra
- first_name: Christoph
full_name: Simon, Christoph
last_name: Simon
- first_name: Felix
full_name: Scholkmann, Felix
last_name: Scholkmann
- first_name: Zahra
full_name: Alirezaei, Zahra
last_name: Alirezaei
- first_name: Jack
full_name: Tuszynski, Jack
last_name: Tuszynski
citation:
ama: Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics
In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark.
2018;23(8):1391-1406. doi:10.2741/4651
apa: Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei,
Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer
diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers
in Bioscience. https://doi.org/10.2741/4651
chicago: Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann,
Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics
In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark.
Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.
ieee: V. Salari et al., “Electromagnetic fields and optomechanics In cancer
diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23,
no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.
ista: Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski
J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment.
Frontiers in Bioscience - Landmark. 23(8), 1391–1406.
mla: Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics
and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers
in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.
short: V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei,
J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.
date_created: 2018-12-11T11:45:37Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:38:14Z
day: '01'
department:
- _id: JoFi
doi: 10.2741/4651
ec_funded: 1
external_id:
isi:
- '000439042800001'
pmid:
- '29293441'
intvolume: ' 23'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.bioscience.org/2018/v23/af/4651/fulltext.htm
month: '03'
oa: 1
oa_version: Submitted Version
page: 1391 - 1406
pmid: 1
project:
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
publication: Frontiers in Bioscience - Landmark
publication_status: published
publisher: Frontiers in Bioscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electromagnetic fields and optomechanics In cancer diagnostics and treatment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2018'
...
---
_id: '425'
abstract:
- lang: eng
text: 'We show that the following algorithmic problem is decidable: given a 2-dimensional
simplicial complex, can it be embedded (topologically, or equivalently, piecewise
linearly) in R3? By a known reduction, it suffices to decide the embeddability
of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which
allows us to simplify X and recurse, is in proving that if X can be embedded in
S3, then there is also an embedding in which X has a short meridian, that is,
an essential curve in the boundary of X bounding a disk in S3 \ X with length
bounded by a computable function of the number of tetrahedra of X.'
article_number: '5'
article_processing_charge: No
article_type: original
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is
decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632
apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability
in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability
in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the
3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.
ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere
is decidable. Journal of the ACM. 65(1), 5.
mla: Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal
of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:46:24Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T13:38:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3078632
ec_funded: 1
external_id:
arxiv:
- '1402.0815'
isi:
- '000425685900006'
intvolume: ' 65'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.0815
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7398'
quality_controlled: '1'
related_material:
record:
- id: '2157'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Embeddability in the 3-Sphere is decidable
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '564'
abstract:
- lang: eng
text: "Maladapted individuals can only colonise a new habitat if they can evolve
a\r\npositive growth rate fast enough to avoid extinction, a process known as
evolutionary\r\nrescue. We treat log fitness at low density in the new habitat
as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow
the evolution\r\nof the growth rate; this assumes that the trait values of offspring
of a\r\nsexual union are normally distributed around the mean of the parents’
trait\r\nvalues, with variance that depends only on the parents’ relatedness.
The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe
mean and genetic variance of the trait in the source population.\r\nThe chance
of success becomes small if migrants come from a population\r\nwith mean growth
rate in the new habitat more than a few standard deviations\r\nbelow zero; this
chance depends roughly equally on the probability\r\nthat the initial founder
is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring
as a result of selection. The loss of genetic variation\r\nduring the founding
event is substantial, but highly variable. With\r\ncontinued migration at rate
M, establishment is inevitable; when migration\r\nis rare, the expected time to
establishment decreases inversely with M.\r\nHowever, above a threshold migration
rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation
is held back by gene flow; above this\r\nthreshold, the expected time to establishment
increases exponentially with M. This threshold behaviour is captured by a deterministic
approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder
population\r\nwith mean and variance evolving deterministically. By assuming a
constant\r\ngenetic variance, we also develop a diffusion approximation for the
joint distribution\r\nof population size and trait mean, which extends to include
stabilising\r\nselection and density regulation. Divergence of the population
from its\r\nancestors causes partial reproductive isolation, which we measure
through\r\nthe reproductive value of migrants into the newly established population."
article_processing_charge: No
article_type: original
author:
- 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: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation.
Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007
apa: Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by
polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007
chicago: Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat
by Polygenic Adaptation.” Theoretical Population Biology. Academic Press,
2018. https://doi.org/10.1016/j.tpb.2017.11.007.
ieee: N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic
adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic
Press, pp. 110–127, 2018.
ista: Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic
adaptation. Theoretical Population Biology. 122(7), 110–127.
mla: Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat
by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no.
7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.
short: N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:41:22Z
day: '01'
ddc:
- '519'
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.11.007
ec_funded: 1
external_id:
isi:
- '000440392900014'
file:
- access_level: open_access
checksum: 0b96f6db47e3e91b5e7d103b847c239d
content_type: application/pdf
creator: nbarton
date_created: 2019-12-21T09:36:39Z
date_updated: 2020-07-14T12:47:09Z
file_id: '7199'
file_name: bartonetheridge.pdf
file_size: 2287682
relation: main_file
file_date_updated: 2020-07-14T12:47:09Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Submitted Version
page: 110-127
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '7250'
quality_controlled: '1'
related_material:
record:
- id: '9842'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Establishment in a new habitat by polygenic adaptation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2018'
...
---
_id: '157'
abstract:
- lang: eng
text: 'Social dilemmas occur when incentives for individuals are misaligned with
group interests 1-7 . According to the ''tragedy of the commons'', these misalignments
can lead to overexploitation and collapse of public resources. The resulting behaviours
can be analysed with the tools of game theory 8 . The theory of direct reciprocity
9-15 suggests that repeated interactions can alleviate such dilemmas, but previous
work has assumed that the public resource remains constant over time. Here we
introduce the idea that the public resource is instead changeable and depends
on the strategic choices of individuals. An intuitive scenario is that cooperation
increases the public resource, whereas defection decreases it. Thus, cooperation
allows the possibility of playing a more valuable game with higher payoffs, whereas
defection leads to a less valuable game. We analyse this idea using the theory
of stochastic games 16-19 and evolutionary game theory. We find that the dependence
of the public resource on previous interactions can greatly enhance the propensity
for cooperation. For these results, the interaction between reciprocity and payoff
feedback is crucial: neither repeated interactions in a constant environment nor
single interactions in a changing environment yield similar cooperation rates.
Our framework shows which feedbacks between exploitation and environment - either
naturally occurring or designed - help to overcome social dilemmas.'
acknowledgement: "European Research Council Start Grant 279307, Austrian Science Fund
(FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme."
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Štepán
full_name: Šimsa, Štepán
last_name: Šimsa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic
games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x
apa: Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of
cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x
chicago: Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak.
“Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.
ieee: C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation
in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group,
pp. 246–249, 2018.
ista: Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in
stochastic games. Nature. 559(7713), 246–249.
mla: Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature,
vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.
short: C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-04T00:00:00Z
date_updated: 2023-09-11T13:43:22Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41586-018-0277-x
ec_funded: 1
external_id:
isi:
- '000438240900054'
file:
- access_level: open_access
checksum: 011ab905cf9a410bc2b96f15174d654d
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:09:57Z
date_updated: 2020-07-14T12:45:02Z
file_id: '7049'
file_name: 2018_Nature_Hilbe.pdf
file_size: 2834442
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 559'
isi: 1
issue: '7713'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 246 - 249
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7764'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/engineering-cooperation/
scopus_import: '1'
status: public
title: Evolution of cooperation in stochastic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 559
year: '2018'
...
---
_id: '384'
abstract:
- lang: eng
text: Can orthologous proteins differ in terms of their ability to be secreted?
To answer this question, we investigated the distribution of signal peptides within
the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons
revealed a large number of signal peptide gain and loss events, in which signal
peptides emerge or disappear in the course of evolution. Signal peptide losses
prevail over gains, an effect which is especially pronounced in the transition
from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate
decline in the number of signal peptide-containing proteins in endosymbionts cannot
be explained by the overall reduction of their genomes. Signal peptides can be
gained and lost either by acquisition/elimination of the corresponding N-terminal
regions or by gradual accumulation of mutations. The evolutionary dynamics of
signal peptides in bacterial proteins represents a powerful mechanism of functional
diversification.
acknowledgement: "his work was supported by the Deutsche Forschungsgemeinschaft (grant
\ number FR 1411/9-1). This work was supported by the German Research Foundation
(DFG) and the Technical University of Munich within the fund- ing programme Open
Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont
status of the organisms and Michael Galperin for\r\nuseful comments. T"
article_processing_charge: No
author:
- first_name: Peter
full_name: Hönigschmid, Peter
last_name: Hönigschmid
- first_name: Nadya
full_name: Bykova, Nadya
last_name: Bykova
- first_name: René
full_name: Schneider, René
last_name: Schneider
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Dmitrij
full_name: Frishman, Dmitrij
last_name: Frishman
citation:
ama: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay
between symbiotic relationships and patterns of signal peptide gain and loss.
Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049
apa: Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D.
(2018). Evolutionary interplay between symbiotic relationships and patterns of
signal peptide gain and loss. Genome Biology and Evolution. Oxford University
Press. https://doi.org/10.1093/gbe/evy049
chicago: Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij
Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns
of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford
University Press, 2018. https://doi.org/10.1093/gbe/evy049.
ieee: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University
Press, pp. 928–938, 2018.
ista: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss. Genome Biology and Evolution. 10(3), 928–938.
mla: Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships
and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution,
vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.
short: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome
Biology and Evolution 10 (2018) 928–938.
date_created: 2018-12-11T11:46:10Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:56:52Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1093/gbe/evy049
external_id:
isi:
- '000429483700022'
file:
- access_level: open_access
checksum: 458a7c2c2e79528567edfeb0f326cbe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:07Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4667'
file_name: IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf
file_size: 691602
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 928 - 938
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7445'
pubrep_id: '999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary interplay between symbiotic relationships and patterns of signal
peptide gain and loss
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2018'
...
---
_id: '563'
abstract:
- lang: eng
text: "In continuous populations with local migration, nearby pairs of individuals
have on average more similar genotypes\r\nthan geographically well separated pairs.
A barrier to gene flow distorts this classical pattern of isolation by distance.
Genetic similarity is decreased for sample pairs on different sides of the barrier
and increased for pairs on the same side near the barrier. Here, we introduce
an inference scheme that utilizes this signal to detect and estimate the strength
of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation
to model the effects of a barrier on the geographical spread of ancestry backwards
in time. This approach allows us to calculate the chance of recent coalescence
and probability of identity by descent. We introduce an inference scheme that
fits these theoretical results to the geographical covariance structure of bialleleic
genetic markers. It can estimate the strength of the barrier as well as several
demographic parameters. We investigate the power of our inference scheme to detect
barriers by applying it to a wide range of simulated data. We also showcase an
example application to a Antirrhinum majus (snapdragon) flower color hybrid zone,
where we do not detect any signal of a strong genome wide barrier to gene flow."
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: David
full_name: Field, David
last_name: Field
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene
flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245.
doi:10.1534/genetics.117.300638
apa: Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating
barriers to gene flow from distorted isolation-by-distance patterns. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.117.300638
chicago: Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton.
“Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.”
Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.
ieee: H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers
to gene flow from distorted isolation-by-distance patterns,” Genetics,
vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.
ista: Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to
gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.
mla: Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted
Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society
of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.
short: H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:42:38Z
day: '01'
department:
- _id: NiBa
- _id: ChLa
doi: 10.1534/genetics.117.300638
external_id:
isi:
- '000426219600025'
intvolume: ' 208'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/205484v1
month: '03'
oa: 1
oa_version: Preprint
page: 1231-1245
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7251'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Estimating barriers to gene flow from distorted isolation-by-distance patterns
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '135'
abstract:
- lang: eng
text: The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by
combining particles with grids. To improve performance, the subsequent narrow
band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid
surface and a traditional grid‐based fluid simulation away from the surface. This
spatially‐limited FLIP simulation significantly reduces the number of particles
and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP
idea even further, by allowing a simulation to transition between a FLIP‐like
fluid simulation and a grid‐based simulation in arbitrary locations, not just
near the surface. This approach leads to even more savings in memory and computation,
because we can concentrate the particles only in areas where they are needed.
More importantly, this new method allows us to seamlessly transition to smooth
implicit surface geometry wherever the particle‐based simulation is unnecessary.
Consequently, our method leads to a practical algorithm for avoiding the noisy
surface artifacts associated with particle‐based liquid simulations, while simultaneously
maintaining the benefits of a FLIP simulation in regions of dynamic motion.
alternative_title:
- Eurographics
article_processing_charge: No
article_type: original
author:
- first_name: Takahiro
full_name: Sato, Takahiro
last_name: Sato
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Takeo
full_name: Igarashi, Takeo
last_name: Igarashi
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
citation:
ama: Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP
for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351
apa: Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended
narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley.
https://doi.org/10.1111/cgf.13351
chicago: Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi
Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics
Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.
ieee: T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow
band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no.
2. Wiley, pp. 169–177, 2018.
ista: Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band
FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.
mla: Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.”
Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.
short: T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum
37 (2018) 169–177.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-05-22T00:00:00Z
date_updated: 2023-09-11T14:00:26Z
day: '22'
ddc:
- '006'
department:
- _id: ChWo
doi: 10.1111/cgf.13351
ec_funded: 1
external_id:
isi:
- '000434085600016'
file:
- access_level: open_access
checksum: 8edb90da8a72395eb5d970580e0925b6
content_type: application/pdf
creator: wojtan
date_created: 2020-10-08T08:38:23Z
date_updated: 2020-10-08T08:38:23Z
file_id: '8627'
file_name: exnbflip.pdf
file_size: 54309947
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:38:23Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 169 - 177
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: Computer Graphics Forum
publication_identifier:
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extended narrow band FLIP for liquid simulations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '316'
abstract:
- lang: eng
text: 'Self-incompatibility (SI) is a genetically based recognition system that
functions to prevent self-fertilization and mating among related plants. An enduring
puzzle in SI is how the high diversity observed in nature arises and is maintained.
Based on the underlying recognition mechanism, SI can be classified into two main
groups: self- and non-self recognition. Most work has focused on diversification
within self-recognition systems despite expected differences between the two groups
in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic
population genetic model and stochastic simulations to investigate how novel S-haplotypes
evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI
system. For this model the pathways for diversification involve either the maintenance
or breakdown of SI and can vary in the order of mutations of the female (SRNase)
and male (SLF) components. We show analytically that diversification can occur
with high inbreeding depression and self-pollination, but this varies with evolutionary
pathway and level of completeness (which determines the number of potential mating
partners in the population), and in general is more likely for lower haplotype
number. The conditions for diversification are broader in stochastic simulations
of finite population size. However, the number of haplotypes observed under high
inbreeding and moderate to high self-pollination is less than that commonly observed
in nature. Diversification was observed through pathways that maintain SI as well
as through self-compatible intermediates. Yet the lifespan of diversified haplotypes
was sensitive to their level of completeness. By examining diversification in
a non-self recognition SI system, this model extends our understanding of the
evolution and maintenance of haplotype diversity observed in a self recognition
system common in flowering plants.'
article_processing_charge: No
article_type: original
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- 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: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.118.300748
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society
of America, 2018. https://doi.org/10.1534/genetics.118.300748.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary
pathways for the generation of new self-incompatibility haplotypes in a non-self
recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America,
pp. 861–883, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 209(3), 861–883.
mla: Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3,
Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018)
861–883.
date_created: 2018-12-11T11:45:47Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:57:43Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1534/genetics.118.300748
ec_funded: 1
external_id:
isi:
- '000437171700017'
intvolume: ' 209'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/node/80098.abstract
month: '07'
oa: 1
oa_version: Preprint
page: 861-883
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genetics
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/
record:
- id: '9813'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '190'
abstract:
- lang: eng
text: The German cockroach, Blattella germanica, is a worldwide pest that infests
buildings, including homes, restaurants, and hospitals, often living in unsanitary
conditions. As a disease vector and producer of allergens, this species has major
health and economic impacts on humans. Factors contributing to the success of
the German cockroach include its resistance to a broad range of insecticides,
immunity to many pathogens, and its ability, as an extreme generalist omnivore,
to survive on most food sources. The recently published genome shows that B. germanica
has an exceptionally high number of protein coding genes. In this study, we investigate
the functions of the 93 significantly expanded gene families with the aim to better
understand the success of B. germanica as a major pest despite such inhospitable
conditions. We find major expansions in gene families with functions related to
the detoxification of insecticides and allelochemicals, defense against pathogens,
digestion, sensory perception, and gene regulation. These expansions might have
allowed B. germanica to develop multiple resistance mechanisms to insecticides
and pathogens, and enabled a broad, flexible diet, thus explaining its success
in unsanitary conditions and under recurrent chemical control. The findings and
resources presented here provide insights for better understanding molecular mechanisms
that will facilitate more effective cockroach control.
article_processing_charge: No
article_type: original
author:
- first_name: Mark
full_name: Harrison, Mark
last_name: Harrison
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Lucas
full_name: Kremer, Lucas
last_name: Kremer
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Maria
full_name: Puilachs, Maria
last_name: Puilachs
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
citation:
ama: 'Harrison M, Arning N, Kremer L, et al. Expansions of key protein families
in the German cockroach highlight the molecular basis of its remarkable success
as a global indoor pest. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824'
apa: 'Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer,
E., … Schal, C. (2018). Expansions of key protein families in the German cockroach
highlight the molecular basis of its remarkable success as a global indoor pest.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution.
Wiley. https://doi.org/10.1002/jez.b.22824'
chicago: 'Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles,
Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families
in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success
as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.'
ieee: 'M. Harrison et al., “Expansions of key protein families in the German
cockroach highlight the molecular basis of its remarkable success as a global
indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution, vol. 330. Wiley, pp. 254–264, 2018.'
ista: 'Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans
AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein
families in the German cockroach highlight the molecular basis of its remarkable
success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 330, 254–264.'
mla: 'Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach
Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.”
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution,
vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824.'
short: 'M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer,
A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental
Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.'
date_created: 2018-12-11T11:45:06Z
date_published: 2018-07-11T00:00:00Z
date_updated: 2023-09-11T13:59:54Z
day: '11'
department:
- _id: BeVi
doi: 10.1002/jez.b.22824
external_id:
isi:
- '000443231000002'
pmid:
- '29998472'
intvolume: ' 330'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824
month: '07'
oa: 1
oa_version: Submitted Version
page: 254-264
pmid: 1
publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution'
publication_status: published
publisher: Wiley
publist_id: '7730'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expansions of key protein families in the German cockroach highlight the molecular
basis of its remarkable success as a global indoor pest
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 330
year: '2018'
...
---
_id: '404'
abstract:
- lang: eng
text: "We construct martingale solutions to stochastic thin-film equations by introducing
a (spatial) semidiscretization and establishing convergence. The discrete scheme
allows for variants of the energy and entropy estimates in the continuous setting
as long as the discrete energy does not exceed certain threshold values depending
on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy
paths constant in time, arbitrary moments of coupled energy/entropy functionals
can be controlled. Having established Hölder regularity of approximate solutions,
the convergence proof is then based on compactness arguments---in particular on
Jakubowski's generalization of Skorokhod's theorem---weak convergence methods,
and recent tools on martingale convergence.\r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Günther
full_name: Grün, Günther
last_name: Grün
citation:
ama: Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film
equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796
apa: Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic
thin-film equations. SIAM Journal on Mathematical Analysis. Society for
Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796
chicago: Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to
Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis.
Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.
ieee: J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic
thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no.
1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.
ista: Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film
equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.
mla: Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic
Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no.
1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.
short: J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.
date_created: 2018-12-11T11:46:17Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2023-09-11T13:59:22Z
day: '30'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1137/16M1098796
external_id:
isi:
- '000426630900015'
file:
- access_level: open_access
checksum: 89a8eae7c52bb356c04f52b44bff4b5a
content_type: application/pdf
creator: dernst
date_created: 2019-11-07T12:20:25Z
date_updated: 2020-07-14T12:46:22Z
file_id: '6992'
file_name: 2018_SIAM_Fischer.pdf
file_size: 557338
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 411 - 455
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7425'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Existence of positive solutions to stochastic thin-film equations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '9813'
abstract:
- lang: eng
text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
S2 contains the code required for a stochastic simulation of the SLF system with
an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- 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: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
material for Bodova et al., 2018.” Genetics Society of America, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.
mla: Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018.
Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-11T13:57:42Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
record:
- id: '316'
relation: used_in_publication
status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '5780'
abstract:
- lang: eng
text: Bioluminescence is found across the entire tree of life, conferring a spectacular
set of visually oriented functions from attracting mates to scaring off predators.
Half a dozen different luciferins, molecules that emit light when enzymatically
oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis
has been described in full, which is found only in bacteria. Here, we report identification
of the fungal luciferase and three other key enzymes that together form the biosynthetic
cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite.
Introduction of the identified genes into the genome of the yeast Pichia pastoris
along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent
in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis
cycle and found that fungal bioluminescence emerged through a series of events
that included two independent gene duplications. The retention of the duplicated
enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication
was followed by functional sequence divergence of enzymes of at least one gene
in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence
proceeded through several closely related stepping stone nonluminescent biochemical
reactions with adaptive roles. The availability of a complete eukaryotic luciferin
biosynthesis pathway provides several applications in biomedicine and bioengineering.
article_processing_charge: No
author:
- first_name: Alexey A.
full_name: Kotlobay, Alexey A.
last_name: Kotlobay
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Yuliana A.
full_name: Mokrushina, Yuliana A.
last_name: Mokrushina
- first_name: Marina
full_name: Marcet-Houben, Marina
last_name: Marcet-Houben
- first_name: Ekaterina O.
full_name: Serebrovskaya, Ekaterina O.
last_name: Serebrovskaya
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Andrey Y.
full_name: Gorokhovatsky, Andrey Y.
last_name: Gorokhovatsky
- first_name: Andrey
full_name: Vvedensky, Andrey
last_name: Vvedensky
- first_name: Konstantin V.
full_name: Purtov, Konstantin V.
last_name: Purtov
- first_name: Valentin N.
full_name: Petushkov, Valentin N.
last_name: Petushkov
- first_name: Natalja S.
full_name: Rodionova, Natalja S.
last_name: Rodionova
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Liliia
full_name: Fakhranurova, Liliia
last_name: Fakhranurova
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Rustam
full_name: Ziganshin, Rustam
last_name: Ziganshin
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Zinaida M.
full_name: Kaskova, Zinaida M.
last_name: Kaskova
- first_name: Victoria
full_name: Shender, Victoria
last_name: Shender
- first_name: Maxim
full_name: Abakumov, Maxim
last_name: Abakumov
- first_name: Tatiana O.
full_name: Abakumova, Tatiana O.
last_name: Abakumova
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Fedor M.
full_name: Eroshkin, Fedor M.
last_name: Eroshkin
- first_name: Andrey G.
full_name: Zaraisky, Andrey G.
last_name: Zaraisky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Tatiana Y.
full_name: Mitiouchkina, Tatiana Y.
last_name: Mitiouchkina
- first_name: Eugene P.
full_name: Kopantzev, Eugene P.
last_name: Kopantzev
- first_name: Hans E.
full_name: Waldenmaier, Hans E.
last_name: Waldenmaier
- first_name: Anderson G.
full_name: Oliveira, Anderson G.
last_name: Oliveira
- first_name: Yuichi
full_name: Oba, Yuichi
last_name: Oba
- first_name: Ekaterina
full_name: Barsova, Ekaterina
last_name: Barsova
- first_name: Ekaterina A.
full_name: Bogdanova, Ekaterina A.
last_name: Bogdanova
- first_name: Toni
full_name: Gabaldón, Toni
last_name: Gabaldón
- first_name: Cassius V.
full_name: Stevani, Cassius V.
last_name: Stevani
- first_name: Sergey
full_name: Lukyanov, Sergey
last_name: Lukyanov
- first_name: Ivan V.
full_name: Smirnov, Ivan V.
last_name: Smirnov
- first_name: Josef I.
full_name: Gitelson, Josef I.
last_name: Gitelson
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
citation:
ama: Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115
apa: Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya,
E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115
chicago: Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben,
Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et
al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.
ieee: A. A. Kotlobay et al., “Genetically encodable bioluminescent system
from fungi,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732,
2018.
ista: Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO,
Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov
VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova
AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin
FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier
HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov
S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable
bioluminescent system from fungi. Proceedings of the National Academy of Sciences
of the United States of America. 115(50), 12728–12732.
mla: Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from
Fungi.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32,
doi:10.1073/pnas.1803615115.
short: A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya,
N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov,
V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya,
R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova,
I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y.
Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova,
E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson,
F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences
of the United States of America 115 (2018) 12728–12732.
date_created: 2018-12-23T22:59:18Z
date_published: 2018-12-11T00:00:00Z
date_updated: 2023-09-11T14:04:05Z
day: '11'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1073/pnas.1803615115
external_id:
isi:
- '000452866000068'
file:
- access_level: open_access
checksum: 46b2c12185eb2ddb598f4c7b4bd267bf
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T15:21:40Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5926'
file_name: 2018_PNAS_Kotlobay.pdf
file_size: 1271988
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 12728-12732
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encodable bioluminescent system from fungi
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '428'
abstract:
- lang: eng
text: The plant hormone gibberellic acid (GA) is a crucial regulator of growth and
development. The main paradigm of GA signaling puts forward transcriptional regulation
via the degradation of DELLA transcriptional repressors. GA has also been shown
to regulate tropic responses by modulation of the plasma membrane incidence of
PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular
and molecular mechanisms by which GA redirects protein trafficking and thus regulates
cell surface functionality. Photoconvertible reporters revealed that GA balances
the protein traffic between the vacuole degradation route and recycling back to
the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple
cargos, including PIN proteins, whereas high GA levels promote their recycling
to the plasma membrane. This GA effect requires components of the retromer complex,
such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated
protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates
the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton
is essential for the GA effect on trafficking. This GA cellular action occurs
through DELLA proteins that regulate the MT and retromer presumably via their
interaction partners Prefoldins (PFDs). Our study identified a branching of the
GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating
transcription, also target by a nontranscriptional mechanism the retromer complex
acting at the intersection of the degradation and recycling trafficking routes.
By this mechanism, GA can redirect receptors and transporters to the cell surface,
thus coregulating multiple processes, including PIN-dependent auxin fluxes during
tropic responses.
acknowledgement: "We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular
y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and
Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology,
Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central
European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for
Science), and Y. Gu (Penn State University) for making available the materials used
in this study;\r\n...funding from the European Research Council (ERC) under the
European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement
282300.\r\nCC BY NC ND"
article_processing_charge: No
author:
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Kaori
full_name: Tabata, Kaori
id: 7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0
last_name: Tabata
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets
the retromer complex to redirect protein trafficking to the plasma membrane. PNAS.
2018;115(14):3716-3721. doi:10.1073/pnas.1721760115
apa: Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc,
M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex
to redirect protein trafficking to the plasma membrane. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1721760115
chicago: Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi
Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the
Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS.
National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.
ieee: Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer
complex to redirect protein trafficking to the plasma membrane,” PNAS,
vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.
ista: Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml
J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect
protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.
mla: Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer
Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS,
vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.
short: Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc,
J. Friml, PNAS 115 (2018) 3716–3721.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-04-03T00:00:00Z
date_updated: 2023-09-11T14:06:34Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1721760115
ec_funded: 1
external_id:
isi:
- '000429012500073'
file:
- access_level: open_access
checksum: 1fcf7223fb8f99559cfa80bd6f24ce44
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:30:14Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5700'
file_name: 2018_PNAS_Salanenka.pdf
file_size: 1924101
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: ' 3716 - 3721'
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7395'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gibberellin DELLA signaling targets the retromer complex to redirect protein
trafficking to the plasma membrane
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '62'
abstract:
- lang: eng
text: Imaging is a dominant strategy for data collection in neuroscience, yielding
stacks of images that often scale to gigabytes of data for a single experiment.
Machine learning algorithms from computer vision can serve as a pair of virtual
eyes that tirelessly processes these images, automatically detecting and identifying
microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction
of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual
clues and requires no training. This approach generalizes across different modalities,
including serially-sectioned scanning electron microscopy (sSEM) of genetically
labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe)
microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue
volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets,
demonstrating the high biological fidelity of the pipeline’s reconstructions.
FLoRIN reconstructions are of sufficient quality for preliminary biological study,
for example examining the distribution and morphology of cells or extracting single
axons from functional data. Compared to existing supervised learning methods,
FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions
that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.
acknowledgement: 'Equipment was generously donated by the NVIDIA Corporation, and
made available by the National Science Foundation (NSF) through grant #CNS-1629914.
This research used resources of the Argonne Leadership Computing Facility, which
is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.'
article_number: '14247'
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Shabazi, Ali
last_name: Shabazi
- first_name: Jeffery
full_name: Kinnison, Jeffery
last_name: Kinnison
- first_name: Rafael
full_name: Vescovi, Rafael
last_name: Vescovi
- first_name: Ming
full_name: Du, Ming
last_name: Du
- first_name: Robert
full_name: Hill, Robert
last_name: Hill
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Marc
full_name: Takeno, Marc
last_name: Takeno
- first_name: Hongkui
full_name: Zeng, Hongkui
last_name: Zeng
- first_name: Nuno
full_name: Da Costa, Nuno
last_name: Da Costa
- first_name: Jaime
full_name: Grutzendler, Jaime
last_name: Grutzendler
- first_name: Narayanan
full_name: Kasthuri, Narayanan
last_name: Kasthuri
- first_name: Walter
full_name: Scheirer, Walter
last_name: Scheirer
citation:
ama: Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation
and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3
apa: Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer,
W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3
chicago: Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian
A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018.
https://doi.org/10.1038/s41598-018-32628-3.
ieee: A. Shabazi et al., “Flexible learning-free segmentation and reconstruction
of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing
Group, 2018.
ista: Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H,
Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free
segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.
mla: Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing
Group, 2018, doi:10.1038/s41598-018-32628-3.
short: A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno,
H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports
8 (2018).
date_created: 2018-12-11T11:44:25Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2023-09-11T14:02:55Z
day: '24'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-018-32628-3
external_id:
isi:
- '000445336600015'
file:
- access_level: open_access
checksum: 1a14ae0666b82fbaa04bef110e3f6bf2
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:22:24Z
date_updated: 2020-07-14T12:47:24Z
file_id: '5699'
file_name: 2018_ScientificReports_Shahbazi.pdf
file_size: 4141645
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intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7992'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: http://doi.org/10.1038/s41598-018-36220-7
scopus_import: '1'
status: public
title: Flexible learning-free segmentation and reconstruction of neural volumes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '437'
abstract:
- lang: eng
text: Dendritic cells (DCs) are sentinels of the adaptive immune system that reside
in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation
and up-regulate the chemokine receptor CCR7 that guides them along gradients of
its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs
present peripherally acquired antigen to naïve T cells, thereby triggering adaptive
immunity.
acknowledged_ssus:
- _id: SSU
acknowledgement: "This work was supported by grants of the European Research Council
(ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific
support units at IST Austria for excellent technical support.\r\nWe thank the scientific
\ support units at IST Austria for excellent technical support. "
article_processing_charge: Yes (via OA deal)
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Hans
full_name: Haecker, Hans
last_name: Haecker
- 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: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast
and efficient genetic engineering of hematopoietic precursor cells for the study
of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077.
doi:10.1002/eji.201747358
apa: Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., &
Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor
cells for the study of dendritic cell migration. European Journal of Immunology.
Wiley-Blackwell. https://doi.org/10.1002/eji.201747358
chicago: Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild,
Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.
ieee: A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M.
K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells
for the study of dendritic cell migration,” European Journal of Immunology,
vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.
ista: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018.
Fast and efficient genetic engineering of hematopoietic precursor cells for the
study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.
mla: Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.
short: A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K.
Sixt, European Journal of Immunology 48 (2018) 1074–1077.
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-09-11T14:01:18Z
day: '13'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1002/eji.201747358
ec_funded: 1
external_id:
isi:
- '000434963700016'
file:
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checksum: 9d5b74cd016505aeb9a4c2d33bbedaeb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5044'
file_name: IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf
file_size: 590106
relation: main_file
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has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1074 - 1077
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: European Journal of Immunology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7386'
pubrep_id: '1067'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and efficient genetic engineering of hematopoietic precursor cells for
the study of dendritic cell migration
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2018'
...
---
_id: '617'
abstract:
- lang: eng
text: Insects are exposed to a variety of potential pathogens in their environment,
many of which can severely impact fitness and health. Consequently, hosts have
evolved resistance and tolerance strategies to suppress or cope with infections.
Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads,
and hosts utilizing tolerance reduce harmful fitness effects per pathogen load.
To understand variation in, and selective pressures on, resistance and tolerance,
we asked to what degree they are shaped by host genetic background, whether plasticity
in these responses depends upon dietary environment, and whether there are interactions
between these two factors. Females from ten wild-type Drosophila melanogaster
genotypes were kept on high- or low-protein (yeast) diets and infected with one
of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila.
We measured host resistance as the inverse of bacterial load in the early infection
phase. The relationship (slope) between fly fecundity and individual-level bacteria
load provided our fecundity tolerance measure. Genotype and dietary yeast determined
host fecundity and strongly affected survival after infection with pathogenic
P. entomophila. There was considerable genetic variation in host resistance, a
commonly found phenomenon resulting from for example varying resistance costs
or frequency-dependent selection. Despite this variation and the reproductive
cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes.
The absence of genetic variation in tolerance may suggest that at this early infection
stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are
not expressed under these infection conditions.
acknowledgement: 'We would like to thank Susann Wicke for performing the genome-wide
SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara
Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical
help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the
Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for
their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG)
priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR
872/1-1). '
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival,
and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
2018;31(1):159-171. doi:10.1111/jeb.13211
apa: Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect
resistance, survival, and fecundity but not fecundity tolerance. Journal of
Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect
Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of
Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.
ieee: M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary
Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.
ista: Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
31(1), 159–171.
mla: Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity
but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31,
no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.
short: M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018)
159–171.
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T14:06:04Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/jeb.13211
external_id:
isi:
- '000419307000014'
pmid:
- '29150962'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13211
month: '01'
oa: 1
oa_version: Published Version
page: 159 - 171
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '7187'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genotype and diet affect resistance, survival, and fecundity but not fecundity
tolerance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 31
year: '2018'
...
---
_id: '5888'
abstract:
- lang: eng
text: "Despite the remarkable number of scientific breakthroughs of the last 100
years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum
disorder, intellectual disability) remains a great challenge. Recent advancements
in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists
to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given
the few hundred risk genes that have been discovered,\r\nthe etiological variability
and the heterogeneous clinical presentation, the need for genotype — along with
phenotype-\r\nbased diagnosis of individual patients has become a requisite. In
this review we look at recent advancements in\r\ngenomic analysis and their translation
into clinical practice."
article_number: '100'
article_processing_charge: No
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an
avenue to personalized medicine. Experimental & Molecular Medicine.
2018;50(8). doi:10.1038/s12276-018-0129-7'
apa: 'Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental
disorders: an avenue to personalized medicine. Experimental & Molecular
Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7'
chicago: 'Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental
Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular
Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.'
ieee: 'D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders:
an avenue to personalized medicine,” Experimental & Molecular Medicine,
vol. 50, no. 8. Springer Nature, 2018.'
ista: 'Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders:
an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8),
100.'
mla: 'Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental
Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular
Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.'
short: D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50
(2018).
date_created: 2019-01-27T22:59:11Z
date_published: 2018-08-07T00:00:00Z
date_updated: 2023-09-11T14:04:41Z
day: '07'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1038/s12276-018-0129-7
external_id:
isi:
- '000441266700006'
pmid:
- '30089840'
file:
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checksum: 4498301c8c53097c9a1a8ef990936eb5
content_type: application/pdf
creator: dernst
date_created: 2019-01-28T15:18:02Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5893'
file_name: 2018_EMM_Tarlungeanu.pdf
file_size: 1237482
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Experimental & Molecular Medicine
publication_identifier:
issn:
- 2092-6413
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomics in neurodevelopmental disorders: an avenue to personalized medicine'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '295'
abstract:
- lang: eng
text: We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional
anyon gas. Our bounds are extensive in the particle number, as for fermions, and
linear in the statistics parameter (Formula presented.). The lower bounds extend
to Lieb–Thirring inequalities for all anyons except bosons.
acknowledgement: Financial support from the Swedish Research Council, grant no. 2013-4734
(D. L.), the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No 694227, R. S.), and by
the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully
acknowledged.
article_processing_charge: No
author:
- first_name: Douglas
full_name: Lundholm, Douglas
last_name: Lundholm
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in
Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y
apa: Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons.
Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y
chicago: Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.”
Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y.
ieee: D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters
in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.
ista: Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters
in Mathematical Physics. 108(11), 2523–2541.
mla: Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.”
Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp.
2523–41, doi:10.1007/s11005-018-1091-y.
short: D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.
date_created: 2018-12-11T11:45:40Z
date_published: 2018-05-11T00:00:00Z
date_updated: 2023-09-11T14:01:57Z
day: '11'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-018-1091-y
ec_funded: 1
external_id:
arxiv:
- '1712.06218'
isi:
- '000446491500008'
file:
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checksum: 8beb9632fa41bbd19452f55f31286a31
content_type: application/pdf
creator: dernst
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date_updated: 2020-07-14T12:45:55Z
file_id: '5698'
file_name: 2018_LettMathPhys_Lundholm.pdf
file_size: 551996
relation: main_file
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has_accepted_license: '1'
intvolume: ' 108'
isi: 1
issue: '11'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2523-2541
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '7586'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fermionic behavior of ideal anyons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 108
year: '2018'
...