---
_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).
corr_author: '1'
date_created: 2019-07-11T12:00:32Z
date_published: 2019-07-07T00:00:00Z
date_updated: 2026-07-01T22:30:49Z
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: '6848'
abstract:
- lang: eng
text: Proton-translocating transhydrogenase (also known as nicotinamide nucleotide
transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner
mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride
between NADH and NADP+, coupled to the translocation of one proton across the
membrane. Its main physiological function is the generation of NADPH, which is
a substrate in anabolic reactions and a regulator of oxidative status; however,
NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid
deficiency in humans and metabolic abnormalities in mice, similar to those observed
in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve
a rotation of around 180° of the entire NADP(H)-binding domain that alternately
participates in hydride transfer and proton-channel gating. However, owing to
the lack of high-resolution structures of intact NNT, the details of this process
remain unclear5,6. Here we present the cryo-electron microscopy structure of intact
mammalian NNT in different conformational states. We show how the NADP(H)-binding
domain opens the proton channel to the opposite sides of the membrane, and we
provide structures of these two states. We also describe the catalytically important
interfaces and linkers between the membrane and the soluble domains and their
roles in nucleotide exchange. These structures enable us to propose a revised
mechanism for a coupling process in NNT that is consistent with a large body of
previous biochemical work. Our results are relevant to the development of currently
unavailable NNT inhibitors, which may have therapeutic potential in ischaemia
reperfusion injury, metabolic syndrome and some cancers7,8,9.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: " We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their
assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing
was performed at the IST high-performance computing cluster.\r\nThis project has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement no. 665385."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
orcid: 0000-0002-6018-3422
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2
apa: Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial
proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019.
https://doi.org/10.1038/s41586-019-1519-2.
ieee: D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating
transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295,
2019.
ista: Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 573(7773), 291–295.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer
Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.
short: D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.
date_created: 2019-09-04T06:21:41Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-07-01T22:31:03Z
day: '12'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-019-1519-2
ec_funded: 1
external_id:
isi:
- '000485415400061'
pmid:
- '31462775'
file:
- access_level: open_access
checksum: 52728cda5210a3e9b74cc204e8aed3d5
content_type: application/pdf
creator: lsazanov
date_created: 2020-11-26T16:33:44Z
date_updated: 2020-11-26T16:33:44Z
file_id: '8821'
file_name: Manuscript_final_acc_withFigs_SI_opt_red.pdf
file_size: 3066206
relation: main_file
success: 1
file_date_updated: 2020-11-26T16:33:44Z
has_accepted_license: '1'
intvolume: ' 573'
isi: 1
issue: '7773'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 291–295
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/
record:
- id: '8340'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of mitochondrial proton-translocating transhydrogenase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 573
year: '2019'
...
---
_id: '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: 2026-07-01T22:31:03Z
day: '04'
ddc:
- '570'
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:
- 1097-4199
issn:
- 0896-6273
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 103
year: '2019'
...
---
_id: '6508'
abstract:
- lang: eng
text: Segregation of maternal determinants within the oocyte constitutes the first
step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming
leads to the segregation of ooplasm from yolk granules along the animal-vegetal
axis of the oocyte. Here, we show that this process does not rely on cortical
actin reorganization, as previously thought, but instead on a cell-cycle-dependent
bulk actin polymerization wave traveling from the animal to the vegetal pole of
the oocyte. This wave functions in segregation by both pulling ooplasm animally
and pushing yolk granules vegetally. Using biophysical experimentation and theory,
we show that ooplasm pulling is mediated by bulk actin network flows exerting
friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism
closely resembling actin comet formation on yolk granules. Our study defines a
novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte
polarization via ooplasmic segregation.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia
Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with
zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful
discussions, and the Bioimaging and zebrafish facilities at IST Austria for their
continuous support. This project has received funding from the European Union (European
Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science
Fund (FWF) (P 31639 to E.H.).
article_processing_charge: No
article_type: original
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- 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: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin
dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18.
doi:10.1016/j.cell.2019.04.030
apa: Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg,
C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030
chicago: Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo,
and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in
Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.
ieee: S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg,
“Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell,
vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.
ista: Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk
actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.
mla: Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030.
short: S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg,
Cell 177 (2019) 1463–1479.e18.
date_created: 2019-06-02T21:59:12Z
date_published: 2019-05-30T00:00:00Z
date_updated: 2026-07-01T22:31:05Z
day: '30'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
- _id: BjHo
doi: 10.1016/j.cell.2019.04.030
ec_funded: 1
external_id:
isi:
- '000469415100013'
pmid:
- '31080065'
file:
- access_level: open_access
checksum: aea43726d80e35ce3885073a5f05c3e3
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T07:22:34Z
date_updated: 2020-10-21T07:22:34Z
file_id: '8686'
file_name: 2019_Cell_Shamipour_accepted.pdf
file_size: 3356292
relation: main_file
success: 1
file_date_updated: 2020-10-21T07:22:34Z
has_accepted_license: '1'
intvolume: ' 177'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.04.030
month: '05'
oa: 1
oa_version: Published Version
page: 1463-1479.e18
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
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/how-the-cytoplasm-separates-from-the-yolk/
record:
- id: '8350'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Bulk actin dynamics drive phase segregation in zebrafish oocytes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 177
year: '2019'
...
---
_id: '7001'
acknowledged_ssus:
- _id: PreCl
- _id: Bio
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: M
full_name: Balda, M
last_name: Balda
- first_name: M
full_name: Tada, M
last_name: Tada
- first_name: K
full_name: Matter, K
last_name: Matter
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight
junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18.
doi:10.1016/j.cell.2019.10.006
apa: Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada,
M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends
on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006
chicago: Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra
Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation
of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell
Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.
ieee: C. Schwayer et al., “Mechanosensation of tight junctions depends on
ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p.
937–952.e18, 2019.
ista: Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter
K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1
phase separation and flow. Cell. 179(4), 937–952.e18.
mla: Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on
ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019,
p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.
short: C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada,
K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.
date_created: 2019-11-12T12:51:06Z
date_published: 2019-10-31T00:00:00Z
date_updated: 2026-07-01T22:31:05Z
day: '31'
ddc:
- '570'
department:
- _id: CaHe
- _id: BjHo
doi: 10.1016/j.cell.2019.10.006
ec_funded: 1
external_id:
isi:
- '000493898000012'
pmid:
- '31675500'
file:
- access_level: open_access
checksum: 33dac4bb77ee630e2666e936b4d57980
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T07:09:45Z
date_updated: 2020-10-21T07:09:45Z
file_id: '8684'
file_name: 2019_Cell_Schwayer_accepted.pdf
file_size: 8805878
relation: main_file
success: 1
file_date_updated: 2020-10-21T07:09:45Z
has_accepted_license: '1'
intvolume: ' 179'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 937-952.e18
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News auf IST Website
relation: press_release
url: https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/
record:
- id: '7186'
relation: dissertation_contains
status: public
- id: '8350'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 179
year: '2019'
...
---
_id: '6260'
abstract:
- lang: eng
text: Polar auxin transport plays a pivotal role in plant growth and development.
PIN auxin efflux carriers regulate directional auxin movement by establishing
local auxin maxima, minima, and gradients that drive multiple developmental processes
and responses to environmental signals. Auxin has been proposed to modulate its
own transport by regulating subcellular PIN trafficking via processes such as
clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further
investigated the mechanisms by which auxin affects PIN trafficking by screening
auxin analogs and identified pinstatic acid (PISA) as a positive modulator of
polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on
hypocotyl elongation and adventitious root formation via positive regulation of
auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN
accumulation at the cell surface by inhibiting PIN internalization from the plasma
membrane. This work demonstrates PISA to be a promising chemical tool to dissect
the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.
acknowledgement: "We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden
University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University
of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis
work was supported by the Ministry of Education, Culture, Sports, Science, and Technology
(Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology
and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.),
and the European Union’s Horizon2020 program (European Research Council grant agreement
no. 742985 to J.F.)."
article_processing_charge: No
article_type: original
author:
- first_name: A
full_name: Oochi, A
last_name: Oochi
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: K
full_name: Fukui, K
last_name: Fukui
- first_name: Y
full_name: Nakao, Y
last_name: Nakao
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: M
full_name: Quareshy, M
last_name: Quareshy
- first_name: K
full_name: Takahashi, K
last_name: Takahashi
- first_name: T
full_name: Kinoshita, T
last_name: Kinoshita
- first_name: SR
full_name: Harborough, SR
last_name: Harborough
- first_name: S
full_name: Kepinski, S
last_name: Kepinski
- first_name: H
full_name: Kasahara, H
last_name: Kasahara
- first_name: RM
full_name: Napier, RM
last_name: Napier
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: KI
full_name: Hayashi, KI
last_name: Hayashi
citation:
ama: Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by
inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165.
doi:10.1104/pp.19.00201
apa: Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., …
Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN
internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201
chicago: Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy,
K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.
ieee: A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting
PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165,
2019.
ista: Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita
T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic
acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology.
180(2), 1152–1165.
mla: Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65,
doi:10.1104/pp.19.00201.
short: A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi,
T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K.
Hayashi, Plant Physiology 180 (2019) 1152–1165.
date_created: 2019-04-09T08:38:20Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2026-07-01T22:31:09Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1104/pp.19.00201
ec_funded: 1
external_id:
isi:
- '000470086100045'
pmid:
- '30936248'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.19.00201
month: '06'
oa: 1
oa_version: Published Version
page: 1152-1165
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Pinstatic acid promotes auxin transport by inhibiting PIN internalization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 180
year: '2019'
...
---
OA_place: publisher
_id: '6435'
abstract:
- lang: eng
text: "Social insect colonies tend to have numerous members which function together
like a single organism in such harmony that the term ``super-organism'' is often
used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells
of a metazoan, while the sterile worker caste corresponds to somatic cells. The
worker castes, like tissues, are\r\nin charge of all functions of a living being,
besides reproduction. The establishment of new super-organismal units\r\n(i.e.
new colonies) is accomplished by the co-dependent castes. The term oftentimes
goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation,
nutrient regulation and gas exchange of a social insect colony. Furthermore, we
assert that the super-organism has an immune system, and benefits from ``social
immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists
to resolve the apparent discrepancy between the expected high frequency of disease
outbreak amongst numerous, closely related tightly-interacting hosts, living in
stable and microbially-rich environments, against the exceptionally scarce epidemic
accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly
of behaviours which have evolved to effectively keep the pathogenic enemies of
a colony at bay. The field of social immunity has drawn interest, as it becomes
increasingly urgent to stop\r\nthe collapse of pollinator species and curb the
growth of invasive pests. In the past decade, several mechanisms of\r\nsocial
immune responses have been dissected, but many more questions remain open.\r\n\r\nI
present my work in two experimental chapters. In the first, I use invasive garden
ants (*Lasius neglectus*) to study how pathogen load and its distribution among
nestmates affect the grooming response of the group. Any given group of ants will
carry out the same total grooming work, but will direct their grooming effort
towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation,
the highest risk of transmission does not stem from grooming highly contaminated
ants, but instead, we suggest that the grooming response likely minimizes spore
loss to the environment, reducing contamination from inadvertent pickup from the
substrate.\r\n\r\nThe second is a comparative developmental approach. I follow
black garden ant queens (*Lasius niger*) and their colonies from mating flight,
through hibernation for a year. Colonies which grow fast from the start, have
a lower chance of survival through hibernation, and those which survive grow at
a lower pace later. This is true for colonies of naive\r\nand challenged queens.
Early pathogen exposure of the queens changes colony dynamics in an unexpected
way: colonies from exposed queens are more likely to grow slowly and recover in
numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental
chapters, this thesis includes a co-authored published review on organisational\r\nimmunity,
where we enlist the experimental evidence and theoretical framework on which this
hypothesis is built,\r\nidentify the caveats and underline how the field is ripe
to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative
efforts, one to develop an image-based tracker, and the second to develop a classifier
for ant\r\nbehaviour."
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: M-Shop
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
citation:
ama: Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen.
2019. doi:10.15479/AT:ISTA:6435
apa: Casillas Perez, B. E. (2019). Collective defenses of garden ants against
a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435
chicago: Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against
a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.
ieee: B. E. Casillas Perez, “Collective defenses of garden ants against a fungal
pathogen,” Institute of Science and Technology Austria, 2019.
ista: Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal
pathogen. Institute of Science and Technology Austria.
mla: Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a
Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.
short: B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal
Pathogen, Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-05-13T08:58:35Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2026-04-08T14:02:12Z
day: '07'
ddc:
- '570'
- '006'
- '578'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:6435
ec_funded: 1
file:
- access_level: open_access
checksum: 6daf2d2086111aa8fd3fbc919a3e2833
content_type: application/pdf
creator: casillas
date_created: 2019-05-13T09:16:20Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-08
file_id: '6438'
file_name: tesisDoctoradoBC.pdf
file_size: 3895187
relation: main_file
- access_level: closed
checksum: 3d221aaff7559a7060230a1ff610594f
content_type: application/zip
creator: casillas
date_created: 2019-05-13T09:16:20Z
date_updated: 2020-07-14T12:47:30Z
embargo_to: open_access
file_id: '6439'
file_name: tesisDoctoradoBC.zip
file_size: 7365118
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
keyword:
- Social Immunity
- Sanitary care
- Social Insects
- Organisational Immunity
- Colony development
- Multi-target tracking
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '183'
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1999'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Collective defenses of garden ants against a fungal pathogen
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
_id: '6780'
abstract:
- lang: eng
text: "In this work, we consider the almost-sure termination problem for probabilistic
programs that asks whether a\r\ngiven probabilistic program terminates with probability
1. Scalable approaches for program analysis often\r\nrely on modularity as their
theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof
Floyd-Hoare logic provides the foundation for modular analysis. Extension of this
rule to almost-sure\r\ntermination of probabilistic programs is quite tricky,
and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic
variant cautiously addresses the key issue of integrability, we show that the
proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic
programs.\r\nBesides establishing unsoundness of the previous rule, our contributions
are as follows: First, we present a\r\nsound modular rule for almost-sure termination
of probabilistic programs. Our approach is based on a novel\r\nnotion of descent
supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat
are linear and show that they can be synthesized in polynomial time. Finally,
we present experimental\r\nresults on a variety of benchmarks and several natural
examples that model various types of nested while\r\nloops in probabilistic programs
and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination
property"
article_number: '129'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mingzhang
full_name: Huang, Mingzhang
last_name: Huang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure
termination of probabilistic programs. In: Proceedings of the 34th ACM International
Conference on Object-Oriented Programming, Systems, Languages, and Applications
. Vol 3. ACM; 2019. doi:10.1145/3360555'
apa: 'Huang, M., Fu, H., Chatterjee, K., & Goharshady, A. K. (2019). Modular
verification for almost-sure termination of probabilistic programs. In Proceedings
of the 34th ACM International Conference on Object-Oriented Programming, Systems,
Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360555'
chicago: Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic
Programs.” In Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications , Vol. 3. ACM, 2019. https://doi.org/10.1145/3360555.
ieee: M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification
for almost-sure termination of probabilistic programs,” in Proceedings of the
34th ACM International Conference on Object-Oriented Programming, Systems, Languages,
and Applications , Athens, Greece, 2019, vol. 3.
ista: 'Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for
almost-sure termination of probabilistic programs. Proceedings of the 34th ACM
International Conference on Object-Oriented Programming, Systems, Languages, and
Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications
vol. 3, 129.'
mla: Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination
of Probabilistic Programs.” Proceedings of the 34th ACM International Conference
on Object-Oriented Programming, Systems, Languages, and Applications , vol.
3, 129, ACM, 2019, doi:10.1145/3360555.
short: M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the
34th ACM International Conference on Object-Oriented Programming, Systems, Languages,
and Applications , ACM, 2019.
conference:
end_date: 2019-10-25
location: Athens, Greece
name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications'
start_date: 2019-10-23
date_created: 2019-08-09T09:54:20Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2026-07-01T22:31:14Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3360555
ec_funded: 1
external_id:
arxiv:
- '1901.06087'
file:
- access_level: open_access
checksum: 3482d8ace6fb4991eb7810e3b70f1b9f
content_type: application/pdf
creator: akafshda
date_created: 2019-08-12T15:40:57Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6807'
file_name: oopsla-2019.pdf
file_size: 1024643
relation: main_file
- access_level: open_access
checksum: 4e5a6fb2b59a75222a4e8335a5a60eac
content_type: application/pdf
creator: dernst
date_created: 2020-05-12T15:15:14Z
date_updated: 2020-07-14T12:47:40Z
file_id: '7821'
file_name: 2019_ACM_Huang.pdf
file_size: 538579
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: 'Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications '
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Modular verification for almost-sure termination of probabilistic programs
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: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2019'
...
---
_id: '6490'
abstract:
- lang: eng
text: "Smart contracts are programs that are stored and executed on the Blockchain
and can receive, manage and transfer money (cryptocurrency units). Two important
problems regarding smart contracts are formal analysis and compiler optimization.
Formal analysis is extremely important, because smart contracts hold funds worth
billions of dollars and their code is immutable after deployment. Hence, an undetected
bug can cause significant financial losses. Compiler optimization is also crucial,
because every action of a smart contract has to be executed by every node in the
Blockchain network. Therefore, optimizations in compiling smart contracts can
lead to significant savings in computation, time and energy.\r\n\r\nTwo classical
approaches in program analysis and compiler optimization are intraprocedural and
interprocedural analysis. In intraprocedural analysis, each function is analyzed
separately, while interprocedural analysis considers the entire program. In both
cases, the analyses are usually reduced to graph problems over the control flow
graph (CFG) of the program. These graph problems are often computationally expensive.
Hence, there has been ample research on exploiting structural properties of CFGs
for efficient algorithms. One such well-studied property is the treewidth, which
is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs
of structured programs have treewidth at most 6, whereas the interprocedural treewidth
cannot be bounded. This result has been used as a basis for many efficient intraprocedural
analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth
of smart contracts for formal analysis and compiler optimization. First, similar
to classical programs, we show that the intraprocedural treewidth of structured
Solidity and Vyper smart contracts is at most 9. Second, for global analysis,
we prove that the interprocedural treewidth of structured smart contracts is bounded
by 10 and, in sharp contrast with classical programs, treewidth-based algorithms
can be easily applied for interprocedural analysis. Finally, we supplement our
theoretical results with experiments using a tool we implemented for computing
treewidth of smart contracts and show that the treewidth is much lower in practice.
We use 36,764 real-world Ethereum smart contracts as benchmarks and find that
they have an average treewidth of at most 3.35 for the intraprocedural case and
3.65 for the interprocedural case.\r\n"
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: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
citation:
ama: 'Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts.
In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part
F147772. ACM; 2019:400-408. doi:10.1145/3297280.3297322'
apa: 'Chatterjee, K., Goharshady, A. K., & Goharshady, E. K. (2019). The treewidth
of smart contracts. In Proceedings of the 34th ACM Symposium on Applied Computing
(Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297322'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady.
“The Treewidth of Smart Contracts.” In Proceedings of the 34th ACM Symposium
on Applied Computing, Part F147772:400–408. ACM, 2019. https://doi.org/10.1145/3297280.3297322.
ieee: K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart
contracts,” in Proceedings of the 34th ACM Symposium on Applied Computing,
Limassol, Cyprus, 2019, vol. Part F147772, pp. 400–408.
ista: 'Chatterjee K, Goharshady AK, Goharshady EK. 2019. The treewidth of smart
contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium
on Applied Computing vol. Part F147772, 400–408.'
mla: Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” Proceedings
of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, 2019,
pp. 400–08, doi:10.1145/3297280.3297322.
short: K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the
34th ACM Symposium on Applied Computing, ACM, 2019, pp. 400–408.
conference:
end_date: 2019-04-12
location: Limassol, Cyprus
name: 'SAC: Symposium on Applied Computing'
start_date: 2019-04-08
corr_author: '1'
date_created: 2019-05-26T21:59:15Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2026-07-01T22:31:14Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3297280.3297322
external_id:
isi:
- '000474685800052'
file:
- access_level: open_access
checksum: dddc20f6d9881f23b8755eb720ec9d6f
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:50:11Z
date_updated: 2020-07-14T12:47:32Z
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language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 400-408
publication: Proceedings of the 34th ACM Symposium on Applied Computing
publication_identifier:
isbn:
- '9781450359337'
publication_status: published
publisher: ACM
pubrep_id: '1070'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The treewidth of smart contracts
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: Part F147772
year: '2019'
...
---
_id: '7158'
abstract:
- lang: eng
text: "Interprocedural analysis is at the heart of numerous applications in programming
languages, such as alias analysis, constant propagation, and so on. Recursive
state machines (RSMs) are standard models for interprocedural analysis. We consider
a general framework with RSMs where the transitions are labeled from a semiring
and path properties are algebraic with semiring operations. RSMs with algebraic
path properties can model interprocedural dataflow analysis problems, the shortest
path problem, the most probable path problem, and so on. The traditional algorithms
for interprocedural analysis focus on path properties where the starting point
is fixed as the entry point of a specific method. In this work, we consider possible
multiple queries as required in many applications such as in alias analysis. The
study of multiple queries allows us to bring in an important algorithmic distinction
between the resource usage of the one-time preprocessing vs for each individual
query. The second aspect we consider is that the control flow graphs for most
programs have constant treewidth.\r\n\r\nOur main contributions are simple and
implementable algorithms that support multiple queries for algebraic path properties
for RSMs that have constant treewidth. Our theoretical results show that our algorithms
have small additional one-time preprocessing but can answer subsequent queries
significantly faster as compared to the current algorithmic solutions for interprocedural
dataflow analysis. We have also implemented our algorithms and evaluated their
performance for performing on-demand interprocedural dataflow analysis on various
domains, such as for live variable analysis and reaching definitions, on a standard
benchmark set. Our experimental results align with our theoretical statements
and show that after a lightweight preprocessing, on-demand queries are answered
much faster than the standard existing algorithmic approaches.\r\n"
article_number: '23'
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Prateesh
full_name: Goyal, Prateesh
last_name: Goyal
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster
algorithms for dynamic algebraic queries in basic RSMs with constant treewidth.
ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3363525
apa: Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., & Pavlogiannis,
A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with
constant treewidth. ACM Transactions on Programming Languages and Systems.
ACM. https://doi.org/10.1145/3363525
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus
Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic
Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming
Languages and Systems. ACM, 2019. https://doi.org/10.1145/3363525.
ieee: K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis,
“Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,”
ACM Transactions on Programming Languages and Systems, vol. 41, no. 4.
ACM, 2019.
ista: Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019.
Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth.
ACM Transactions on Programming Languages and Systems. 41(4), 23.
mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries
in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages
and Systems, vol. 41, no. 4, 23, ACM, 2019, doi:10.1145/3363525.
short: K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis,
ACM Transactions on Programming Languages and Systems 41 (2019).
date_created: 2019-12-09T08:33:33Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2026-07-01T22:31:14Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3363525
ec_funded: 1
external_id:
isi:
- '000564108400004'
file:
- access_level: open_access
checksum: 291cc86a07bd010d4815e177dac57b70
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T12:58:10Z
date_updated: 2020-10-08T12:58:10Z
file_id: '8632'
file_name: 2019_ACMTransactions_Chatterjee.pdf
file_size: 667357
relation: main_file
success: 1
file_date_updated: 2020-10-08T12:58:10Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: ACM Transactions on Programming Languages and Systems
publication_identifier:
issn:
- 0164-0925
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Faster algorithms for dynamic algebraic queries in basic RSMs with constant
treewidth
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 41
year: '2019'
...
---
_id: '6378'
abstract:
- lang: eng
text: 'In today''s cryptocurrencies, Hashcash proof of work is the most commonly-adopted
approach to mining. In Hashcash, when a miner decides to add a block to the chain,
she has to solve the difficult computational puzzle of inverting a hash function.
While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it
has attracted significant and harsh criticism due to its massive waste of electricity,
its carbon footprint and environmental effects, and the inherent lack of usefulness
in inverting a hash function. Various other mining protocols have been suggested,
including proof of stake, in which a miner''s chance of adding the next block
is proportional to her current balance. However, such protocols lead to a higher
entry cost for new miners who might not still have any stake in the cryptocurrency,
and can in the worst case lead to an oligopoly, where the rich have complete control
over mining. In this paper, we propose Hybrid Mining: a new mining protocol that
combines solving real-world useful problems with Hashcash. Our protocol allows
new miners to join the network by taking part in Hashcash mining without having
to own an initial stake. It also allows nodes of the network to submit hard computational
problems whose solutions are of interest in the real world, e.g.~protein folding
problems. Then, miners can choose to compete in solving these problems, in lieu
of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners
to solve useful problems, such as hard computational problems arising in biology,
in a distributed manner. It also gives researchers in other areas an easy-to-use
tool to outsource their hard computations to the blockchain network, which has
enormous computational power, by paying a reward to the miner who solves the problem
for them. Moreover, our protocol provides strong security guarantees and is at
least as resilient to double spending as Bitcoin.'
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: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s
computational power for distributed problem solving. In: Proceedings of the
34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381.
doi:10.1145/3297280.3297319'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining:
Exploiting blockchain’s computational power for distributed problem solving. In
Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772,
pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem
Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing,
Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving,” in Proceedings
of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol.
Part F147772, pp. 374–381.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving. Proceedings
of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing
vol. Part F147772, 374–381.'
mla: 'Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational
Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium
on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the
34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.
conference:
end_date: 2019-04-12
location: Limassol, Cyprus
name: ACM Symposium on Applied Computing
start_date: 2019-04-08
date_created: 2019-05-06T12:11:36Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2026-07-01T22:31:14Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3297280.3297319
ec_funded: 1
external_id:
isi:
- '000474685800049'
file:
- access_level: open_access
checksum: fbfbcd5a0c7a743862bfc3045539a614
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:09:27Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6379'
file_name: 2019_ACM_Chatterjee.pdf
file_size: 1023934
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 374-381
project:
- _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
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the 34th ACM Symposium on Applied Computing
publication_identifier:
isbn:
- '9781450359337'
publication_status: published
publisher: ACM
pubrep_id: '1069'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Hybrid Mining: Exploiting blockchain’s computational power for distributed
problem solving'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: Part F147772
year: '2019'
...
---
_id: '6175'
abstract:
- lang: eng
text: "We consider the problem of expected cost analysis over nondeterministic probabilistic
programs,\r\nwhich aims at automated methods for analyzing the resource-usage
of such programs.\r\nPrevious approaches for this problem could only handle nonnegative
bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis
of cryptocurrency protocols,\r\nboth 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\r\nexpected accumulated
cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a)
general positive and negative costs with bounded updates in\r\nvariables; and
(b) nonnegative costs with general updates to variables.\r\nWe show that several
natural examples which could not be\r\nhandled by previous approaches are captured
in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time
algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs
could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our
approach using experimental results on a variety of programs for which we efficiently
synthesize tight resource-usage bounds."
article_processing_charge: No
arxiv: 1
author:
- first_name: Peixin
full_name: Wang, Peixin
last_name: Wang
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Xudong
full_name: Qin, Xudong
last_name: Qin
- first_name: Wenjun
full_name: Shi, Wenjun
last_name: Shi
citation:
ama: 'Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of
nondeterministic probabilistic programs. In: PLDI 2019: Proceedings of the
40th ACM SIGPLAN Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2019:204-220. doi:10.1145/3314221.3314581'
apa: 'Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., & Shi, W.
(2019). Cost analysis of nondeterministic probabilistic programs. In PLDI 2019:
Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design
and Implementation (pp. 204–220). Phoenix, AZ, United States: Association
for Computing Machinery. https://doi.org/10.1145/3314221.3314581'
chicago: 'Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee,
Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.”
In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming
Language Design and Implementation, 204–20. Association for Computing Machinery,
2019. https://doi.org/10.1145/3314221.3314581.'
ieee: 'P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost
analysis of nondeterministic probabilistic programs,” in PLDI 2019: Proceedings
of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation,
Phoenix, AZ, United States, 2019, pp. 204–220.'
ista: 'Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis
of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th
ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI:
Conference on Programming Language Design and Implementation, 204–220.'
mla: 'Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.”
PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language
Design and Implementation, Association for Computing Machinery, 2019, pp.
204–20, doi:10.1145/3314221.3314581.'
short: 'P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI
2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2019, pp. 204–220.'
conference:
end_date: 2019-06-26
location: Phoenix, AZ, United States
name: 'PLDI: Conference on Programming Language Design and Implementation'
start_date: 2019-06-22
date_created: 2019-03-25T10:13:25Z
date_published: 2019-06-08T00:00:00Z
date_updated: 2026-07-01T22:31:15Z
day: '08'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3314221.3314581
ec_funded: 1
external_id:
arxiv:
- '1902.04659'
isi:
- '000523190300014'
file:
- access_level: open_access
checksum: 703a5e9b8c8587f2a44085ffd9a4db64
content_type: application/pdf
creator: akafshda
date_created: 2019-03-25T10:11:22Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6176'
file_name: paper.pdf
file_size: 4051066
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
isi: 1
keyword:
- Program Cost Analysis
- Program Termination
- Probabilistic Programs
- Martingales
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 204-220
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: 'PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming
Language Design and Implementation'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5457'
relation: earlier_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cost analysis of nondeterministic probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '7014'
abstract:
- lang: eng
text: "We study the problem of developing efficient approaches for proving\r\nworst-case
bounds of non-deterministic recursive programs. Ranking functions\r\nare sound
and complete for proving termination and worst-case bounds of\r\nnonrecursive
programs. First, we apply ranking functions to recursion,\r\nresulting in measure
functions. We show that measure functions provide a sound\r\nand complete approach
to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second
contribution is the synthesis of measure functions in\r\nnonpolynomial forms.
We show that non-polynomial measure functions with\r\nlogarithm and exponentiation
can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms,
Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous
methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds
of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$
is not an integer. We present\r\nexperimental results to demonstrate that our
approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms
such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair
problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii)
Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm
for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that
$r$ is not an integer and\r\nclose to the best-known bounds for the respective
algorithms."
article_number: '20'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive
programs. ACM Transactions on Programming Languages and Systems. 2019;41(4).
doi:10.1145/3339984
apa: Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case
analysis of recursive programs. ACM Transactions on Programming Languages and
Systems. ACM. https://doi.org/10.1145/3339984
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial
Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming
Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984.
ieee: K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis
of recursive programs,” ACM Transactions on Programming Languages and Systems,
vol. 41, no. 4. ACM, 2019.
ista: Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis
of recursive programs. ACM Transactions on Programming Languages and Systems.
41(4), 20.
mla: Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive
Programs.” ACM Transactions on Programming Languages and Systems, vol.
41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.
short: K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages
and Systems 41 (2019).
date_created: 2019-11-13T08:33:43Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2026-07-01T22:31:15Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3339984
ec_funded: 1
external_id:
arxiv:
- '1705.00317'
isi:
- '000564108400001'
intvolume: ' 41'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/1705.00317
month: '10'
oa: 1
oa_version: Preprint
project:
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grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: ACM Transactions on Programming Languages and Systems
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '639'
relation: earlier_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-polynomial worst-case analysis of recursive programs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2019'
...
---
OA_place: publisher
OA_type: hybrid
_id: '6380'
abstract:
- lang: eng
text: 'There is a huge gap between the speeds of modern caches and main memories,
and therefore cache misses account for a considerable loss of efficiency in programs.
The predominant technique to address this issue has been Data Packing: data elements
that are frequently accessed within time proximity are packed into the same cache
block, thereby minimizing accesses to the main memory. We consider the algorithmic
problem of Data Packing on a two-level memory system. Given a reference sequence
R of accesses to data elements, the task is to partition the elements into cache
blocks such that the number of cache misses on R is minimized. The problem is
notoriously difficult: it is NP-hard even when the cache has size 1, and is hard
to approximate for any cache size larger than 4. Therefore, all existing techniques
for Data Packing are based on heuristics and lack theoretical guarantees. In this
work, we present the first positive theoretical results for Data Packing, along
with new and stronger negative results. We consider the problem under the lens
of the underlying access hypergraphs, which are hypergraphs of affinities between
the data elements, where the order of an access hypergraph corresponds to the
size of the affinity group. We study the problem parameterized by the treewidth
of access hypergraphs, which is a standard notion in graph theory to measure the
closeness of a graph to a tree. Our main results are as follows: We show there
is a number q* depending on the cache parameters such that (a) if the access hypergraph
of order q* has constant treewidth, then there is a linear-time algorithm for
Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph
of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy
depending on a single parameter, namely, the highest order among access hypegraphs
that have constant treewidth; and establish the optimal value q* of this parameter.
Finally, we present an experimental evaluation of a prototype implementation of
our algorithm. Our results demonstrate that, in practice, access hypergraphs of
many commonly-used algorithms have small treewidth. We compare our approach with
several state-of-the-art heuristic-based algorithms and show that our algorithm
leads to significantly fewer cache-misses. '
acknowledgement: "The research was partially supported by Vienna Science and Technology
Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23
(RiSE/SHiNE), ERC\r\nStarting Grant (279307: Graph Games), and the IBM PhD Fellowship
program."
article_number: '53'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Nastaran
full_name: Okati, Nastaran
last_name: Okati
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
2019;3(POPL). doi:10.1145/3290366
apa: Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019).
Efficient parameterized algorithms for data packing. Proceedings of the ACM
on Programming Languages. ACM. https://doi.org/10.1145/3290366
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas
Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings
of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.
ieee: K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient
parameterized algorithms for data packing,” Proceedings of the ACM on Programming
Languages, vol. 3, no. POPL. ACM, 2019.
ista: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
3(POPL), 53.
mla: Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data
Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no.
POPL, 53, ACM, 2019, doi:10.1145/3290366.
short: K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of
the ACM on Programming Languages 3 (2019).
date_created: 2019-05-06T12:18:17Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2026-07-01T22:31:15Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3290366
ec_funded: 1
file:
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checksum: c157752f96877b36685ad7063ada4524
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:23:11Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6381'
file_name: 2019_ACM_POPL_Chatterjee.pdf
file_size: 1294962
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 3'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
issn:
- 2475-1421
publication_status: published
publisher: ACM
pubrep_id: '1056'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Efficient parameterized algorithms for data packing
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: 3
year: '2019'
...
---
_id: '6056'
abstract:
- lang: eng
text: In today's programmable blockchains, smart contracts are limited to being
deterministic and non-probabilistic. This lack of randomness is a consequential
limitation, given that a wide variety of real-world financial contracts, such
as casino games and lotteries, depend entirely on randomness. As a result, several
ad-hoc random number generation approaches have been developed to be used in smart
contracts. These include ideas such as using an oracle or relying on the block
hash. However, these approaches are manipulatable, i.e. their output can be tampered
with by parties who might not be neutral, such as the owner of the oracle or the
miners.We propose a novel game-theoretic approach for generating provably unmanipulatable
pseudorandom numbers on the blockchain. Our approach allows smart contracts to
access a trustworthy source of randomness that does not rely on potentially compromised
miners or oracles, hence enabling the creation of a new generation of smart contracts
that are not limited to being non-probabilistic and can be drawn from the much
more general class of probabilistic programs.
article_number: '8751326'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts:
Secure randomness on the blockchain. In: IEEE International Conference on Blockchain
and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic
smart contracts: Secure randomness on the blockchain. In IEEE International
Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE
International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart
contracts: Secure randomness on the blockchain,” in IEEE International Conference
on Blockchain and Cryptocurrency, Seoul, Korea, 2019.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts:
Secure randomness on the blockchain. IEEE International Conference on Blockchain
and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency,
8751326.'
mla: 'Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness
on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency,
8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International
Conference on Blockchain and Cryptocurrency, IEEE, 2019.
conference:
end_date: 2019-05-17
location: Seoul, Korea
name: IEEE International Conference on Blockchain and Cryptocurrency
start_date: 2019-05-14
date_created: 2019-02-26T09:03:15Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2026-07-01T22:31:15Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/BLOC.2019.8751326
ec_funded: 1
external_id:
arxiv:
- '1902.07986'
isi:
- '000491257000076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07986
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies
publication: IEEE International Conference on Blockchain and Cryptocurrency
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Probabilistic smart contracts: Secure randomness on the blockchain'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2019'
...
---
OA_place: publisher
_id: '6849'
abstract:
- lang: eng
text: 'Brain function is mediated by complex dynamical interactions between excitatory
and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons)
are one of the least studied types, despite being suspected to play important
roles in cognitive processes. We studied the network effects of optogenetic silencing
of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states.
The cell firing pattern in response to light pulses allowed us to classify the
recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal
cell and interneurons, and the inhibited interneurons corresponding to the CCK
group. The light application, which inhibited the activity of CCK interneurons
triggered wider changes in the firing dynamics of cells. We observed rate changes
(i.e. remapping) of pyramidal cells during the exploration session in which the
light was applied relative to the previous control session that was not restricted
neither in time nor space to the light delivery. Also, the disinhibited pyramidal
cells had higher increase in bursting than in single spike firing rate as a result
of CCK silencing. In addition, the firing activity patterns during exploratory
periods were more weakly reactivated in sleep for those periods in which CCK-interneuron
were silenced than in the unaffected periods. Furthermore, light pulses during
sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK
neurons during exploration suppressed the reactivation of waking firing patterns
in sleep and CCK interneuron activity was also required during sleep for the normal
reactivation of waking patterns. These findings demonstrate the involvement of
CCK cells in reactivation-related memory consolidation. An important part of our
analysis was to test the relationship of the identified CCKinterneurons to brain
oscillations. Our findings showed that these cells exhibited different oscillatory
behaviour during anaesthesia and natural waking and sleep conditions. We showed
that: 1) Contrary to the past studies performed under anaesthesia, the identified
CCKinterneurons fired on the descending portion of the theta phase in waking exploration.
2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3)
Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons
increased around the peak activity of the sharp-wave ripple (SWR) events in natural
sleep, which is congruent with new reports about their functional connectivity.
We also found that light driven CCK-interneuron silencing altered the dynamics
on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted
their preferred theta phases when the light was applied, while interneurons responses
were less consistent. 2) As a population, pyramidal cells negatively shifted their
preferred activity during gamma oscillations, albeit we did not find gamma modulation
differences related to the light application when pyramidal cells were subdivided
into the disinhibited and unaffected groups. 3) During the peak of SWR events,
all but the CCK-interneurons had a reduction in their relative firing rate change
during the light application as compared to the change observed at SWR initiation.
Finally, regarding to the place field activity of the recorded pyramidal neurons,
we showed that the disinhibited pyramidal cells had reduced place field similarity,
coherence and spatial information, but only during the light application. The
mechanisms behind such observed behaviours might involve eCB signalling and plastic
changes in CCK-interneuron synapses. In conclusion, the observed changes related
to the light-mediated silencing of CCKinterneurons have unravelled characteristics
of this interneuron subpopulation that might change the understanding not only
of their particular network interactions, but also of the current theories about
the emergence of certain cognitive processes such as place coding needed for navigation
or hippocampus-dependent memory consolidation. '
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
citation:
ama: Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal
network dynamics. 2019. doi:10.15479/AT:ISTA:6849
apa: Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating
hippocampal network dynamics. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6849
chicago: Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating
Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:6849.
ieee: D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal
network dynamics,” Institute of Science and Technology Austria, 2019.
ista: Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal
network dynamics. Institute of Science and Technology Austria.
mla: Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.
short: D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics, Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-09-06T06:54:16Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2026-04-08T13:56:53Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6849
file:
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file_name: Thesis_Damaris_Rangel_source.docx
file_size: 18253100
relation: source_file
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checksum: 59c73be40eeaa1c4db24067270151555
content_type: application/pdf
creator: drangel
date_created: 2019-09-09T13:09:52Z
date_updated: 2020-09-11T22:30:04Z
embargo: 2020-09-10
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language:
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month: '09'
oa: 1
oa_version: Published Version
page: '97'
publication_identifier:
isbn:
- 978-3-99078-003-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5914'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The role of CCK-interneurons in regulating hippocampal network dynamics
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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
arxiv: 1
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: 2026-07-01T22:31:17Z
day: '22'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.122.114502
external_id:
arxiv:
- '1809.06358'
isi:
- '000461922000006'
pmid:
- '30951357'
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
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 122
year: '2019'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2019-09-19T08:19:44Z
date_published: 2019-07-24T00:00:00Z
date_updated: 2026-06-18T17:44:11Z
day: '24'
ddc:
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file_size: 52787224
relation: main_file
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keyword:
- cell biology
- immunology
- leukocyte
- migration
- microfluidics
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month: '07'
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oa_version: Published Version
page: '171'
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publication_identifier:
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isbn:
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status: public
supervisor:
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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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
_id: '6187'
abstract:
- lang: eng
text: Aberrant display of the truncated core1 O-glycan T-antigen is a common feature
of human cancer cells that correlates with metastasis. Here we show that T-antigen
in Drosophila melanogaster macrophages is involved in their developmentally programmed
tissue invasion. Higher macrophage T-antigen levels require an atypical major
facilitator superfamily (MFS) member that we named Minerva which enables macrophage
dissemination and invasion. We characterize for the first time the T and Tn glycoform
O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva
increases the presence of T-antigen on proteins in pathways previously linked
to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required
for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the
minerva mutant’s migration and T-antigen glycosylation defects. We thus identify
a key conserved regulator that orchestrates O-glycosylation on a protein subset
to activate a program governing migration steps important for both development
and cancer metastasis.
acknowledged_ssus:
- _id: LifeSc
article_number: e41801
article_processing_charge: No
author:
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
orcid: 0000-0002-7926-0221
- first_name: Julia
full_name: Biebl, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Biebl
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Michaela
full_name: Misova, Michaela
id: 495A3C32-F248-11E8-B48F-1D18A9856A87
last_name: Misova
orcid: 0000-0003-2427-6856
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Patricia
full_name: Dos Reis Rodrigues, Patricia
id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F
last_name: Dos Reis Rodrigues
orcid: 0000-0003-1681-508X
- first_name: Katerina
full_name: Shkarina, Katerina
last_name: Shkarina
- first_name: Ida Signe Bohse
full_name: Larsen, Ida Signe Bohse
last_name: Larsen
- first_name: Sergey Y
full_name: Vakhrushev, Sergey Y
last_name: Vakhrushev
- first_name: Henrik
full_name: Clausen, Henrik
last_name: Clausen
- 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: Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily
member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion.
eLife. 2019;8. doi:10.7554/elife.41801
apa: Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M.,
… Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates
a subset of O-glycosylation to aid macrophage tissue invasion. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.41801
chicago: Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila
György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator
Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage
Tissue Invasion.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.41801.
ieee: K. Valosková et al., “A conserved major facilitator superfamily member
orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” eLife,
vol. 8. eLife Sciences Publications, 2019.
ista: Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh
A, Dos Reis Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus
DE. 2019. A conserved major facilitator superfamily member orchestrates a subset
of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.
mla: Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member
Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife,
vol. 8, e41801, eLife Sciences Publications, 2019, doi:10.7554/elife.41801.
short: K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A.
Ratheesh, P. Dos Reis Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev,
H. Clausen, D.E. Siekhaus, ELife 8 (2019).
date_created: 2019-03-28T13:37:45Z
date_published: 2019-03-26T00:00:00Z
date_updated: 2026-07-01T22:31:19Z
day: '26'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/elife.41801
ec_funded: 1
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grant_number: '24283'
name: Examination of the role of a MFS transporter in the migration of Drosophila
immune cells
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call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
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call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
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relation: press_release
url: https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/
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status: public
title: A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation
to aid macrophage tissue invasion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
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...
---
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_id: '6546'
abstract:
- lang: eng
text: "Invasive migration plays a crucial role not only during development and homeostasis
but also in pathological states, such as tumor metastasis. Drosophila macrophage
migration into the extended germband is an interesting system to study invasive
migration. It carries similarities to immune cell transmigration and cancer cell
invasion, therefore studying this process could also bring new understanding of
invasion in higher organisms. In our work, we uncover a highly conserved member
of the major facilitator family that plays a role in tissue invasion through regulation
of glycosylation on a subgroup of proteins and/or by aiding the precise timing
of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1
O-glycan T-antigen is a common feature of human cancer cells that correlates with
metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages
is involved in their developmentally programmed tissue invasion. Higher macrophage
T-antigen levels require an atypical major facilitator superfamily (MFS) member
that we named Minerva which enables macrophage dissemination and invasion. We
characterize for the first time the T and Tn glycoform O-glycoproteome of the
Drosophila melanogaster embryo, and determine that Minerva increases the presence
of T-antigen on proteins in pathways previously linked to cancer, most strongly
on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue
entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration
and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator
that orchestrates O-glycosylation on a protein subset to activate \r\na program
governing migration steps important for both development and cancer metastasis.
\r\n"
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
orcid: 0000-0002-7926-0221
citation:
ama: Valosková K. The role of a highly conserved major facilitator superfamily member
in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546
apa: Valosková, K. (2019). The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546
chicago: Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator
Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of
Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.
ieee: K. Valosková, “The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration,” Institute of Science and
Technology Austria, 2019.
ista: Valosková K. 2019. The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration. Institute of Science and
Technology Austria.
mla: Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily
Member in Drosophila Embryonic Macrophage Migration. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.
short: K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily
Member in Drosophila Embryonic Macrophage Migration, Institute of Science and
Technology Austria, 2019.
corr_author: '1'
date_created: 2019-06-07T12:49:19Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2026-04-08T13:58:36Z
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immune cells
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full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: The role of a highly conserved major facilitator superfamily member in Drosophila
embryonic macrophage migration
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...