---
_id: '6947'
abstract:
- lang: eng
text: Lymph nodes are es s ential organs of the immune s ys tem where adaptive
immune responses originate, and consist of various leukocyte populations and a
stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells
and form a sponge-like extracellular matrix network, called conduits , which they thems
elves enwrap and contract. Lymph, containing s oluble antigens , arrive
in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps
ular s inus and conduit network. According to the current paradigm, the conduit network dis
tributes afferent lymph through lymph nodes and thus provides acces
s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the
immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the
size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s
ize remains remarkedly s table under homeostatic conditions. It is only
partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is
able to swell in inflammation. The role of the FRC network in lymph node s
welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s
tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal
metastases.We examined the role of a mechanical feedback in regulation of lymph node
swelling. Using parallel plate compression and UV-las er cutting experiments we dis
s ected the mechanical force dynamics of the whole lymph node, and individually
for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens
ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis
s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells
∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps
ule, and how are lymphocytes able to enter in conditions that resist
swelling remain open ques tions . We s how that tens ion on the FRC network is important
to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion.
This is illustrated by interfering with FRC contractility, which leads to faster
swelling rates and a dis organized FRC network in the inflamed lymph node.
Growth of the FRC network in turn is expected to releas e tens ion on thes
e s tructures and lowers the res is tance to swelling, thereby allowing
more lymphocytes to enter the organ and drive more swelling. Halt of swelling
coincides with a thickening of the caps ule, which forms a thick res
is tant band around the organ and lowers tens ion on the FRC network to form
a new force equilibrium.The FRC and conduit network are further believed to be a privileged s
ite of s oluble information within the lymph node, although many details remain uns
olved. We s how by 3D ultra-recons truction that FRCs and antigen pres
enting cells cover the s urface of conduit s ys tem for more than 99%
and we dis cus s the implications for s oluble information exchangeat the conduit
level.Finally, there is an ongoing debate in the cancer field whether and how
cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus
ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels.
Once in the blood circulation, these cells are able to form metastases in
distal tissues.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
citation:
ama: 'Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility,
morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947'
apa: 'Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between
stroma contractility, morphology and lymphocyte trafficking. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947'
chicago: 'Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between
Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.'
ieee: 'F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma
contractility, morphology and lymphocyte trafficking,” Institute of Science and
Technology Austria, 2019.'
ista: 'Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma
contractility, morphology and lymphocyte trafficking. Institute of Science and
Technology Austria.'
mla: 'Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between
Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of
Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.'
short: 'F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma
Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and
Technology Austria, 2019.'
date_created: 2019-10-14T16:54:52Z
date_published: 2019-10-09T00:00:00Z
date_updated: 2023-09-13T08:50:57Z
day: '9'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:6947
file:
- access_level: closed
checksum: 53a739752a500f84d0f8ec953cbbd0b6
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: fassen
date_created: 2019-11-06T12:30:02Z
date_updated: 2020-11-07T23:30:03Z
embargo_to: open_access
file_id: '6990'
file_name: PhDthesis_FrankAssen_revised2.docx
file_size: 214172667
relation: source_file
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checksum: 8c156b65d9347bb599623a4b09f15d15
content_type: application/pdf
creator: fassen
date_created: 2019-11-06T12:30:57Z
date_updated: 2020-11-07T23:30:03Z
embargo: 2020-11-06
file_id: '6991'
file_name: PhDthesis_FrankAssen_revised2.pdf
file_size: 83637532
relation: main_file
file_date_updated: 2020-11-07T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '142'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '664'
relation: part_of_dissertation
status: public
- id: '402'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: 'Lymph node mechanics: Deciphering the interplay between stroma contractility,
morphology and lymphocyte trafficking'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6955'
abstract:
- lang: eng
text: We study few-body bound states of charged particles subject to attractive
zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic
length scales of the system at zero energy are set by the Coulomb length scale
D and the Coulomb-modified effective range r eff. We study shallow bound states
of charged particles with D >> r eff and show that these systems obey universal
scaling laws different from neutral particles. An accurate description of these
states requires both the Coulomb-modified scattering length and the effective
range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant
for bound states whose spatial extent is significantly larger than the range of
the attractive potential. These states enjoy universality – their character is
independent of the shape of the short-range potential.
article_number: '135016'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: C.H.
full_name: Schmickler, C.H.
last_name: Schmickler
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of
a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016
apa: Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics
of bound states of a few charged particles. Physics Letters B. Elsevier.
https://doi.org/10.1016/j.physletb.2019.135016
chicago: Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics
of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier,
2019. https://doi.org/10.1016/j.physletb.2019.135016.
ieee: C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound
states of a few charged particles,” Physics Letters B, vol. 798. Elsevier,
2019.
ista: Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states
of a few charged particles. Physics Letters B. 798, 135016.
mla: Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged
Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016.
short: C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).
date_created: 2019-10-18T18:33:32Z
date_published: 2019-11-10T00:00:00Z
date_updated: 2023-08-30T07:06:42Z
day: '10'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1016/j.physletb.2019.135016
external_id:
arxiv:
- '1904.00913'
isi:
- '000494939000086'
file:
- access_level: open_access
checksum: d27f983b34ea7dafdf356afbf9472fbf
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:47:04Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6974'
file_name: 2019_PhysicsLettersB_Schmickler.pdf
file_size: 528362
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 798'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
publication: Physics Letters B
publication_identifier:
issn:
- 0370-2693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universal physics of bound states of a few charged particles
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: 798
year: '2019'
...
---
_id: '6957'
abstract:
- lang: eng
text: "In many shear flows like pipe flow, plane Couette flow, plane Poiseuille
flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough
perturbations, the flow becomes turbulent in spite of the laminar base flow being
linearly stable. The nature of this instability has puzzled the scientific community
for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally
intermittent. In pipe flow the localized turbulent structures are referred to
as puffs and in planar flows like plane Couette and channel flow, patches arise
in the form of localized oblique bands. In this thesis, we study the onset of
turbulence in channel flow in direct numerical simulations from a dynamical system
theory perspective, as well as by performing experiments in a large aspect ratio
channel.\r\n\r\nThe aim of the experimental work is to determine the critical
Reynolds number where turbulence first becomes sustained. Recently, the onset
of turbulence has been described in analogy to absorbing state phase transition
(i.e. directed percolation). In particular, it has been shown that the critical
point can be estimated from the competition between spreading and decay processes.
Here, by performing experiments, we identify the mechanisms underlying turbulence
proliferation in channel flow and find the critical Reynolds number, above which
turbulence becomes sustained. Above the critical point, the continuous growth
at the tip of the stripes outweighs the stochastic shedding of turbulent patches
at the tail and the stripes expand. For growing stripes, the probability to decay
decreases while the probability of stripe splitting increases. Consequently, and
unlike for the puffs in pipe flow, neither of these two processes is time-independent
i.e. memoryless. Coupling between stripe expansion and creation of new stripes
via splitting leads to a significantly lower critical point ($Re_c=670+/-10$)
than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light
on how turbulence first becomes sustained, it provides no insight into the origin
of the stripes themselves. In the numerical part of the thesis we investigate
how turbulent stripes form from invariant solutions of the Navier-Stokes equations.
The origin of these turbulent stripes can be identified by applying concepts from
the dynamical system theory. In doing so, we identify the exact coherent structures
underlying stripes and their bifurcations and how they give rise to the turbulent
attractor in phase space. We first report a family of localized nonlinear traveling
wave solutions of the Navier-Stokes equations in channel flow. These solutions
show structural similarities with turbulent stripes in experiments like obliqueness,
quasi-streamwise streaks and vortices, etc. A parametric study of these traveling
wave solution is performed, with parameters like Reynolds number, stripe tilt
angle and domain size, including the stability of the solutions. These solutions
emerge through saddle-node bifurcations and form a phase space skeleton for the
turbulent stripes observed in the experiments. The lower branches of these TW
solutions at different tilt angles undergo Hopf bifurcation and new solutions
branches of relative periodic orbits emerge. These RPO solutions do not belong
to the same family and therefore the routes to chaos for different angles are
different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature.
\ Consequently,turbulence can not be tracked to lower Reynolds numbers, where
the dynamics may simplify. Before this happens, turbulence becomes short-lived
and laminarizes. In the last part of the thesis, we show that using numerical
simulations we can continue turbulent stripes in channel flow past the 'relaminarization
barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies
and the fluctuations are no longer stochastic and the stripe settles down to a
relative periodic orbit. This relative periodic orbit originates from the aforementioned
traveling wave solutions. Starting from the relative periodic orbit, a small increase
in speed i.e. Reynolds number gives rise to chaos and the attractor dimension
sharply increases in contrast to the classical transition scenario where the instabilities
affect the flow globally and give rise to much more gradual route to turbulence."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
citation:
ama: Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957
apa: Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957
chicago: Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957.
ieee: C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute
of Science and Technology Austria, 2019.
ista: Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute
of Science and Technology Austria.
mla: Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957.
short: C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of
Science and Technology Austria, 2019.
date_created: 2019-10-22T12:08:43Z
date_published: 2019-10-24T00:00:00Z
date_updated: 2023-09-07T12:53:25Z
day: '24'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: BjHo
doi: 10.15479/AT:ISTA:6957
file:
- access_level: closed
checksum: 7ba298ba0ce7e1d11691af6b8eaf0a0a
content_type: application/zip
creator: cparanjape
date_created: 2019-10-23T09:54:43Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6962'
file_name: Chaitanya_Paranjape_source_files_tex_figures.zip
file_size: 45828099
relation: source_file
- access_level: open_access
checksum: 642697618314e31ac31392da7909c2d9
content_type: application/pdf
creator: cparanjape
date_created: 2019-10-23T10:37:09Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6963'
file_name: Chaitanya_Paranjape_Thesis.pdf
file_size: 19504197
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
keyword:
- Instabilities
- Turbulence
- Nonlinear dynamics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Onset of turbulence in plane Poiseuille flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6972'
abstract:
- lang: eng
text: 'We give fault-tolerant algorithms for establishing synchrony in distributed
systems in which each of thennodes has its own clock. Our algorithms operate in
a very strong fault model: we require self-stabilisation, i.e.,the initial state
of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471
apa: Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471
chicago: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock
Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM,
2019. https://doi.org/10.1145/3339471.
ieee: C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM,
2019.
ista: Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. 66(5), 32.
mla: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation
Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32,
ACM, 2019, doi:10.1145/3339471.
short: C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).
date_created: 2019-10-24T17:12:48Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-30T07:07:23Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3339471
ec_funded: 1
external_id:
arxiv:
- '1705.06173'
isi:
- '000496514100001'
file:
- access_level: open_access
checksum: 7e5d95c478e0e393f4927fcf7e48194e
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:58:38Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6975'
file_name: 2019_JACM_Lenzen.pdf
file_size: 2183085
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-stabilising Byzantine clock synchronisation is almost as easy as consensus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 66
year: '2019'
...
---
_id: '6978'
abstract:
- lang: eng
text: In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent
work, we study numerically the localized turbulence in pipe flow and elucidate
astate space structure that gives rise to transient chaos. Starting from the basin
boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence
of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe
homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which
wasconjectured in various earlier studies. By mapping the transverse intersections
between thestable and unstable manifold of a periodic orbit, we identify the gateways
that promote anescape from turbulence.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Akshunna
full_name: Dogra, Akshunna
last_name: Dogra
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401
apa: Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos
in streamwise-localized pipe flow turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401
chicago: Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient
Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids.
American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401.
ieee: N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized
pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American
Physical Society, p. 102401, 2019.
ista: Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 4(10), 102401.
mla: Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized
Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American
Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.
short: N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.
date_created: 2019-11-04T10:04:01Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:20:03Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.4.102401
external_id:
arxiv:
- '1810.02211'
isi:
- '000493510400001'
intvolume: ' 4'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.02211
month: '10'
oa: 1
oa_version: Preprint
page: '102401'
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of transient chaos in streamwise-localized pipe flow turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2019'
...
---
_id: '6979'
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial
cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068'
apa: 'Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal
epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068'
chicago: 'Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of
Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press,
2019. https://doi.org/10.1016/j.cub.2019.08.068.'
ieee: 'A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal
epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20.
Cell Press, pp. R1091–R1093, 2019.'
ista: 'Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial
cells in tissue renewal. Current Biology. 29(20), R1091–R1093.'
mla: 'Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal
Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20,
Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068.'
short: A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.
date_created: 2019-11-04T15:18:29Z
date_published: 2019-10-21T00:00:00Z
date_updated: 2023-09-05T12:43:43Z
day: '21'
department:
- _id: MiSi
doi: 10.1016/j.cub.2019.08.068
external_id:
isi:
- '000491286200016'
pmid:
- '31639357'
intvolume: ' 29'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa_version: None
page: R1091-R1093
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gut homeostasis: Active migration of intestinal epithelial cells in tissue
renewal'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2019'
...
---
_id: '6980'
abstract:
- lang: eng
text: Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal
coordination of mechanical and chemical signals. Extensive work on how mechanical
forces together with the well‐established morphogen signalling pathways can actively
shape living tissues has revealed evolutionary conserved mechanochemical features
of embryonic development. More recently, attention has been drawn to the description
of tissue material properties and how they can influence certain morphogenetic
processes. Interestingly, besides the role of tissue material properties in determining
how much tissues deform in response to force application, there is increasing
theoretical and experimental evidence, suggesting that tissue material properties
can abruptly and drastically change in development. These changes resemble phase
transitions, pointing at the intriguing possibility that important morphogenetic
processes in development, such as symmetry breaking and self‐organization, might
be mediated by tissue phase transitions. In this review, we summarize recent findings
on the regulation and role of tissue material properties in the context of the
developing embryo. We posit that abrupt changes of tissue rheological properties
may have important implications in maintaining the balance between robustness
and adaptability during embryonic development.
article_number: e102497
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Nicoletta
full_name: Petridou, Nicoletta
id: 2A003F6C-F248-11E8-B48F-1D18A9856A87
last_name: Petridou
orcid: 0000-0002-8451-1195
- 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: Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The
EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497
apa: Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic
organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497
chicago: Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in
Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497.
ieee: N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,”
The EMBO Journal, vol. 38, no. 20. EMBO, 2019.
ista: Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization.
The EMBO Journal. 38(20), e102497.
mla: Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic
Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019,
doi:10.15252/embj.2019102497.
short: N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).
date_created: 2019-11-04T15:24:29Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-09-05T13:04:13Z
day: '15'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.15252/embj.2019102497
ec_funded: 1
external_id:
isi:
- '000485561900001'
pmid:
- '31512749'
file:
- access_level: open_access
checksum: 76f7f4e79ab6d850c30017a69726fd85
content_type: application/pdf
creator: dernst
date_created: 2019-11-04T15:30:08Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6981'
file_name: 2019_Embo_Petridou.pdf
file_size: 847356
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
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: 2693FD8C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00736
name: Tissue material properties in embryonic development
publication: The EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: EMBO
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tissue rheology in embryonic organization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2019'
...
---
_id: '6982'
abstract:
- lang: eng
text: "We present an efficient algorithm for a problem in the interface between
clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold
M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint
Jordan arcs between the corresponding vertices. In applications in clustering,
cartography, and visualization, nearby vertices and edges are often bundled to
the same point or overlapping arcs due to data compression or low resolution.
This raises the computational problem of deciding whether a given map ϕ : G →
M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed
into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖
is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings
has recently been found by Fulek and Kynčl. It reduces the problem to solving
a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where
ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices
and edges of G. We improve the running time to O(n log n). Our algorithm is also
conceptually simpler: We perform a sequence of local operations that gradually
“untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak
embedding. It combines local constraints on the orientation of subgraphs directly,
thereby eliminating the need for solving large systems of linear equations.\r\n"
article_number: '50'
article_type: original
arxiv: 1
author:
- first_name: Hugo
full_name: Akitaya, Hugo
last_name: Akitaya
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Csaba
full_name: Tóth, Csaba
last_name: Tóth
citation:
ama: Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions
on Algorithms. 2019;15(4). doi:10.1145/3344549
apa: Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings
of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549
chicago: Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings
of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549.
ieee: H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,”
ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.
ista: Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM
Transactions on Algorithms. 15(4), 50.
mla: Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions
on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.
short: H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).
date_created: 2019-11-04T15:45:17Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-15T12:19:31Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3344549
external_id:
arxiv:
- '1709.09209'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.09209
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: ACM Transactions on Algorithms
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '309'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Recognizing weak embeddings of graphs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...
---
_id: '6983'
abstract:
- lang: eng
text: Malaria, a disease caused by parasites of the Plasmodium genus, begins when
Plasmodium-infected mosquitoes inject malaria sporozoites while searching for
blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes,
and form liver stages which in mice 48 h later escape into blood and cause clinical
malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating
and eliminating all liver stages in 48 h, thus preventing the blood-stage disease.
However, the rules of how CD8 T cells are able to locate all liver stages within
a relatively short time period remains poorly understood. We recently reported
formation of clusters consisting of variable numbers of activated CD8 T cells
around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental
data and mathematical models we now provide additional insights into mechanisms
of formation of these clusters. First, we show that a model in which cluster formation
is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness”
of different liver stages, cannot explain distribution of cluster sizes in different
experimental conditions. In contrast, the model in which cluster formation is
driven by the positive feedback loop (i.e., larger clusters attract more CD8 T
cells) can accurately explain the available data. Second, while both Py-specific
CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are
attracted to the clusters, we found no evidence that non-specific CD8 T cells
play a role in cluster formation. Third and finally, mathematical modeling suggested
that formation of clusters occurs rapidly, within few hours after adoptive transfer
of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their
targets in complex peripheral organs, such as the liver. Taken together, our analysis
provides novel insights into and attempts to discriminate between alternative
mechanisms driving the formation of clusters of antigen-specific CD8 T cells in
the liver.
article_number: '2153'
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: H
full_name: Rajakaruna, H
last_name: Rajakaruna
- first_name: IA
full_name: Cockburn, IA
last_name: Cockburn
- first_name: VV
full_name: Ganusov, VV
last_name: Ganusov
citation:
ama: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8
T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153
apa: Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering
of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153
chicago: Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering
of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven
by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.
ieee: R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of
activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers,
2019.
ista: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated
CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 10, 2153.
mla: Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected
Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in
Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.
short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology
10 (2019).
date_created: 2019-11-04T15:50:06Z
date_published: 2019-09-20T00:00:00Z
date_updated: 2023-08-30T07:18:23Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3389/fimmu.2019.02153
external_id:
isi:
- '000487187000001'
pmid:
- '31616407'
file:
- access_level: open_access
checksum: 68d1708f7aa412544159b498ef17a6b9
content_type: application/pdf
creator: dernst
date_created: 2019-11-04T15:54:00Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6984'
file_name: 2019_FrontiersImmonology_Kelemen.pdf
file_size: 2083061
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is
rapid and is driven by antigen-specific cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6985'
abstract:
- lang: eng
text: In this paper, we introduce a novel method to interpret recurrent neural networks
(RNNs), particularly long short-term memory networks (LSTMs) at the cellular level.
We propose a systematic pipeline for interpreting individual hidden state dynamics
within the network using response characterization methods. The ranked contribution
of individual cells to the network's output is computed by analyzing a set of
interpretable metrics of their decoupled step and sinusoidal responses. As a result,
our method is able to uniquely identify neurons with insightful dynamics, quantify
relationships between dynamical properties and test accuracy through ablation
analysis, and interpret the impact of network capacity on a network's dynamical
distribution. Finally, we demonstrate the generalizability and scalability of
our method by evaluating a series of different benchmark sequential datasets.
article_number: '8851954'
arxiv: 1
author:
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Felix
full_name: Naser, Felix
last_name: Naser
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization
for auditing cell dynamics in long short-term memory networks. In: Proceedings
of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954'
apa: 'Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., & Rus, D. (2019).
Response characterization for auditing cell dynamics in long short-term memory
networks. In Proceedings of the International Joint Conference on Neural Networks.
Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954'
chicago: Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu,
and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long
Short-Term Memory Networks.” In Proceedings of the International Joint Conference
on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954.
ieee: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response
characterization for auditing cell dynamics in long short-term memory networks,”
in Proceedings of the International Joint Conference on Neural Networks,
Budapest, Hungary, 2019.
ista: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization
for auditing cell dynamics in long short-term memory networks. Proceedings of
the International Joint Conference on Neural Networks. IJCNN: International Joint
Conference on Neural Networks, 8851954.'
mla: Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics
in Long Short-Term Memory Networks.” Proceedings of the International Joint
Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954.
short: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings
of the International Joint Conference on Neural Networks, IEEE, 2019.
conference:
end_date: 2019-07-19
location: Budapest, Hungary
name: 'IJCNN: International Joint Conference on Neural Networks'
start_date: 2019-07-14
date_created: 2019-11-04T15:59:58Z
date_published: 2019-09-30T00:00:00Z
date_updated: 2021-01-12T08:11:19Z
day: '30'
department:
- _id: ToHe
doi: 10.1109/ijcnn.2019.8851954
external_id:
arxiv:
- '1809.03864'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.03864
month: '09'
oa: 1
oa_version: Preprint
publication: Proceedings of the International Joint Conference on Neural Networks
publication_identifier:
isbn:
- '9781728119854'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: 1
status: public
title: Response characterization for auditing cell dynamics in long short-term memory
networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6986'
abstract:
- lang: eng
text: 'Li-Nadler proposed a conjecture about traces of Hecke categories, which implies
the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler
in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds
in the natural generality of reflection groups in Euclidean or hyperbolic space.
As a corollary, we give an expression of the centralizer of a finite order element
in a reflection group using homotopy theory. '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Penghui
full_name: Li, Penghui
id: 42A24CCC-F248-11E8-B48F-1D18A9856A87
last_name: Li
citation:
ama: Li P. A colimit of traces of reflection groups. Proceedings of the American
Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586
apa: Li, P. (2019). A colimit of traces of reflection groups. Proceedings of
the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586
chicago: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings
of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586.
ieee: P. Li, “A colimit of traces of reflection groups,” Proceedings of the American
Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.
ista: Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American
Mathematical Society. 147(11), 4597–4604.
mla: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of
the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604,
doi:10.1090/proc/14586.
short: P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604.
date_created: 2019-11-04T16:10:50Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-05T12:22:21Z
day: '01'
department:
- _id: TaHa
doi: 10.1090/proc/14586
ec_funded: 1
external_id:
arxiv:
- '1810.07039'
isi:
- '000488621700004'
intvolume: ' 147'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.07039
month: '11'
oa: 1
oa_version: Preprint
page: 4597-4604
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Proceedings of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6826
issn:
- 0002-9939
publication_status: published
publisher: AMS
quality_controlled: '1'
scopus_import: '1'
status: public
title: A colimit of traces of reflection groups
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 147
year: '2019'
...
---
_id: '6987'
abstract:
- lang: eng
text: Cells are arranged into species-specific patterns during early embryogenesis.
Such cell division patterns are important since they often reflect the distribution
of localized cortical factors from eggs/fertilized eggs to specific cells as well
as the emergence of organismal form. However, it has proven difficult to reveal
the mechanisms that underlie the emergence of cell positioning patterns that underlie
embryonic shape, likely because a systems-level approach is required that integrates
cell biological, genetic, developmental, and mechanical parameters. The choice
of organism to address such questions is also important. Because ascidians display
the most extreme form of invariant cleavage pattern among the metazoans, we have
been analyzing the cell biological mechanisms that underpin three aspects of cell
division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous
cell cycles) which affect the overall shape of the blastula-stage ascidian embryo
composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell
stage that in turn undergo two further successive rounds of UCD. Starting at the
16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides
before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages.
Perturbing either UCD or the alternate cell division rhythm perturbs cell position.
We propose that dynamic cell shape changes propagate throughout the embryo via
cell-cell contacts to create the ascidian-specific invariant cleavage pattern.
alternative_title:
- RESULTS
article_processing_charge: No
author:
- first_name: Alex
full_name: McDougall, Alex
last_name: McDougall
- first_name: Janet
full_name: Chenevert, Janet
last_name: Chenevert
- first_name: Benoit G
full_name: Godard, Benoit G
id: 33280250-F248-11E8-B48F-1D18A9856A87
last_name: Godard
- first_name: Remi
full_name: Dumollard, Remi
last_name: Dumollard
citation:
ama: 'McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape
during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model
Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154.
doi:10.1007/978-3-030-23459-1_6'
apa: 'McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence
of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski
(Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol.
68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6'
chicago: 'McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard.
“Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model
Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and
Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.'
ieee: 'A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of
embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in
cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski,
Eds. Springer Nature, 2019, pp. 127–154.'
ista: 'McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo
shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental
biology. RESULTS, vol. 68, 127–154.'
mla: 'McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.”
Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by
Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp.
127–54, doi:10.1007/978-3-030-23459-1_6.'
short: 'A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo,
S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology,
Springer Nature, 2019, pp. 127–154.'
date_created: 2019-11-04T16:20:19Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-09-05T15:01:12Z
day: '10'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1007/978-3-030-23459-1_6
editor:
- first_name: Waclaw
full_name: Tworzydlo, Waclaw
last_name: Tworzydlo
- first_name: Szczepan M.
full_name: Bilinski, Szczepan M.
last_name: Bilinski
external_id:
pmid:
- '31598855'
file:
- access_level: open_access
checksum: 7f43e1e3706d15061475c5c57efc2786
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T10:09:30Z
date_updated: 2020-07-14T12:47:46Z
file_id: '7829'
file_name: 2019_RESULTS_McDougall.pdf
file_size: 19317348
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 68'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 127-154
pmid: 1
publication: 'Evo-Devo: Non-model species in cell and developmental biology'
publication_identifier:
eissn:
- 1861-0412
isbn:
- '9783030234584'
- '9783030234591'
issn:
- 0080-1844
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of embryo shape during cleavage divisions
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 68
year: '2019'
...
---
_id: '6988'
abstract:
- lang: eng
text: 'Platelets are central players in thrombosis and hemostasis but are increasingly
recognized as key components of the immune system. They shape ensuing immune responses
by recruiting leukocytes, and support the development of adaptive immunity. Recent
data shed new light on the complex role of platelets in immunity. Here, we summarize
experimental and clinical data on the role of platelets in host defense against
bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet
proinflammatory effector functions and cross-talk with the coagulation system,
can also result in damage to the host (e.g., acute lung injury and sepsis). Novel
clinical insights support this dichotomy: platelet inhibition/thrombocytopenia
can be either harmful or protective, depending on pathophysiological context.
Clinical studies are currently addressing this aspect in greater depth.'
article_processing_charge: No
article_type: review
author:
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: 'Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental
and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004'
apa: 'Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host
defense: Experimental and clinical insights. Trends in Immunology. Cell
Press. https://doi.org/10.1016/j.it.2019.08.004'
chicago: 'Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host
Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell
Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.'
ieee: 'L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental
and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press,
pp. 922–938, 2019.'
ista: 'Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental
and clinical insights. Trends in Immunology. 40(10), 922–938.'
mla: 'Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical
Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp.
922–38, doi:10.1016/j.it.2019.08.004.'
short: L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.
date_created: 2019-11-04T16:27:36Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:19:23Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.it.2019.08.004
ec_funded: 1
external_id:
isi:
- '000493292100005'
pmid:
- '31601520'
intvolume: ' 40'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 922-938
pmid: 1
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Trends in Immunology
publication_identifier:
issn:
- 1471-4906
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Platelets in host defense: Experimental and clinical insights'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2019'
...
---
_id: '6989'
abstract:
- lang: eng
text: 'When can a polyomino piece of paper be folded into a unit cube? Prior work
studied tree-like polyominoes, but polyominoes with holes remain an intriguing
open problem. We present sufficient conditions for a polyomino with hole(s) to
fold into a cube, and conditions under which cube folding is impossible. In particular,
we show that all but five special simple holes guarantee foldability. '
acknowledgement: This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank
all other participants for a fruitful atmosphere.
article_processing_charge: No
arxiv: 1
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Hugo A
full_name: Akitaya, Hugo A
last_name: Akitaya
- first_name: Kenneth C
full_name: Cheung, Kenneth C
last_name: Cheung
- first_name: Erik D
full_name: Demaine, Erik D
last_name: Demaine
- first_name: Martin L
full_name: Demaine, Martin L
last_name: Demaine
- first_name: Sandor P
full_name: Fekete, Sandor P
last_name: Fekete
- first_name: Linda
full_name: Kleist, Linda
last_name: Kleist
- first_name: Irina
full_name: Kostitsyna, Irina
last_name: Kostitsyna
- first_name: Maarten
full_name: Löffler, Maarten
last_name: Löffler
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Klara
full_name: Mundilova, Klara
last_name: Mundilova
- first_name: Christiane
full_name: Schmidt, Christiane
last_name: Schmidt
citation:
ama: 'Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes
into a cube. In: Proceedings of the 31st Canadian Conference on Computational
Geometry. Canadian Conference on Computational Geometry; 2019:164-170.'
apa: 'Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M.
L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a
cube. In Proceedings of the 31st Canadian Conference on Computational Geometry
(pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.'
chicago: Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin
L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes
into a Cube.” In Proceedings of the 31st Canadian Conference on Computational
Geometry, 164–70. Canadian Conference on Computational Geometry, 2019.
ieee: O. Aichholzer et al., “Folding polyominoes with holes into a cube,”
in Proceedings of the 31st Canadian Conference on Computational Geometry,
Edmonton, Canada, 2019, pp. 164–170.
ista: 'Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist
L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding
polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference
on Computational Geometry. CCCG: Canadian Conference in Computational Geometry,
164–170.'
mla: Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings
of the 31st Canadian Conference on Computational Geometry, Canadian Conference
on Computational Geometry, 2019, pp. 164–70.
short: O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P.
Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt,
in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian
Conference on Computational Geometry, 2019, pp. 164–170.
conference:
end_date: 2019-08-10
location: Edmonton, Canada
name: 'CCCG: Canadian Conference in Computational Geometry'
start_date: 2019-08-08
date_created: 2019-11-04T16:46:11Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-04T10:57:42Z
day: '01'
department:
- _id: HeEd
external_id:
arxiv:
- '1910.09917'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://cccg.ca/proceedings/2019/proceedings.pdf
month: '08'
oa: 1
oa_version: Published Version
page: 164-170
publication: Proceedings of the 31st Canadian Conference on Computational Geometry
publication_status: published
publisher: Canadian Conference on Computational Geometry
quality_controlled: '1'
related_material:
record:
- id: '8317'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: Folding polyominoes with holes into a cube
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2019'
...
---
_id: '6999'
abstract:
- lang: eng
text: Plasmodesmata (PD) are plant-specific membrane-lined channels that create
cytoplasmic and membrane continuities between adjacent cells, thereby facilitating
cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms
to regulate PD plasticity in response to numerous environmental stimuli. In particular,
during defense against plant pathogens, the defense hormone, salicylic acid (SA),
plays a crucial role in the regulation of PD permeability in a callose-dependent
manner. Here, we uncover a mechanism by which plants restrict the spreading of
virus and PD cargoes using SA signaling by increasing lipid order and closure
of PD. We showed that exogenous SA application triggered the compartmentalization
of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein,
Remorin (REM). Genetic studies, superresolution imaging, and transmission electron
microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3
are crucial for plasma membrane nanodomain assembly to control PD aperture and
functionality. In addition, we also found that a 14-3-3 epsilon protein modulates
REM clustering and membrane nanodomain compartmentalization through its direct
interaction with REM proteins. This study unveils a molecular mechanism by which
the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization,
thereby regulating PD closure to impede virus spreading.
article_processing_charge: No
article_type: original
author:
- first_name: D
full_name: Huang, D
last_name: Huang
- first_name: Y
full_name: Sun, Y
last_name: Sun
- first_name: Z
full_name: Ma, Z
last_name: Ma
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: Y
full_name: Cui, Y
last_name: Cui
- first_name: Z
full_name: Chen, Z
last_name: Chen
- first_name: C
full_name: Chen, C
last_name: Chen
- first_name: C
full_name: Ji, C
last_name: Ji
- first_name: TM
full_name: Tran, TM
last_name: Tran
- first_name: L
full_name: Yang, L
last_name: Yang
- first_name: SM
full_name: Lam, SM
last_name: Lam
- first_name: Y
full_name: Han, Y
last_name: Han
- first_name: G
full_name: Shu, G
last_name: Shu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Miao, Y
last_name: Miao
- first_name: L
full_name: Jiang, L
last_name: Jiang
- first_name: X
full_name: Chen, X
last_name: Chen
citation:
ama: Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via
Remorin-dependent lipid organization. Proceedings of the National Academy of
Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116
apa: Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic
acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116
chicago: Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated
Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.
ieee: D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via
Remorin-dependent lipid organization,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 42. Proceedings
of the National Academy of Sciences, pp. 21274–21284, 2019.
ista: Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam
S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated
plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of
the National Academy of Sciences of the United States of America. 116(42), 21274–21284.
mla: Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent
Lipid Organization.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 116, no. 42, Proceedings of the National Academy
of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.
short: D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran,
L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings
of the National Academy of Sciences of the United States of America 116 (2019)
21274–21284.
date_created: 2019-11-12T11:42:05Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-10-17T12:32:37Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1911892116
external_id:
isi:
- '000490183000068'
pmid:
- '31575745'
file:
- access_level: open_access
checksum: 258c666bc6253eab81961f61169eefae
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:22:28Z
date_updated: 2020-07-14T12:47:46Z
file_id: '7012'
file_name: 2019_PNAS_Huang.pdf
file_size: 3287466
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 116'
isi: 1
issue: '42'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 21274-21284
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2004738117
scopus_import: '1'
status: public
title: Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '7000'
abstract:
- lang: eng
text: The main contributions of this paper are the proposition and the convergence
analysis of a class of inertial projection-type algorithm for solving variational
inequality problems in real Hilbert spaces where the underline operator is monotone
and uniformly continuous. We carry out a unified analysis of the proposed method
under very mild assumptions. In particular, weak convergence of the generated
sequence is established and nonasymptotic O(1 / n) rate of convergence is established,
where n denotes the iteration counter. We also present some experimental results
to illustrate the profits gained by introducing the inertial extrapolation steps.
article_number: '161'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Xiao-Huan
full_name: Li, Xiao-Huan
last_name: Li
- first_name: Qiao-Li
full_name: Dong, Qiao-Li
last_name: Dong
citation:
ama: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method
for variational inequalities. Computational and Applied Mathematics. 2019;38(4).
doi:10.1007/s40314-019-0955-9
apa: Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence
analysis of projection method for variational inequalities. Computational and
Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9
chicago: Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence
Analysis of Projection Method for Variational Inequalities.” Computational
and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9.
ieee: Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of
projection method for variational inequalities,” Computational and Applied
Mathematics, vol. 38, no. 4. Springer Nature, 2019.
ista: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection
method for variational inequalities. Computational and Applied Mathematics. 38(4),
161.
mla: Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational
Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161,
Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.
short: Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics
38 (2019).
date_created: 2019-11-12T12:41:44Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:20:32Z
day: '01'
ddc:
- '510'
- '515'
- '518'
department:
- _id: VlKo
doi: 10.1007/s40314-019-0955-9
ec_funded: 1
external_id:
arxiv:
- '2101.09081'
isi:
- '000488973100005'
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s40314-019-0955-9
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Computational and Applied Mathematics
publication_identifier:
eissn:
- 1807-0302
issn:
- 2238-3603
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence analysis of projection method for variational inequalities
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
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: 2024-03-25T23:30:21Z
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:
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content_type: application/pdf
creator: dernst
date_created: 2020-10-21T07:09:45Z
date_updated: 2020-10-21T07:09:45Z
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language:
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oa: 1
oa_version: Submitted Version
page: 937-952.e18
pmid: 1
project:
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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: '7002'
abstract:
- lang: eng
text: Multiple Importance Sampling (MIS) is a key technique for achieving robustness
of Monte Carlo estimators in computer graphics and other fields. We derive optimal
weighting functions for MIS that provably minimize the variance of an MIS estimator,
given a set of sampling techniques. We show that the resulting variance reduction
over the balance heuristic can be higher than predicted by the variance bounds
derived by Veach and Guibas, who assumed only non-negative weights in their proof.
We theoretically analyze the variance of the optimal MIS weights and show the
relation to the variance of the balance heuristic. Furthermore, we establish a
connection between the new weighting functions and control variates as previously
applied to mixture sampling. We apply the new optimal weights to integration problems
in light transport and show that they allow for new design considerations when
choosing the appropriate sampling techniques for a given integration problem.
article_number: '37'
article_processing_charge: No
article_type: original
author:
- first_name: Ivo
full_name: Kondapaneni, Ivo
last_name: Kondapaneni
- first_name: Petr
full_name: Vevoda, Petr
last_name: Vevoda
- first_name: Pascal
full_name: Grittmann, Pascal
last_name: Grittmann
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Philipp
full_name: Slusallek, Philipp
last_name: Slusallek
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
citation:
ama: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal
multiple importance sampling. ACM Transactions on Graphics. 2019;38(4).
doi:10.1145/3306346.3323009
apa: Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., &
Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3306346.3323009
chicago: Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp
Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM
Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.
ieee: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J.
Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics,
vol. 38, no. 4. ACM, 2019.
ista: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J.
2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4),
37.
mla: Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions
on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.
short: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek,
ACM Transactions on Graphics 38 (2019).
date_created: 2019-11-12T13:05:40Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-30T07:21:25Z
day: '01'
department:
- _id: ChWo
doi: 10.1145/3306346.3323009
ec_funded: 1
external_id:
isi:
- '000475740600011'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal multiple importance sampling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '7005'
abstract:
- lang: eng
text: Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during
intense neuronal activity via a two-step process. First, bulk endosomes are formed
direct from the plasma membrane from which SVs are then generated. SV generation
from bulk endosomes requires the efflux of previously accumulated calcium and
activation of the protein phosphatase calcineurin. However, it is still unknown
how calcineurin mediates SV generation. We addressed this question using a series
of acute interventions that decoupled the generation of SVs from bulk endosomes
in rat primary neuronal culture. This was achieved by either disruption of protein–protein
interactions via delivery of competitive peptides, or inhibition of enzyme activity
by known inhibitors. SV generation was monitored using either a morphological
horseradish peroxidase assay or an optical assay that monitors the replenishment
of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides
that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity
and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin
I interaction. Peptides that disrupted syndapin I interactions with eps15 homology
domain-containing proteins had no effect. This revealed that (i) calcineurin must
be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity
is essential for SV fission and (iii) the calcineurin-dependent interaction between
dynamin I and syndapin I is essential for SV generation. We therefore propose
that a calcineurin-dependent dephosphorylation cascade that requires both dynamin
I GTPase and syndapin I lipid-deforming activity is essential for SV generation
from bulk endosomes.
article_processing_charge: No
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Michael A.
full_name: Cousin, Michael A.
last_name: Cousin
citation:
ama: Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk
endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction.
Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862
apa: Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from
activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin
interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862
chicago: Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation
from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent
Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019.
https://doi.org/10.1111/jnc.14862.
ieee: G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent
bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,”
Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.
ista: Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent
bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction.
Journal of Neurochemistry. 151(5), 570–583.
mla: Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from
Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin
Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019,
pp. 570–83, doi:10.1111/jnc.14862.
short: G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.
date_created: 2019-11-12T14:37:08Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:21:50Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1111/jnc.14862
external_id:
isi:
- '000490703100001'
pmid:
- '31479508'
file:
- access_level: open_access
checksum: ec1fb2aebb874009bc309adaada6e1d7
content_type: application/pdf
creator: dernst
date_created: 2020-02-05T10:30:02Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7452'
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file_size: 4334962
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has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 570-583
pmid: 1
publication: Journal of Neurochemistry
publication_identifier:
eissn:
- 1471-4159
issn:
- 0022-3042
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptic vesicle generation from activity‐dependent bulk endosomes requires
a dephosphorylation‐dependent dynamin–syndapin interaction
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: 151
year: '2019'
...
---
_id: '7007'
abstract:
- lang: eng
text: 'We consider the primitive relay channel, where the source sends a message
to the relay and to the destination, and the relay helps the communication by
transmitting an additional message to the destination via a separate channel.
Two well-known coding techniques have been introduced for this setting: decode-and-forward
and compress-and-forward. In decode-and-forward, the relay completely decodes
the message and sends some information to the destination; in compress-and-forward,
the relay does not decode, and it sends a compressed version of the received signal
to the destination using Wyner–Ziv coding. In this paper, we present a novel coding
paradigm that provides an improved achievable rate for the primitive relay channel.
The idea is to combine compress-and-forward and decode-and-forward via a chaining
construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward;
and, in the second block, we use decode-and-forward. More specifically, in the
first block, the relay does not decode, it compresses the received signal via
Wyner–Ziv, and it sends only part of the compression to the destination. In the
second block, the relay completely decodes the message, it sends some information
to the destination, and it also sends the remaining part of the compression coming
from the first block. By doing so, we are able to strictly outperform both compress-and-forward
and decode-and-forward. Note that the proposed coding scheme can be implemented
with polar codes. As such, it has the typical attractive properties of polar coding
schemes, namely, quasi-linear encoding and decoding complexity, and error probability
that decays at super-polynomial speed. As a running example, we take into account
the special case of the erasure relay channel, and we provide a comparison between
the rates achievable by our proposed scheme and the existing upper and lower bounds.'
article_number: '218'
article_type: original
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: S. Hamed
full_name: Hassani, S. Hamed
last_name: Hassani
- first_name: Rüdiger
full_name: Urbanke, Rüdiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive
relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218
apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm
for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218
chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm
for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.
ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the
primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.
ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive
relay channel. Algorithms. 12(10), 218.
mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.”
Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218.
short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).
date_created: 2019-11-12T14:46:19Z
date_published: 2019-10-18T00:00:00Z
date_updated: 2023-02-23T12:49:28Z
day: '18'
ddc:
- '510'
department:
- _id: MaMo
doi: 10.3390/a12100218
external_id:
arxiv:
- '1801.03153'
file:
- access_level: open_access
checksum: 267756d8f9db572f496cd1663c89d59a
content_type: application/pdf
creator: dernst
date_created: 2019-11-12T14:48:45Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7008'
file_name: 2019_Algorithms_Mondelli.pdf
file_size: 696791
relation: main_file
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Algorithms
publication_identifier:
issn:
- 1999-4893
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
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- id: '6675'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: A new coding paradigm for the primitive relay channel
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: 12
year: '2019'
...