---
_id: '1289'
abstract:
- lang: eng
text: 'Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI)
magnifying endoscopic (ME) images of the stomach, we combine methods from image
processing, topology, geometry, and machine learning to classify patterns into
three classes: oval, tubular and irregular. Training the algorithm on a small
number of images of each type, we achieve a high rate of correct classifications.
The analysis of the learning algorithm reveals that a handful of geometric and
topological features are responsible for the overwhelming majority of decisions.'
article_processing_charge: No
author:
- first_name: Olga
full_name: Dunaeva, Olga
last_name: Dunaeva
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Lukyanov, Anton
last_name: Lukyanov
- first_name: Michael
full_name: Machin, Michael
last_name: Machin
- first_name: Daria
full_name: Malkova, Daria
last_name: Malkova
- first_name: Roman
full_name: Kuvaev, Roman
last_name: Kuvaev
- first_name: Sergey
full_name: Kashin, Sergey
last_name: Kashin
citation:
ama: Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy
images with persistent homology. Pattern Recognition Letters. 2016;83(1):13-22.
doi:10.1016/j.patrec.2015.12.012
apa: Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev,
R., & Kashin, S. (2016). The classification of endoscopy images with persistent
homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2015.12.012
chicago: Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria
Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images
with Persistent Homology.” Pattern Recognition Letters. Elsevier, 2016.
https://doi.org/10.1016/j.patrec.2015.12.012.
ieee: O. Dunaeva et al., “The classification of endoscopy images with persistent
homology,” Pattern Recognition Letters, vol. 83, no. 1. Elsevier, pp. 13–22,
2016.
ista: Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin
S. 2016. The classification of endoscopy images with persistent homology. Pattern
Recognition Letters. 83(1), 13–22.
mla: Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent
Homology.” Pattern Recognition Letters, vol. 83, no. 1, Elsevier, 2016,
pp. 13–22, doi:10.1016/j.patrec.2015.12.012.
short: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev,
S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.
date_created: 2018-12-11T11:51:10Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T10:04:40Z
day: '01'
ddc:
- '004'
- '514'
department:
- _id: HeEd
doi: 10.1016/j.patrec.2015.12.012
file:
- access_level: open_access
checksum: 33458bbb8c32a339e1adeca6d5a1112d
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:55:51Z
date_updated: 2020-07-14T12:44:42Z
file_id: '6334'
file_name: 2016-Edelsbrunner_The_classification.pdf
file_size: 1921113
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 83'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Submitted Version
page: 13 - 22
publication: Pattern Recognition Letters
publication_status: published
publisher: Elsevier
publist_id: '6027'
pubrep_id: '975'
quality_controlled: '1'
related_material:
record:
- id: '1568'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: The classification of endoscopy images with persistent homology
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: 83
year: '2016'
...
---
_id: '1164'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C1, … , Ck with common center c, and edges are drawn radially: every edge
intersects every circle centered at c at most once. G is radial planar if it has
a radial embedding, that is, a crossing-free radial drawing. If the vertices of
G are ordered or partitioned into ordered levels (as they are for leveled graphs),
we require that the assignment of vertices to circles corresponds to the given
ordering or leveling. A pair of edges e and f in a graph is independent if e and
f do not share a vertex. We show that a graph G is radial planar if G has a radial
drawing in which every two independent edges cross an even number of times; the
radial embedding has the same leveling as the radial drawing. In other words,
we establish the strong Hanani-Tutte theorem for radial planarity. This characterization
yields a very simple algorithm for radial planarity testing.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In:
Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36'
apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial
planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and
Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36'
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.
ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity
II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece,
2016, vol. 9801, pp. 468–481.'
ista: 'Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity
II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.'
mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801,
Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36.
short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:29Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-02-23T10:05:57Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_36
ec_funded: 1
external_id:
arxiv:
- '1608.08662'
intvolume: ' 9801'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.08662
month: '12'
oa: 1
oa_version: Preprint
page: 468 - 481
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6193'
quality_controlled: '1'
related_material:
record:
- id: '1113'
relation: later_version
status: public
- id: '1595'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity II
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9801
year: '2016'
...
---
_id: '1592'
abstract:
- lang: eng
text: A modular approach to constructing cryptographic protocols leads to simple
designs but often inefficient instantiations. On the other hand, ad hoc constructions
may yield efficient protocols at the cost of losing conceptual simplicity. We
suggest a new design paradigm, structure-preserving cryptography, that provides
a way to construct modular protocols with reasonable efficiency while retaining
conceptual simplicity. A cryptographic scheme over a bilinear group is called
structure-preserving if its public inputs and outputs consist of elements from
the bilinear groups and their consistency can be verified by evaluating pairing-product
equations. As structure-preserving schemes smoothly interoperate with each other,
they are useful as building blocks in modular design of cryptographic applications.
This paper introduces structure-preserving commitment and signature schemes over
bilinear groups with several desirable properties. The commitment schemes include
homomorphic, trapdoor and length-reducing commitments to group elements, and the
structure-preserving signature schemes are the first ones that yield constant-size
signatures on multiple group elements. A structure-preserving signature scheme
is called automorphic if the public keys lie in the message space, which cannot
be achieved by compressing inputs via a cryptographic hash function, as this would
destroy the mathematical structure we are trying to preserve. Automorphic signatures
can be used for building certification chains underlying privacy-preserving protocols.
Among a vast number of applications of structure-preserving protocols, we present
an efficient round-optimal blind-signature scheme and a group signature scheme
with an efficient and concurrently secure protocol for enrolling new members.
acknowledgement: The authors would like to thank the anonymous reviewers of this paper.
We also would like to express our appreciation to the program committee and the
anonymous reviewers for CRYPTO 2010. The first author thanks Sherman S. M. Chow
for his comment on group signatures in Sect. 7.1.
author:
- first_name: Masayuki
full_name: Abe, Masayuki
last_name: Abe
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Jens
full_name: Groth, Jens
last_name: Groth
- first_name: Kristiyan
full_name: Haralambiev, Kristiyan
last_name: Haralambiev
- first_name: Miyako
full_name: Ohkubo, Miyako
last_name: Ohkubo
citation:
ama: Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. Structure preserving
signatures and commitments to group elements. Journal of Cryptology. 2016;29(2):363-421.
doi:10.1007/s00145-014-9196-7
apa: Abe, M., Fuchsbauer, G., Groth, J., Haralambiev, K., & Ohkubo, M. (2016).
Structure preserving signatures and commitments to group elements. Journal
of Cryptology. Springer. https://doi.org/10.1007/s00145-014-9196-7
chicago: Abe, Masayuki, Georg Fuchsbauer, Jens Groth, Kristiyan Haralambiev, and
Miyako Ohkubo. “Structure Preserving Signatures and Commitments to Group Elements.”
Journal of Cryptology. Springer, 2016. https://doi.org/10.1007/s00145-014-9196-7.
ieee: M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, and M. Ohkubo, “Structure
preserving signatures and commitments to group elements,” Journal of Cryptology,
vol. 29, no. 2. Springer, pp. 363–421, 2016.
ista: Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. 2016. Structure preserving
signatures and commitments to group elements. Journal of Cryptology. 29(2), 363–421.
mla: Abe, Masayuki, et al. “Structure Preserving Signatures and Commitments to Group
Elements.” Journal of Cryptology, vol. 29, no. 2, Springer, 2016, pp. 363–421,
doi:10.1007/s00145-014-9196-7.
short: M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, M. Ohkubo, Journal of Cryptology
29 (2016) 363–421.
date_created: 2018-12-11T11:52:54Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:51:49Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00145-014-9196-7
intvolume: ' 29'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 363 - 421
publication: Journal of Cryptology
publication_status: published
publisher: Springer
publist_id: '5579'
quality_controlled: '1'
scopus_import: 1
status: public
title: Structure preserving signatures and commitments to group elements
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1599'
abstract:
- lang: eng
text: "The addition of polysialic acid to N- and/or O-linked glycans, referred to
as polysialylation, is a rare posttranslational modification that is mainly known
to control the developmental plasticity of the nervous system. Here we show that
CCR7, the central chemokine receptor controlling immune cell trafficking to secondary
lymphatic organs, carries polysialic acid. This modification is essential for
the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking
is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed
lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function
analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited
conformation, which is released upon interaction with polysialic acid. Thus, we
describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic
basis.\r\n"
acknowledged_ssus:
- _id: SSU
acknowledgement: 'We thank S. Schüchner and E. Ogris for kindly providing the antibody
to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific
Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for
critically reading the manuscript. '
article_processing_charge: No
article_type: original
author:
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Rita
full_name: Gerardy Schahn, Rita
last_name: Gerardy Schahn
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Friedrich
full_name: Freiberger, Friedrich
last_name: Freiberger
- first_name: Richard
full_name: Imre, Richard
last_name: Imre
- first_name: Deni
full_name: Taleski, Deni
last_name: Taleski
- first_name: Richard
full_name: Payne, Richard
last_name: Payne
- first_name: Asolina
full_name: Braun, Asolina
last_name: Braun
- first_name: Reinhold
full_name: Förster, Reinhold
last_name: Förster
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Martina
full_name: Mühlenhoff, Martina
last_name: Mühlenhoff
- first_name: Brian
full_name: Volkman, Brian
last_name: Volkman
- 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: Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic
cell trafficking by regulating chemokine recognition. Science. 2016;351(6269):186-190.
doi:10.1126/science.aad0512
apa: Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy Schahn, R., de Vries, I.,
Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking
by regulating chemokine recognition. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aad0512
chicago: Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy
Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation
Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science.
American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aad0512.
ieee: E. Kiermaier et al., “Polysialylation controls dendritic cell trafficking
by regulating chemokine recognition,” Science, vol. 351, no. 6269. American
Association for the Advancement of Science, pp. 186–190, 2016.
ista: Kiermaier E, Moussion C, Veldkamp C, Gerardy Schahn R, de Vries I, Williams
L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster
R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls
dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269),
186–190.
mla: Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking
by Regulating Chemokine Recognition.” Science, vol. 351, no. 6269, American
Association for the Advancement of Science, 2016, pp. 186–90, doi:10.1126/science.aad0512.
short: E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy Schahn, I. de Vries,
L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne,
A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science
351 (2016) 186–190.
date_created: 2018-12-11T11:52:57Z
date_published: 2016-01-08T00:00:00Z
date_updated: 2021-01-12T06:51:52Z
day: '08'
department:
- _id: MiSi
doi: 10.1126/science.aad0512
ec_funded: 1
external_id:
pmid:
- '26657283'
intvolume: ' 351'
issue: '6269'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/
month: '01'
oa: 1
oa_version: Submitted Version
page: 186 - 190
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25A76F58-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '289720'
name: Stromal Cell-immune Cell Interactions in Health and Disease
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5570'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polysialylation controls dendritic cell trafficking by regulating chemokine
recognition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 351
year: '2016'
...
---
_id: '1597'
abstract:
- lang: eng
text: Chemokines are the main guidance cues directing leukocyte migration. Opposed
to early assumptions, chemokines do not necessarily act as soluble cues but are
often immobilized within tissues, e.g., dendritic cell migration toward lymphatic
vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled
assay systems to quantitatively study haptotaxis in vitro are still missing. In
this chapter, we describe an in vitro haptotaxis assay optimized for the unique
properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive
state, using laser-assisted protein adsorption by photobleaching. The cells follow
this immobilized CCL21 gradient in a haptotaxis chamber, which provides three
dimensionally confined migration conditions.
acknowledged_ssus:
- _id: Bio
acknowledgement: This work was supported by the Boehringer Ingelheim Fonds, the European
Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation
(FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input
and the Imaging Facility of IST Austria for excellent support.
article_processing_charge: No
article_type: original
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- 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: Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. Methods
in Enzymology. 2016;570:567-581. doi:10.1016/bs.mie.2015.11.004
apa: Schwarz, J., & Sixt, M. K. (2016). Quantitative analysis of dendritic cell
haptotaxis. Methods in Enzymology. Elsevier. https://doi.org/10.1016/bs.mie.2015.11.004
chicago: Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell
Haptotaxis.” Methods in Enzymology. Elsevier, 2016. https://doi.org/10.1016/bs.mie.2015.11.004.
ieee: J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,”
Methods in Enzymology, vol. 570. Elsevier, pp. 567–581, 2016.
ista: Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis.
Methods in Enzymology. 570, 567–581.
mla: Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell
Haptotaxis.” Methods in Enzymology, vol. 570, Elsevier, 2016, pp. 567–81,
doi:10.1016/bs.mie.2015.11.004.
short: J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581.
date_created: 2018-12-11T11:52:56Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:51Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/bs.mie.2015.11.004
ec_funded: 1
external_id:
pmid:
- '26921962'
intvolume: ' 570'
language:
- iso: eng
month: '01'
oa_version: None
page: 567 - 581
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Methods in Enzymology
publication_status: published
publisher: Elsevier
publist_id: '5573'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative analysis of dendritic cell haptotaxis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 570
year: '2016'
...
---
_id: '1608'
abstract:
- lang: eng
text: 'We show that the Anderson model has a transition from localization to delocalization
at exactly 2 dimensional growth rate on antitrees with normalized edge weights
which are certain discrete graphs. The kinetic part has a one-dimensional structure
allowing a description through transfer matrices which involve some Schur complement.
For such operators we introduce the notion of having one propagating channel and
extend theorems from the theory of one-dimensional Jacobi operators that relate
the behavior of transfer matrices with the spectrum. These theorems are then applied
to the considered model. In essence, in a certain energy region the kinetic part
averages the random potentials along shells and the transfer matrices behave similar
as for a one-dimensional operator with random potential of decaying variance.
At d dimensional growth for d>2 this effective decay is strong enough to obtain
absolutely continuous spectrum, whereas for some uniform d dimensional growth
with d<2 one has pure point spectrum in this energy region. At exactly uniform
2 dimensional growth also some singular continuous spectrum appears, at least
at small disorder. As a corollary we also obtain a change from singular spectrum
(d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type
rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete
adjacency operator (Laplacian) on ℤd and λ a random potential. '
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
citation:
ama: Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and
spectral theory for operators with one propagating channel. Annales Henri Poincare.
2016;17(7):1631-1675. doi:10.1007/s00023-015-0456-3
apa: Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees
and spectral theory for operators with one propagating channel. Annales Henri
Poincare. Birkhäuser. https://doi.org/10.1007/s00023-015-0456-3
chicago: Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on
Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales
Henri Poincare. Birkhäuser, 2016. https://doi.org/10.1007/s00023-015-0456-3.
ieee: C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and
spectral theory for operators with one propagating channel,” Annales Henri
Poincare, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016.
ista: Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees
and spectral theory for operators with one propagating channel. Annales Henri
Poincare. 17(7), 1631–1675.
mla: Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees
and Spectral Theory for Operators with One Propagating Channel.” Annales Henri
Poincare, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:10.1007/s00023-015-0456-3.
short: C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.
date_created: 2018-12-11T11:53:00Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:51:58Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00023-015-0456-3
ec_funded: 1
intvolume: ' 17'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04287
month: '07'
oa: 1
oa_version: Preprint
page: 1631 - 1675
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '5558'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anderson transition at 2 dimensional growth rate on antitrees and spectral
theory for operators with one propagating channel
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1612'
abstract:
- lang: eng
text: We prove that whenever A is a 3-conservative relational structure with only
binary and unary relations,then the algebra of polymorphisms of A either has no
Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety
(i.e.,CSP(A)has bounded width).
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
citation:
ama: Kazda A. CSP for binary conservative relational structures. Algebra Universalis.
2016;75(1):75-84. doi:10.1007/s00012-015-0358-8
apa: Kazda, A. (2016). CSP for binary conservative relational structures. Algebra
Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8
chicago: Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra
Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8.
ieee: A. Kazda, “CSP for binary conservative relational structures,” Algebra
Universalis, vol. 75, no. 1. Springer, pp. 75–84, 2016.
ista: Kazda A. 2016. CSP for binary conservative relational structures. Algebra
Universalis. 75(1), 75–84.
mla: Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra
Universalis, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:10.1007/s00012-015-0358-8.
short: A. Kazda, Algebra Universalis 75 (2016) 75–84.
date_created: 2018-12-11T11:53:01Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00012-015-0358-8
intvolume: ' 75'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1112.1099
month: '02'
oa: 1
oa_version: Preprint
page: 75 - 84
publication: Algebra Universalis
publication_status: published
publisher: Springer
publist_id: '5554'
quality_controlled: '1'
scopus_import: 1
status: public
title: CSP for binary conservative relational structures
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2016'
...
---
_id: '1617'
abstract:
- lang: eng
text: 'We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d
is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of
equal measure and placing a random point inside each of the N=md cubes. We prove
that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d,
where the upper bound with an unspecified constant Cd was proven earlier by Beck.
Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality
and a suitably taylored Bernstein inequality; we have reasons to believe that
the upper bound has the sharp scaling in N. Additional heuristics suggest that
jittered sampling should be able to improve known bounds on the inverse of the
star-discrepancy in the regime N≳dd. We also prove a partition principle showing
that every partition of [0,1]d combined with a jittered sampling construction
gives rise to a set whose expected squared L2-discrepancy is smaller than that
of purely random points.'
acknowledgement: We are grateful to the referee whose suggestions greatly improved
the quality and clarity of the exposition.
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Stefan
full_name: Steinerberger, Stefan
last_name: Steinerberger
citation:
ama: Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. Journal
of Complexity. 2016;33:199-216. doi:10.1016/j.jco.2015.11.003
apa: Pausinger, F., & Steinerberger, S. (2016). On the discrepancy of jittered
sampling. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.11.003
chicago: Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered
Sampling.” Journal of Complexity. Academic Press, 2016. https://doi.org/10.1016/j.jco.2015.11.003.
ieee: F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,”
Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016.
ista: Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling.
Journal of Complexity. 33, 199–216.
mla: Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered
Sampling.” Journal of Complexity, vol. 33, Academic Press, 2016, pp. 199–216,
doi:10.1016/j.jco.2015.11.003.
short: F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.
date_created: 2018-12-11T11:53:03Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:02Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jco.2015.11.003
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.00251
month: '04'
oa: 1
oa_version: Submitted Version
page: 199 - 216
publication: Journal of Complexity
publication_status: published
publisher: Academic Press
publist_id: '5549'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the discrepancy of jittered sampling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2016'
...
---
_id: '1620'
abstract:
- lang: eng
text: We consider the Bardeen–Cooper–Schrieffer free energy functional for particles
interacting via a two-body potential on a microscopic scale and in the presence
of weak external fields varying on a macroscopic scale. We study the influence
of the external fields on the critical temperature. We show that in the limit
where the ratio between the microscopic and macroscopic scale tends to zero, the
next to leading order of the critical temperature is determined by the lowest
eigenvalue of the linearization of the Ginzburg–Landau equation.
acknowledgement: The authors are grateful to I. M. Sigal for useful discussions. Financial
support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432
(R.L.F.), from the Danish council for independent research and from ERC Advanced
Grant 321029 (J.P.S.) is acknowledged.
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of
the BCS critical temperature. Communications in Mathematical Physics. 2016;342(1):189-216.
doi:10.1007/s00220-015-2526-2
apa: Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2016). The external
field dependence of the BCS critical temperature. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-015-2526-2
chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The
External Field Dependence of the BCS Critical Temperature.” Communications
in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-015-2526-2.
ieee: R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence
of the BCS critical temperature,” Communications in Mathematical Physics,
vol. 342, no. 1. Springer, pp. 189–216, 2016.
ista: Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence
of the BCS critical temperature. Communications in Mathematical Physics. 342(1),
189–216.
mla: Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.”
Communications in Mathematical Physics, vol. 342, no. 1, Springer, 2016,
pp. 189–216, doi:10.1007/s00220-015-2526-2.
short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical
Physics 342 (2016) 189–216.
date_created: 2018-12-11T11:53:04Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:52:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-015-2526-2
intvolume: ' 342'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.2352
month: '02'
oa: 1
oa_version: Submitted Version
page: 189 - 216
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5546'
quality_controlled: '1'
scopus_import: 1
status: public
title: The external field dependence of the BCS critical temperature
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 342
year: '2016'
...
---
_id: '1622'
abstract:
- lang: eng
text: We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities
for many-body quantum systems with fractional kinetic operators and homogeneous
interaction potentials, where no anti-symmetry on the wave functions is assumed.
These many-body inequalities imply interesting one-body interpolation inequalities,
and we show that the corresponding one- and many-body inequalities are actually
equivalent in certain cases.
acknowledgement: "We thank Jan Philip Solovej, Robert Seiringer and Vladimir Maz’ya
for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for
useful comments. Part of this work has been carried out during a visit at the Institut
Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW
2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research
Council grant no. 2013-4734. P.T.N. is supported by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement no. 291734. F.P. acknowledges support from the ERC project
no. 321029 “The\r\nmathematics of the structure of matter”."
author:
- first_name: Douglas
full_name: Lundholm, Douglas
last_name: Lundholm
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Fabian
full_name: Portmann, Fabian
last_name: Portmann
citation:
ama: Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities
for interacting systems. Archive for Rational Mechanics and Analysis. 2016;219(3):1343-1382.
doi:10.1007/s00205-015-0923-5
apa: Lundholm, D., Nam, P., & Portmann, F. (2016). Fractional Hardy–Lieb–Thirring
and related Inequalities for interacting systems. Archive for Rational Mechanics
and Analysis. Springer. https://doi.org/10.1007/s00205-015-0923-5
chicago: Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring
and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics
and Analysis. Springer, 2016. https://doi.org/10.1007/s00205-015-0923-5.
ieee: D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and
related Inequalities for interacting systems,” Archive for Rational Mechanics
and Analysis, vol. 219, no. 3. Springer, pp. 1343–1382, 2016.
ista: Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related
Inequalities for interacting systems. Archive for Rational Mechanics and Analysis.
219(3), 1343–1382.
mla: Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities
for Interacting Systems.” Archive for Rational Mechanics and Analysis,
vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:10.1007/s00205-015-0923-5.
short: D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis
219 (2016) 1343–1382.
date_created: 2018-12-11T11:53:05Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:52:04Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00205-015-0923-5
ec_funded: 1
intvolume: ' 219'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04570
month: '03'
oa: 1
oa_version: Submitted Version
page: 1343 - 1382
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '5542'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 219
year: '2016'
...
---
_id: '1631'
abstract:
- lang: eng
text: 'Ancestral processes are fundamental to modern population genetics and spatial
structure has been the subject of intense interest for many years. Despite this
interest, almost nothing is known about the distribution of the locations of pedigree
or genetic ancestors. Using both spatially continuous and stepping-stone models,
we show that the distribution of pedigree ancestors approaches a travelling wave,
for which we develop two alternative approximations. The speed and width of the
wave are sensitive to the local details of the model. After a short time, genetic
ancestors spread far more slowly than pedigree ancestors, ultimately diffusing
out with radius ## rather than spreading at constant speed. In contrast to the
wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the
local details of the models.'
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic
ancestry in spatially distributed populations. Theoretical Population Biology.
2016;108:1-12. doi:10.1016/j.tpb.2015.10.008
apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread
of pedigree versus genetic ancestry in spatially distributed populations. Theoretical
Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008
chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton.
“Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.”
Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.
ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree
versus genetic ancestry in spatially distributed populations,” Theoretical
Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.
ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus
genetic ancestry in spatially distributed populations. Theoretical Population
Biology. 108, 1–12.
mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially
Distributed Populations.” Theoretical Population Biology, vol. 108, Academic
Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.
short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population
Biology 108 (2016) 1–12.
date_created: 2018-12-11T11:53:08Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2015.10.008
ec_funded: 1
file:
- access_level: open_access
checksum: 6a65ba187994d4ad86c1c509e0ff482a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:12Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4865'
file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf
file_size: 1684043
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 108'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 12
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '5524'
pubrep_id: '465'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spread of pedigree versus genetic ancestry in spatially distributed populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2016'
...
---
_id: '1641'
abstract:
- lang: eng
text: The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant
growth and development including embryo and root patterning, lateral organ formation
and growth responses to environmental stimuli. Auxin is directionally transported
from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)]
and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations
are aligned with the direction of the auxin flow. Auxin itself regulates its own
transport by modulation of the expression and subcellular localization of the
auxin transporters. Increased auxin levels promote the transcription of PIN2 and
AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged
auxin exposure increases the turnover of PIN proteins and their degradation in
the vacuole. In this study, we applied a forward genetic approach, to identify
molecular components playing a role in the auxin-mediated degradation. We generated
EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations
and designed a screen for mutants with persistently strong fluorescent signals
of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin
2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation
mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and
established a role for auxin-mediated degradation in plant development.
acknowledgement: 'European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science
Foundation GAČR (GA13-40637S) to JF. '
author:
- first_name: Radka
full_name: Zemová, Radka
last_name: Zemová
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen
for new regulators of auxin mediated degradation of auxin transport proteins in
Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476.
doi:10.1007/s00344-015-9553-2
apa: Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A
forward genetic screen for new regulators of auxin mediated degradation of auxin
transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation.
Springer. https://doi.org/10.1007/s00344-015-9553-2
chicago: Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří
Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation
of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth
Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2.
ieee: R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic
screen for new regulators of auxin mediated degradation of auxin transport proteins
in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35,
no. 2. Springer, pp. 465–476, 2016.
ista: Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic
screen for new regulators of auxin mediated degradation of auxin transport proteins
in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.
mla: Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin
Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal
of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.
short: R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant
Growth Regulation 35 (2016) 465–476.
date_created: 2018-12-11T11:53:12Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:52:11Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1007/s00344-015-9553-2
file:
- access_level: open_access
checksum: 0dc6a300cde6536ceedd2bcdd2060efb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:34Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4695'
file_name: IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf
file_size: 5637591
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Preprint
page: 465 - 476
publication: Journal of Plant Growth Regulation
publication_status: published
publisher: Springer
publist_id: '5512'
pubrep_id: '1001'
quality_controlled: '1'
scopus_import: 1
status: public
title: A forward genetic screen for new regulators of auxin mediated degradation of
auxin transport proteins in Arabidopsis thaliana
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1225'
abstract:
- lang: eng
text: At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model
construction of efficient roundoptimal blind signatures that does not require
complexity leveraging. It is conceptually simple and builds on the primitive of
structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the
unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme
and hardness of a version of the DH inversion problem. Blindness under adversarially
chosen keys is proven under an interactive variant of the DDH assumption. We propose
a variant of their scheme whose blindness can be proven under a non-interactive
assumption, namely a variant of the bilinear DDH assumption. We moreover prove
its unforgeability assuming only unforgeability of the underlying SPS-EQ but no
additional assumptions as needed for the FHS scheme.
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Christian
full_name: Hanser, Christian
last_name: Hanser
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Daniel
full_name: Slamanig, Daniel
last_name: Slamanig
citation:
ama: 'Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. Practical round-optimal
blind signatures in the standard model from weaker assumptions. In: Vol 9841.
Springer; 2016:391-408. doi:10.1007/978-3-319-44618-9_21'
apa: 'Fuchsbauer, G., Hanser, C., Kamath Hosdurg, C., & Slamanig, D. (2016).
Practical round-optimal blind signatures in the standard model from weaker assumptions
(Vol. 9841, pp. 391–408). Presented at the SCN: Security and Cryptography for
Networks, Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-44618-9_21'
chicago: Fuchsbauer, Georg, Christian Hanser, Chethan Kamath Hosdurg, and Daniel
Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model from
Weaker Assumptions,” 9841:391–408. Springer, 2016. https://doi.org/10.1007/978-3-319-44618-9_21.
ieee: 'G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, and D. Slamanig, “Practical
round-optimal blind signatures in the standard model from weaker assumptions,”
presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy, 2016,
vol. 9841, pp. 391–408.'
ista: 'Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. 2016. Practical round-optimal
blind signatures in the standard model from weaker assumptions. SCN: Security
and Cryptography for Networks, LNCS, vol. 9841, 391–408.'
mla: Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the
Standard Model from Weaker Assumptions. Vol. 9841, Springer, 2016, pp. 391–408,
doi:10.1007/978-3-319-44618-9_21.
short: G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, D. Slamanig, in:, Springer,
2016, pp. 391–408.
conference:
end_date: 2016-09-02
location: Amalfi, Italy
name: 'SCN: Security and Cryptography for Networks'
start_date: 2016-08-31
date_created: 2018-12-11T11:50:49Z
date_published: 2016-08-11T00:00:00Z
date_updated: 2023-02-23T10:08:16Z
day: '11'
department:
- _id: KrPi
doi: 10.1007/978-3-319-44618-9_21
ec_funded: 1
intvolume: ' 9841'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/662
month: '08'
oa: 1
oa_version: Submitted Version
page: 391 - 408
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6109'
quality_controlled: '1'
related_material:
record:
- id: '1647'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Practical round-optimal blind signatures in the standard model from weaker
assumptions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9841
year: '2016'
...
---
_id: '1653'
abstract:
- lang: eng
text: "A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs
(ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x)
using a public hashing-key hk. Furthermore, there is a way to set up the hash
key hk to make it statistically binding on some arbitrary hidden position i, meaning
that: (1) the digest y completely determines the i’th bit (or symbol) of x so
that all pre-images of y have the same value in the i’th position, (2) it is computationally
infeasible to distinguish the position i on which hk is statistically binding
from any other position i’. Lastly, the hash should have a local opening property
analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should
be possible to create a short proof π that certifies the value of the i’th bit
(or symbol) of x without having to provide the entire input x. A similar primitive
called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC
’15) further supports dynamic updates of the hashed value. These tools, which
are interesting in their own right, also serve as one of the main technical components
in several recent works building advanced applications from indistinguishability
obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional
accumulators required fully homomorphic encryption (FHE) and iO respectively.
In this work, we give new constructions of these tools based on well studied number-theoretic
assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction
from lossy/injective functions."
alternative_title:
- LNCS
author:
- first_name: Tatsuaki
full_name: Okamoto, Tatsuaki
last_name: Okamoto
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Brent
full_name: Waters, Brent
last_name: Waters
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically
binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145.
doi:10.1007/978-3-662-48797-6_6'
apa: 'Okamoto, T., Pietrzak, K. Z., Waters, B., & Wichs, D. (2016). New realizations
of somewhere statistically binding hashing and positional accumulators (Vol. 9452,
pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology
and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48797-6_6'
chicago: Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs.
“New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,”
9452:121–45. Springer, 2016. https://doi.org/10.1007/978-3-662-48797-6_6.
ieee: 'T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of
somewhere statistically binding hashing and positional accumulators,” presented
at the ASIACRYPT: Theory and Application of Cryptology and Information Security,
Auckland, New Zealand, 2016, vol. 9452, pp. 121–145.'
ista: 'Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere
statistically binding hashing and positional accumulators. ASIACRYPT: Theory and
Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.'
mla: Okamoto, Tatsuaki, et al. New Realizations of Somewhere Statistically Binding
Hashing and Positional Accumulators. Vol. 9452, Springer, 2016, pp. 121–45,
doi:10.1007/978-3-662-48797-6_6.
short: T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp.
121–145.
conference:
end_date: 2015-12-03
location: Auckland, New Zealand
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
start_date: 2015-11-29
date_created: 2018-12-11T11:53:16Z
date_published: 2016-01-08T00:00:00Z
date_updated: 2021-01-12T06:52:16Z
day: '08'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/978-3-662-48797-6_6
ec_funded: 1
file:
- access_level: open_access
checksum: a57711cb660c5b17b42bb47275a00180
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:05Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4923'
file_name: IST-2016-677-v1+1_869.pdf
file_size: 580088
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9452'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 121 - 145
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5497'
pubrep_id: '677'
quality_controlled: '1'
scopus_import: 1
status: public
title: New realizations of somewhere statistically binding hashing and positional
accumulators
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9452
year: '2016'
...
---
_id: '1148'
abstract:
- lang: eng
text: Continuous-time Markov chain (CTMC) models have become a central tool for
understanding the dynamics of complex reaction networks and the importance of
stochasticity in the underlying biochemical processes. When such models are employed
to answer questions in applications, in order to ensure that the model provides
a sufficiently accurate representation of the real system, it is of vital importance
that the model parameters are inferred from real measured data. This, however,
is often a formidable task and all of the existing methods fail in one case or
the other, usually because the underlying CTMC model is high-dimensional and computationally
difficult to analyze. The parameter inference methods that tend to scale best
in the dimension of the CTMC are based on so-called moment closure approximations.
However, there exists a large number of different moment closure approximations
and it is typically hard to say a priori which of the approximations is the most
suitable for the inference procedure. Here, we propose a moment-based parameter
inference method that automatically chooses the most appropriate moment closure
method. Accordingly, contrary to existing methods, the user is not required to
be experienced in moment closure techniques. In addition to that, our method adaptively
changes the approximation during the parameter inference to ensure that always
the best approximation is used, even in cases where different approximations are
best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd
acknowledgement: This work is based on the CMSB 2015 paper “Adaptive moment closure
for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015).
The work was partly supported by the German Research Foundation (DFG) as part of
the Transregional Collaborative Research Center “Automatic Verification and Analysis
of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under
grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23
(RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People
Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme
(FP7/2007-2013) under REA grant agreement no. 291734.
author:
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment
closure for parameter inference of biochemical reaction networks. Biosystems.
2016;149:15-25. doi:10.1016/j.biosystems.2016.07.005
apa: Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., & Ruess,
J. (2016). Adaptive moment closure for parameter inference of biochemical reaction
networks. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2016.07.005
chicago: Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski,
and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical
Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005.
ieee: C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive
moment closure for parameter inference of biochemical reaction networks,” Biosystems,
vol. 149. Elsevier, pp. 15–25, 2016.
ista: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive
moment closure for parameter inference of biochemical reaction networks. Biosystems.
149, 15–25.
mla: Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference
of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016,
pp. 15–25, doi:10.1016/j.biosystems.2016.07.005.
short: C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems
149 (2016) 15–25.
date_created: 2018-12-11T11:50:24Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T10:08:46Z
day: '01'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1016/j.biosystems.2016.07.005
ec_funded: 1
intvolume: ' 149'
language:
- iso: eng
month: '11'
oa_version: None
page: 15 - 25
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biosystems
publication_status: published
publisher: Elsevier
publist_id: '6210'
quality_controlled: '1'
related_material:
record:
- id: '1658'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Adaptive moment closure for parameter inference of biochemical reaction networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 149
year: '2016'
...
---
_id: '1705'
abstract:
- lang: eng
text: Hybrid systems represent an important and powerful formalism for modeling
real-world applications such as embedded systems. A verification tool like SpaceEx
is based on the exploration of a symbolic search space (the region space). As
a verification tool, it is typically optimized towards proving the absence of
errors. In some settings, e.g., when the verification tool is employed in a feedback-directed
design cycle, one would like to have the option to call a version that is optimized
towards finding an error trajectory in the region space. A recent approach in
this direction is based on guided search. Guided search relies on a cost function
that indicates which states are promising to be explored, and preferably explores
more promising states first. In this paper, we propose an abstraction-based cost
function based on coarse-grained space abstractions for guiding the reachability
analysis. For this purpose, a suitable abstraction technique that exploits the
flexible granularity of modern reachability analysis algorithms is introduced.
The new cost function is an effective extension of pattern database approaches
that have been successfully applied in other areas. The approach has been implemented
in the SpaceEx model checker. The evaluation shows its practical potential.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Alexandre
full_name: Donzé, Alexandre
last_name: Donzé
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
- first_name: Hamed
full_name: Ladan, Hamed
last_name: Ladan
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Martin
full_name: Wehrle, Martin
last_name: Wehrle
citation:
ama: Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based
on coarse-grained space abstractions. International Journal on Software Tools
for Technology Transfer. 2016;18(4):449-467. doi:10.1007/s10009-015-0393-y
apa: Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., …
Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space
abstractions. International Journal on Software Tools for Technology Transfer.
Springer. https://doi.org/10.1007/s10009-015-0393-y
chicago: Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson,
Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems
Based on Coarse-Grained Space Abstractions.” International Journal on Software
Tools for Technology Transfer. Springer, 2016. https://doi.org/10.1007/s10009-015-0393-y.
ieee: S. Bogomolov et al., “Guided search for hybrid systems based on coarse-grained
space abstractions,” International Journal on Software Tools for Technology
Transfer, vol. 18, no. 4. Springer, pp. 449–467, 2016.
ista: Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle
M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions.
International Journal on Software Tools for Technology Transfer. 18(4), 449–467.
mla: Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained
Space Abstractions.” International Journal on Software Tools for Technology
Transfer, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:10.1007/s10009-015-0393-y.
short: S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski,
M. Wehrle, International Journal on Software Tools for Technology Transfer 18
(2016) 449–467.
date_created: 2018-12-11T11:53:34Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10009-015-0393-y
ec_funded: 1
file:
- access_level: open_access
checksum: 31561d7705599a9bd4ea816accc0752e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:26Z
date_updated: 2020-07-14T12:45:13Z
file_id: '5146'
file_name: IST-2016-457-v1+1_s10009-015-0393-y.pdf
file_size: 2296522
relation: main_file
file_date_updated: 2020-07-14T12:45:13Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 449 - 467
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Journal on Software Tools for Technology Transfer
publication_status: published
publisher: Springer
publist_id: '5431'
pubrep_id: '457'
quality_controlled: '1'
scopus_import: 1
status: public
title: Guided search for hybrid systems based on coarse-grained space abstractions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '1707'
abstract:
- lang: eng
text: "Volunteer supporters play an important role in modern crisis and disaster
management. In the times of mobile Internet devices, help from thousands of volunteers
can be requested within a short time span, thus relieving professional helpers
from minor chores or geographically spread-out tasks. However, the simultaneous
availability of many volunteers also poses new problems. In particular, the volunteer
efforts must be well coordinated, or otherwise situations might emerge in which
too many idle volunteers at one location become more of a burden than a relief
to the professionals.\r\nIn this work, we study the task of optimally assigning
volunteers to selected locations, e.g. in order to perform regular measurements,
to report on damage, or to distribute information or resources to the population
in a crisis situation. We formulate the assignment tasks as an optimization problem
and propose an effective and efficient solution procedure. Experiments on real
data of the Team Österreich, consisting of over 36,000 Austrian volunteers, show
the effectiveness and efficiency of our approach."
acknowledgement: The DRIVER FP7 project has received funding from the European Unions
Seventh Framework Programme for research, technological development and demonstration
under grant agreement no 607798. RE-ACTA was funded within the framework of the
Austrian Security Research Programme KIRAS by the Federal Ministry for Transport,
Innovation and Technology.
article_number: '7402041'
author:
- first_name: Jasmin
full_name: Pielorz, Jasmin
id: 49BC895A-F248-11E8-B48F-1D18A9856A87
last_name: Pielorz
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pielorz J, Lampert C. Optimal geospatial allocation of volunteers for crisis
management. In: IEEE; 2016. doi:10.1109/ICT-DM.2015.7402041'
apa: 'Pielorz, J., & Lampert, C. (2016). Optimal geospatial allocation of volunteers
for crisis management. Presented at the ICT-DM: Information and Communication
Technologies for Disaster Management, Rennes, France: IEEE. https://doi.org/10.1109/ICT-DM.2015.7402041'
chicago: Pielorz, Jasmin, and Christoph Lampert. “Optimal Geospatial Allocation
of Volunteers for Crisis Management.” IEEE, 2016. https://doi.org/10.1109/ICT-DM.2015.7402041.
ieee: 'J. Pielorz and C. Lampert, “Optimal geospatial allocation of volunteers for
crisis management,” presented at the ICT-DM: Information and Communication Technologies
for Disaster Management, Rennes, France, 2016.'
ista: 'Pielorz J, Lampert C. 2016. Optimal geospatial allocation of volunteers for
crisis management. ICT-DM: Information and Communication Technologies for Disaster
Management, 7402041.'
mla: Pielorz, Jasmin, and Christoph Lampert. Optimal Geospatial Allocation of
Volunteers for Crisis Management. 7402041, IEEE, 2016, doi:10.1109/ICT-DM.2015.7402041.
short: J. Pielorz, C. Lampert, in:, IEEE, 2016.
conference:
end_date: 2015-12-02
location: Rennes, France
name: 'ICT-DM: Information and Communication Technologies for Disaster Management'
start_date: 2015-11-30
date_created: 2018-12-11T11:53:35Z
date_published: 2016-02-11T00:00:00Z
date_updated: 2021-01-12T06:52:39Z
day: '11'
department:
- _id: ChLa
doi: 10.1109/ICT-DM.2015.7402041
language:
- iso: eng
month: '02'
oa_version: None
publication_status: published
publisher: IEEE
publist_id: '5429'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal geospatial allocation of volunteers for crisis management
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1833'
abstract:
- lang: eng
text: 'Relational models for contingency tables are generalizations of log-linear
models, allowing effects associated with arbitrary subsets of cells in the table,
and not necessarily containing the overall effect, that is, a common parameter
in every cell. Similarly to log-linear models, relational models can be extended
to non-negative distributions, but the extension requires more complex methods.
An extended relational model is defined as an algebraic variety, and it turns
out to be the closure of the original model with respect to the Bregman divergence.
In the extended relational model, the MLE of the cell parameters always exists
and is unique, but some of its properties may be different from those of the MLE
under log-linear models. The MLE can be computed using a generalized iterative
scaling procedure based on Bregman projections. '
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. On the closure of relational models. Journal of Multivariate
Analysis. 2016;143:440-452. doi:10.1016/j.jmva.2015.10.005
apa: Klimova, A., & Rudas, T. (2016). On the closure of relational models. Journal
of Multivariate Analysis. Elsevier. https://doi.org/10.1016/j.jmva.2015.10.005
chicago: Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.”
Journal of Multivariate Analysis. Elsevier, 2016. https://doi.org/10.1016/j.jmva.2015.10.005.
ieee: A. Klimova and T. Rudas, “On the closure of relational models,” Journal
of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.
ista: Klimova A, Rudas T. 2016. On the closure of relational models. Journal of
Multivariate Analysis. 143, 440–452.
mla: Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal
of Multivariate Analysis, vol. 143, Elsevier, 2016, pp. 440–52, doi:10.1016/j.jmva.2015.10.005.
short: A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452.
date_created: 2018-12-11T11:54:15Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:30Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jmva.2015.10.005
intvolume: ' 143'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00600
month: '01'
oa: 1
oa_version: Preprint
page: 440 - 452
publication: Journal of Multivariate Analysis
publication_status: published
publisher: Elsevier
publist_id: '5270'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the closure of relational models
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1881'
abstract:
- lang: eng
text: 'We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric
or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal
random matrix of size N with i.i.d.\ entries that are independent of W. We assume
subexponential decay for the matrix entries of W and we choose λ∼1, so that the
eigenvalues of W and λV are typically of the same order. Further, we assume that
the density of the entries of V is supported on a single interval and is convex
near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such
that the largest eigenvalues of H are in the limit of large N determined by the
order statistics of V for λ>λ+. In particular, the largest eigenvalue of H
has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently
large, we show that the eigenvectors associated to the largest eigenvalues are
partially localized for λ>λ+, while they are completely delocalized for λ<λ+.
Similar results hold for the lowest eigenvalues. '
acknowledgement: "Most of the presented work was obtained while Kevin Schnelli was
staying at the IAS with the support of\r\nThe Fund For Math."
author:
- first_name: Jioon
full_name: Lee, Jioon
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Extremal eigenvalues and eigenvectors of deformed Wigner
matrices. Probability Theory and Related Fields. 2016;164(1-2):165-241.
doi:10.1007/s00440-014-0610-8
apa: Lee, J., & Schnelli, K. (2016). Extremal eigenvalues and eigenvectors of
deformed Wigner matrices. Probability Theory and Related Fields. Springer.
https://doi.org/10.1007/s00440-014-0610-8
chicago: Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors
of Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer,
2016. https://doi.org/10.1007/s00440-014-0610-8.
ieee: J. Lee and K. Schnelli, “Extremal eigenvalues and eigenvectors of deformed
Wigner matrices,” Probability Theory and Related Fields, vol. 164, no.
1–2. Springer, pp. 165–241, 2016.
ista: Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed
Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241.
mla: Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed
Wigner Matrices.” Probability Theory and Related Fields, vol. 164, no.
1–2, Springer, 2016, pp. 165–241, doi:10.1007/s00440-014-0610-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.
date_created: 2018-12-11T11:54:31Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00440-014-0610-8
ec_funded: 1
intvolume: ' 164'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.7057
month: '02'
oa: 1
oa_version: Preprint
page: 165 - 241
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '5215'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extremal eigenvalues and eigenvectors of deformed Wigner matrices
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 164
year: '2016'
...
---
_id: '1411'
abstract:
- lang: eng
text: We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn
on a compact two-dimensional surface M with boundary. Each αi and each βj is either
an arc meeting the boundary of M at its two endpoints, or a closed curve. The
αi are pairwise disjoint except for possibly sharing endpoints, and similarly
for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of
M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise
such that the total number of crossings of the ai with the φ(βj) is as small as
possible. This problem is motivated by an application in the algorithmic theory
of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with
h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently
of h), which is asymptotically tight, as an easy lower bound shows. In general,
for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable
or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent
of h and g. The proofs rely, among other things, on a result concerning simultaneous
planar drawings of graphs by Erten and Kobourov.
acknowledgement: 'Supported by the ERC Adv anced Grant No. 267165. '
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing
curves. Israel Journal of Mathematics. 2016;212(1):37-79. doi:10.1007/s11856-016-1294-9
apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2016). Untangling
two systems of noncrossing curves. Israel Journal of Mathematics. Springer.
https://doi.org/10.1007/s11856-016-1294-9
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling
Two Systems of Noncrossing Curves.” Israel Journal of Mathematics. Springer,
2016. https://doi.org/10.1007/s11856-016-1294-9.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems
of noncrossing curves,” Israel Journal of Mathematics, vol. 212, no. 1.
Springer, pp. 37–79, 2016.
ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of
noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79.
mla: Matoušek, Jiří, et al. “Untangling Two Systems of Noncrossing Curves.” Israel
Journal of Mathematics, vol. 212, no. 1, Springer, 2016, pp. 37–79, doi:10.1007/s11856-016-1294-9.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics
212 (2016) 37–79.
date_created: 2018-12-11T11:51:52Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-23T10:34:31Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s11856-016-1294-9
intvolume: ' 212'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1302.6475
month: '05'
oa: 1
oa_version: Preprint
page: 37 - 79
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '5796'
quality_controlled: '1'
related_material:
record:
- id: '2244'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Untangling two systems of noncrossing curves
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2016'
...
---
_id: '1479'
abstract:
- lang: eng
text: "Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule
stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That
is, by conditioning on A the entropy of X can decrease by at most the bitlength
|A| of A. Such chain rules are known to hold for some computational entropy notions
like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue
of min-entropy, the chain rule is of special interest and has found many applications,
including leakage-resilient cryptography, deterministic encryption, and memory
delegation. These applications rely on restricted special cases of the chain rule.
Whether the chain rule for conditional HILL entropy holds in general was an open
problem for which we give a strong negative answer: we construct joint distributions
(X,Z,A), where A is a distribution over a single bit, such that the HILL entropy
H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample
just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption
that injective one-way function exist, we can make all the distributions efficiently
samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic
objects like lossy functions can be used to sample a distribution constituting
a counterexample to the chain rule making only a single invocation to the underlying
object."
acknowledgement: "This work was partly funded by the European Research Council under
ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n"
author:
- first_name: Stephan
full_name: Krenn, Stephan
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Akshay
full_name: Wadia, Akshay
last_name: Wadia
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule
for conditional HILL entropy. Computational Complexity. 2016;25(3):567-605.
doi:10.1007/s00037-015-0120-9
apa: Krenn, S., Pietrzak, K. Z., Wadia, A., & Wichs, D. (2016). A counterexample
to the chain rule for conditional HILL entropy. Computational Complexity.
Springer. https://doi.org/10.1007/s00037-015-0120-9
chicago: Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A
Counterexample to the Chain Rule for Conditional HILL Entropy.” Computational
Complexity. Springer, 2016. https://doi.org/10.1007/s00037-015-0120-9.
ieee: S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the
chain rule for conditional HILL entropy,” Computational Complexity, vol.
25, no. 3. Springer, pp. 567–605, 2016.
ista: Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain
rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.
mla: Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional
HILL Entropy.” Computational Complexity, vol. 25, no. 3, Springer, 2016,
pp. 567–605, doi:10.1007/s00037-015-0120-9.
short: S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25
(2016) 567–605.
date_created: 2018-12-11T11:52:16Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-02-23T11:05:09Z
day: '01'
ddc:
- '004'
department:
- _id: KrPi
doi: 10.1007/s00037-015-0120-9
ec_funded: 1
file:
- access_level: open_access
checksum: 7659296174fa75f5f0364f31f46f4bcf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:29Z
date_updated: 2020-07-14T12:44:56Z
file_id: '5012'
file_name: IST-2017-766-v1+1_678.pdf
file_size: 483258
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 567 - 605
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Computational Complexity
publication_status: published
publisher: Springer
publist_id: '5715'
pubrep_id: '766'
quality_controlled: '1'
related_material:
record:
- id: '2940'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: A counterexample to the chain rule for conditional HILL entropy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '478'
abstract:
- lang: eng
text: 'Magic: the Gathering is a game about magical combat for any number of players.
Formally it is a zero-sum, imperfect information stochastic game that consists
of a potentially unbounded number of steps. We consider the problem of deciding
if a move is legal in a given single step of Magic. We show that the problem is
(a) coNP-complete in general; and (b) in P if either of two small sets of cards
are not used. Our lower bound holds even for single-player Magic games. The significant
aspects of our results are as follows: First, in most real-life game problems,
the task of deciding whether a given move is legal in a single step is trivial,
and the computationally hard task is to find the best sequence of legal moves
in the presence of multiple players. In contrast, quite uniquely our hardness
result holds for single step and with only one-player. Second, we establish efficient
algorithms for important special cases of Magic.'
alternative_title:
- Frontiers in Artificial Intelligence and Applications
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single
step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:10.3233/978-1-61499-672-9-1432'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2016). The complexity of deciding
legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented
at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands:
IOS Press. https://doi.org/10.3233/978-1-61499-672-9-1432'
chicago: 'Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding
Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016.
https://doi.org/10.3233/978-1-61499-672-9-1432.'
ieee: 'K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of
a single step of magic: The gathering,” presented at the ECAI: European Conference
on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439.'
ista: 'Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of
a single step of magic: The gathering. ECAI: European Conference on Artificial
Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285,
1432–1439.'
mla: 'Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Deciding
Legality of a Single Step of Magic: The Gathering. Vol. 285, IOS Press, 2016,
pp. 1432–39, doi:10.3233/978-1-61499-672-9-1432.'
short: K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.
conference:
end_date: 2016-09-02
location: The Hague, Netherlands
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2016-08-29
date_created: 2018-12-11T11:46:41Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:00:54Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.3233/978-1-61499-672-9-1432
file:
- access_level: open_access
checksum: 848043c812ace05e459579c923f3d3cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:59Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4658'
file_name: IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf
file_size: 2116225
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 285'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 1432 - 1439
publication_status: published
publisher: IOS Press
publist_id: '7342'
pubrep_id: '950'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The complexity of deciding legality of a single step of magic: The gathering'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2016'
...
---
_id: '479'
abstract:
- lang: eng
text: Clinical guidelines and decision support systems (DSS) play an important role
in daily practices of medicine. Many text-based guidelines have been encoded for
work-flow simulation of DSS to automate health care. During the collaboration
with Carle hospital to develop a DSS, we identify that, for some complex and life-critical
diseases, it is highly desirable to automatically rigorously verify some complex
temporal properties in guidelines, which brings new challenges to current simulation
based DSS with limited support of automatical formal verification and real-time
data analysis. In this paper, we conduct the first study on applying runtime verification
to cooperate with current DSS based on real-time data. Within the proposed technique,
a user-friendly domain specific language, named DRTV, is designed to specify vital
real-time data sampled by medical devices and temporal properties originated from
clinical guidelines. Some interfaces are developed for data acquisition and communication.
Then, for medical practice scenarios described in DRTV model, we will automatically
generate event sequences and runtime property verifier automata. If a temporal
property violates, real-time warnings will be produced by the formal verifier
and passed to medical DSS. We have used DRTV to specify different kinds of medical
care scenarios, and applied the proposed technique to assist existing DSS. As
presented in experiment results, in terms of warning detection, it outperforms
the only use of DSS or human inspection, and improves the quality of clinical
health care of hospital
acknowledgement: "This work is supported by NSF CNS 13-30077, NSF CNS 13-29886, NSF
CNS 15-45002, and NSFC 61303014.\r\nThe authors thank Dr. Bobby and Dr. Hill at
Carle Hospital, Urbana, IL for their help with the discussion on medical knowledge.\r\n\r\n"
alternative_title:
- Proceedings International Conference on Software Engineering
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Rui
full_name: Wang, Rui
last_name: Wang
- first_name: Mohamad
full_name: Hosseini, Mohamad
last_name: Hosseini
- first_name: Jiaguang
full_name: Sun, Jiaguang
last_name: Sun
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: 'Jiang Y, Liu H, Kong H, et al. Use runtime verification to improve the quality
of medical care practice. In: Proceedings of the 38th International Conference
on Software Engineering Companion . IEEE; 2016:112-121. doi:10.1145/2889160.2889233'
apa: 'Jiang, Y., Liu, H., Kong, H., Wang, R., Hosseini, M., Sun, J., & Sha,
L. (2016). Use runtime verification to improve the quality of medical care practice.
In Proceedings of the 38th International Conference on Software Engineering
Companion (pp. 112–121). Austin, TX, USA: IEEE. https://doi.org/10.1145/2889160.2889233'
chicago: Jiang, Yu, Han Liu, Hui Kong, Rui Wang, Mohamad Hosseini, Jiaguang Sun,
and Lui Sha. “Use Runtime Verification to Improve the Quality of Medical Care
Practice.” In Proceedings of the 38th International Conference on Software
Engineering Companion , 112–21. IEEE, 2016. https://doi.org/10.1145/2889160.2889233.
ieee: Y. Jiang et al., “Use runtime verification to improve the quality of
medical care practice,” in Proceedings of the 38th International Conference
on Software Engineering Companion , Austin, TX, USA, 2016, pp. 112–121.
ista: 'Jiang Y, Liu H, Kong H, Wang R, Hosseini M, Sun J, Sha L. 2016. Use runtime
verification to improve the quality of medical care practice. Proceedings of the
38th International Conference on Software Engineering Companion . ICSE: International
Conference on Software Engineering, Proceedings International Conference on Software
Engineering, , 112–121.'
mla: Jiang, Yu, et al. “Use Runtime Verification to Improve the Quality of Medical
Care Practice.” Proceedings of the 38th International Conference on Software
Engineering Companion , IEEE, 2016, pp. 112–21, doi:10.1145/2889160.2889233.
short: Y. Jiang, H. Liu, H. Kong, R. Wang, M. Hosseini, J. Sun, L. Sha, in:, Proceedings
of the 38th International Conference on Software Engineering Companion , IEEE,
2016, pp. 112–121.
conference:
end_date: 2016-05-22
location: Austin, TX, USA
name: 'ICSE: International Conference on Software Engineering'
start_date: 2016-05-14
date_created: 2018-12-11T11:46:42Z
date_published: 2016-05-14T00:00:00Z
date_updated: 2021-01-12T08:00:55Z
day: '14'
department:
- _id: ToHe
doi: 10.1145/2889160.2889233
language:
- iso: eng
month: '05'
oa_version: None
page: 112 - 121
publication: 'Proceedings of the 38th International Conference on Software Engineering
Companion '
publication_status: published
publisher: IEEE
publist_id: '7341'
quality_controlled: '1'
scopus_import: 1
status: public
title: Use runtime verification to improve the quality of medical care practice
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '480'
abstract:
- lang: eng
text: Graph games provide the foundation for modeling and synthesizing reactive
processes. In the synthesis of stochastic reactive processes, the traditional
model is perfect-information stochastic games, where some transitions of the game
graph are controlled by two adversarial players, and the other transitions are
executed probabilistically. We consider such games where the objective is the
conjunction of several quantitative objectives (specified as mean-payoff conditions),
which we refer to as generalized mean-payoff objectives. The basic decision problem
asks for the existence of a finite-memory strategy for a player that ensures the
generalized mean-payoff objective be satisfied with a desired probability against
all strategies of the opponent. A special case of the decision problem is the
almost-sure problem where the desired probability is 1. Previous results presented
a semi-decision procedure for -approximations of the almost-sure problem. In this
work, we show that both the almost-sure problem as well as the general basic decision
problem are coNP-complete, significantly improving the previous results. Moreover,
we show that in the case of 1-player stochastic games, randomized memoryless strategies
are sufficient and the problem can be solved in polynomial time. In contrast,
in two-player stochastic games, we show that even with randomized strategies exponential
memory is required in general, and present a matching exponential upper bound.
We also study the basic decision problem with infinite-memory strategies and present
computational complexity results for the problem. Our results are relevant in
the synthesis of stochastic reactive systems with multiple quantitative requirements.
alternative_title:
- Proceedings Symposium on Logic in Computer Science
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Perfect-information stochastic games with generalized
mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:10.1145/2933575.2934513'
apa: 'Chatterjee, K., & Doyen, L. (2016). Perfect-information stochastic games
with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented
at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934513'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic
Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE,
2016. https://doi.org/10.1145/2933575.2934513.
ieee: 'K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized
mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New
York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256.'
ista: 'Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized
mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium
on Logic in Computer Science, vol. 05-08-July-2016, 247–256.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Perfect-Information Stochastic
Games with Generalized Mean-Payoff Objectives. Vol. 05-08-July-2016, IEEE,
2016, pp. 247–56, doi:10.1145/2933575.2934513.
short: K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:46:42Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T08:00:56Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2934513
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.06376
month: '07'
oa: 1
oa_version: Preprint
page: 247 - 256
project:
- _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: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: IEEE
publist_id: '7340'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perfect-information stochastic games with generalized mean-payoff objectives
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 05-08-July-2016
year: '2016'
...
---
_id: '1379'
abstract:
- lang: eng
text: We investigate the complexity of finding an embedded non-orientable surface
of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural
question in low-dimensional topology, and as a first non-trivial instance of embeddability
of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding
to the relatively few hardness results that are currently known in 3-manifold
topology. In addition, we show that the problem lies in NP when the Euler genus
g is odd, and we give an explicit algorithm in this case.
alternative_title:
- LIPIcs
author:
- first_name: Benjamin
full_name: Burton, Benjamin
last_name: Burton
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds.
In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing;
2016:24.1-24.15. doi:10.4230/LIPIcs.SoCG.2016.24'
apa: 'Burton, B., de Mesmay, A. N., & Wagner, U. (2016). Finding non-orientable
surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium
on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.24'
chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable
Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur
Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.24.
ieee: 'B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces
in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford,
MA, USA, 2016, vol. 51, p. 24.1-24.15.'
ista: 'Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in
3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.'
mla: Burton, Benjamin, et al. Finding Non-Orientable Surfaces in 3-Manifolds.
Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing,
2016, p. 24.1-24.15, doi:10.4230/LIPIcs.SoCG.2016.24.
short: B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-23T12:23:20Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.24
file:
- access_level: open_access
checksum: f04248a61c24297cfabd30c5f8e0deb9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:12Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4930'
file_name: IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf
file_size: 574770
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 24.1 - 24.15
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
publist_id: '5832'
pubrep_id: '622'
quality_controlled: '1'
related_material:
record:
- id: '534'
relation: later_version
status: public
scopus_import: 1
status: public
title: Finding non-orientable surfaces in 3-manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1477'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs) with ω-regular
conditions specified as parity objectives. The class of ω-regular languages provides
a robust specification language to express properties in verification, and parity
objectives are canonical forms to express them. The qualitative analysis problem
given a POMDP and a parity objective asks whether there is a strategy to ensure
that the objective is satisfied with probability 1 (resp. positive probability).
While the qualitative analysis problems are undecidable even for special cases
of parity objectives, we establish decidability (with optimal complexity) for
POMDPs with all parity objectives under finite-memory strategies. We establish
optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative
analysis problems under finite-memory strategies for POMDPs with parity objectives.
We also present a practical approach, where we design heuristics to deal with
the exponential complexity, and have applied our implementation on a number of
POMDP examples.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Mathieu
full_name: Tracol, Mathieu
id: 3F54FA38-F248-11E8-B48F-1D18A9856A87
last_name: Tracol
citation:
ama: Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable
Markov decision processes with ω-regular objectives. Journal of Computer and
System Sciences. 2016;82(5):878-911. doi:10.1016/j.jcss.2016.02.009
apa: Chatterjee, K., Chmelik, M., & Tracol, M. (2016). What is decidable about
partially observable Markov decision processes with ω-regular objectives. Journal
of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.02.009
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable
about Partially Observable Markov Decision Processes with ω-Regular Objectives.”
Journal of Computer and System Sciences. Elsevier, 2016. https://doi.org/10.1016/j.jcss.2016.02.009.
ieee: K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially
observable Markov decision processes with ω-regular objectives,” Journal of
Computer and System Sciences, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.
ista: Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially
observable Markov decision processes with ω-regular objectives. Journal of Computer
and System Sciences. 82(5), 878–911.
mla: Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable
Markov Decision Processes with ω-Regular Objectives.” Journal of Computer and
System Sciences, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:10.1016/j.jcss.2016.02.009.
short: K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences
82 (2016) 878–911.
date_created: 2018-12-11T11:52:15Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-02-23T12:24:38Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2016.02.009
ec_funded: 1
external_id:
arxiv:
- '1309.2802'
intvolume: ' 82'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.2802
month: '08'
oa: 1
oa_version: Preprint
page: 878 - 911
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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '5718'
quality_controlled: '1'
related_material:
record:
- id: '2295'
relation: earlier_version
status: public
- id: '5400'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: What is decidable about partially observable Markov decision processes with
ω-regular objectives
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2016'
...
---
_id: '1529'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
a set of target states and an integer cost associated with every transition. The
optimization objective we study asks to minimize the expected total cost of reaching
a state in the target set, while ensuring that the target set is reached almost
surely (with probability 1). We show that for integer costs approximating the
optimal cost is undecidable. For positive costs, our results are as follows: (i)
we establish matching lower and upper bounds for the optimal cost, both double
exponential in the POMDP state space size; (ii) we show that the problem of approximating
the optimal cost is decidable and present approximation algorithms developing
on the existing algorithms for POMDPs with finite-horizon objectives. While the
worst-case running time of our algorithm is double exponential, we also present
efficient stopping criteria for the algorithm and show experimentally that it
performs well in many examples of interest.'
acknowledgement: 'We thank Blai Bonet for helping us with RTDP-Bel. The research was
partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant
No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty
fellows award.'
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: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability
in POMDPs. Artificial Intelligence. 2016;234:26-48. doi:10.1016/j.artint.2016.01.007
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2016). Optimal cost
almost-sure reachability in POMDPs. Artificial Intelligence. Elsevier.
https://doi.org/10.1016/j.artint.2016.01.007
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
“Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence.
Elsevier, 2016. https://doi.org/10.1016/j.artint.2016.01.007.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure
reachability in POMDPs,” Artificial Intelligence, vol. 234. Elsevier, pp.
26–48, 2016.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure
reachability in POMDPs. Artificial Intelligence. 234, 26–48.
mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.”
Artificial Intelligence, vol. 234, Elsevier, 2016, pp. 26–48, doi:10.1016/j.artint.2016.01.007.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence
234 (2016) 26–48.
date_created: 2018-12-11T11:52:33Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-23T12:25:49Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.artint.2016.01.007
ec_funded: 1
external_id:
arxiv:
- '1411.3880'
intvolume: ' 234'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1411.3880
month: '05'
oa: 1
oa_version: Preprint
page: 26 - 48
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Artificial Intelligence
publication_status: published
publisher: Elsevier
publist_id: '5642'
quality_controlled: '1'
related_material:
record:
- id: '1820'
relation: earlier_version
status: public
- id: '5425'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 234
year: '2016'
...
---
_id: '5445'
abstract:
- lang: eng
text: 'We consider the quantitative analysis problem for interprocedural control-flow
graphs (ICFGs). The input consists of an ICFG, a positive weight function that
assigns every transition a positive integer-valued number, and a labelling of
the transitions (events) as good, bad, and neutral events. The weight function
assigns to each transition a numerical value that represents ameasure of how good
or bad an event is. The quantitative analysis problem asks whether there is a
run of the ICFG where the ratio of the sum of the numerical weights of good events
versus the sum of weights of bad events in the long-run is at least a given threshold
(or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
The quantitative analysis problem for ICFGs can be solved in polynomial time,
and we present an efficient and practical algorithm for the problem. We show that
several problems relevant for static program analysis, such as estimating the
worst-case execution time of a program or the average energy consumption of a
mobile application, can be modeled in our framework. We have implemented our algorithm
as a tool in the Java Soot framework. We demonstrate the effectiveness of our
approach with two case studies. First, we show that our framework provides a sound
approach (no false positives) for the analysis of inefficiently-used containers.
Second, we show that our approach can also be used for static profiling of programs
which reasons about methods that are frequently invoked. Our experimental results
show that our tool scales to relatively large benchmarks, and discovers relevant
and useful information that can be used to optimize performance of the programs. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative Interprocedural Analysis.
IST Austria; 2016. doi:10.15479/AT:IST-2016-523-v1-1
apa: Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2016). Quantitative
interprocedural analysis. IST Austria. https://doi.org/10.15479/AT:IST-2016-523-v1-1
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. Quantitative
Interprocedural Analysis. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-523-v1-1.
ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, Quantitative interprocedural
analysis. IST Austria, 2016.
ista: Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural
analysis, IST Austria, 33p.
mla: Chatterjee, Krishnendu, et al. Quantitative Interprocedural Analysis.
IST Austria, 2016, doi:10.15479/AT:IST-2016-523-v1-1.
short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis,
IST Austria, 2016.
date_created: 2018-12-12T11:39:22Z
date_published: 2016-03-31T00:00:00Z
date_updated: 2023-02-23T10:06:22Z
day: '31'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-523-v1-1
file:
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checksum: cef516fa091925b5868813e355268fb4
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date_created: 2018-12-12T11:53:52Z
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language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '523'
related_material:
record:
- id: '1604'
relation: later_version
status: public
status: public
title: Quantitative interprocedural analysis
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1166'
abstract:
- lang: eng
text: POMDPs are standard models for probabilistic planning problems, where an agent
interacts with an uncertain environment. We study the problem of almost-sure reachability,
where given a set of target states, the question is to decide whether there is
a policy to ensure that the target set is reached with probability 1 (almost-surely).
While in general the problem is EXPTIMEcomplete, in many practical cases policies
with a small amount of memory suffice. Moreover, the existing solution to the
problem is explicit, which first requires to construct explicitly an exponential
reduction to a belief-support MDP. In this work, we first study the existence
of observation-stationary strategies, which is NP-complete, and then small-memory
strategies. We present a symbolic algorithm by an efficient encoding to SAT and
using a SAT solver for the problem. We report experimental results demonstrating
the scalability of our symbolic (SAT-based) approach. © 2016, Association for
the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Jessica
full_name: Davies, Jessica
id: 378E0060-F248-11E8-B48F-1D18A9856A87
last_name: Davies
citation:
ama: 'Chatterjee K, Chmelik M, Davies J. A symbolic SAT based algorithm for almost
sure reachability with small strategies in pomdps. In: Proceedings of the Thirtieth
AAAI Conference on Artificial Intelligence. Vol 2016. AAAI Press; 2016:3225-3232.'
apa: 'Chatterjee, K., Chmelik, M., & Davies, J. (2016). A symbolic SAT based
algorithm for almost sure reachability with small strategies in pomdps. In Proceedings
of the Thirtieth AAAI Conference on Artificial Intelligence (Vol. 2016, pp.
3225–3232). Phoenix, AZ, USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. “A Symbolic
SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.”
In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence,
2016:3225–32. AAAI Press, 2016.
ieee: K. Chatterjee, M. Chmelik, and J. Davies, “A symbolic SAT based algorithm
for almost sure reachability with small strategies in pomdps,” in Proceedings
of the Thirtieth AAAI Conference on Artificial Intelligence, Phoenix, AZ,
USA, 2016, vol. 2016, pp. 3225–3232.
ista: 'Chatterjee K, Chmelik M, Davies J. 2016. A symbolic SAT based algorithm for
almost sure reachability with small strategies in pomdps. Proceedings of the Thirtieth
AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence
vol. 2016, 3225–3232.'
mla: Chatterjee, Krishnendu, et al. “A Symbolic SAT Based Algorithm for Almost Sure
Reachability with Small Strategies in Pomdps.” Proceedings of the Thirtieth
AAAI Conference on Artificial Intelligence, vol. 2016, AAAI Press, 2016, pp.
3225–32.
short: K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI
Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232.
conference:
end_date: 2016-02-17
location: Phoenix, AZ, USA
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2016-02-12
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-02T00:00:00Z
date_updated: 2023-02-23T12:26:41Z
day: '02'
department:
- _id: KrCh
- _id: ToHe
ec_funded: 1
intvolume: ' 2016'
language:
- iso: eng
month: '12'
oa_version: None
page: 3225 - 3232
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '6191'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: https://dl.acm.org/citation.cfm?id=3016355
record:
- id: '5443'
relation: earlier_version
status: public
status: public
title: A symbolic SAT based algorithm for almost sure reachability with small strategies
in pomdps
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '5449'
abstract:
- lang: eng
text: "The fixation probability is the probability that a new mutant introduced
in a homogeneous population eventually takes over the entire population.\r\nThe
fixation probability is a fundamental quantity of natural selection, and known
to depend on the population structure.\r\nAmplifiers of natural selection are
population structures which increase the fixation probability of advantageous
mutants, as compared to the baseline case of well-mixed populations. In this work
we focus on symmetric population structures represented as undirected graphs.
In the regime of undirected graphs, the strongest amplifier known has been the
Star graph, and the existence of undirected graphs with stronger amplification
properties has remained open for over a decade.\r\nIn this work we present the
Comet and Comet-swarm families of undirected graphs. We show that for a range
of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation
probability strictly larger than the fixation probability of the Star graph, for
fixed population size and at the limit of large populations, respectively."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on Undirected
Population Structures: Comets Beat Stars. IST Austria; 2016. doi:10.15479/AT:IST-2016-648-v1-1'
apa: 'Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Amplification
on undirected population structures: Comets beat stars. IST Austria. https://doi.org/10.15479/AT:IST-2016-648-v1-1'
chicago: 'Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Amplification on Undirected Population Structures: Comets Beat Stars.
IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-648-v1-1.'
ieee: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Amplification
on undirected population structures: Comets beat stars. IST Austria, 2016.'
ista: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on
undirected population structures: Comets beat stars, IST Austria, 22p.'
mla: 'Pavlogiannis, Andreas, et al. Amplification on Undirected Population Structures:
Comets Beat Stars. IST Austria, 2016, doi:10.15479/AT:IST-2016-648-v1-1.'
short: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected
Population Structures: Comets Beat Stars, IST Austria, 2016.'
date_created: 2018-12-12T11:39:24Z
date_published: 2016-11-09T00:00:00Z
date_updated: 2023-02-23T12:22:21Z
day: '09'
ddc:
- '519'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-648-v1-1
file:
- access_level: open_access
checksum: 8345a8c1e7d7f0cd92516d182b7fc59e
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:07Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5529'
file_name: IST-2016-648-v1+1_tr.pdf
file_size: 1264221
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Updated Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '648'
related_material:
record:
- id: '512'
relation: later_version
status: public
status: public
title: 'Amplification on undirected population structures: Comets beat stars'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5453'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers
of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-749-v3-1
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Arbitrarily
strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2017-749-v3-1
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria,
2016. https://doi.org/10.15479/AT:IST-2017-749-v3-1.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong
amplifiers of natural selection. IST Austria, 2016.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong
amplifiers of natural selection, IST Austria, 34p.
mla: Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection.
IST Austria, 2016, doi:10.15479/AT:IST-2017-749-v3-1.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong
Amplifiers of Natural Selection, IST Austria, 2016.
date_created: 2018-12-12T11:39:25Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2023-02-23T12:27:07Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-749-v3-1
file:
- access_level: open_access
checksum: 83b0313dab3bff4bdb6ac38695026fda
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:13Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5474'
file_name: IST-2017-749-v3+1_main.pdf
file_size: 1015647
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '34'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '755'
related_material:
record:
- id: '5452'
relation: earlier_version
status: public
status: public
title: Arbitrarily strong amplifiers of natural selection
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5451'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Strong Amplifiers of Natural
Selection. IST Austria; 2016. doi:10.15479/AT:IST-2016-728-v1-1
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Strong
amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2016-728-v1-1
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-728-v1-1.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Strong amplifiers
of natural selection. IST Austria, 2016.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers
of natural selection, IST Austria, 34p.
mla: Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection.
IST Austria, 2016, doi:10.15479/AT:IST-2016-728-v1-1.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of
Natural Selection, IST Austria, 2016.
date_created: 2018-12-12T11:39:24Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2023-02-23T12:27:05Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-728-v1-1
file:
- access_level: open_access
checksum: 7b8bb17c322c0556acba6ac169fa71c1
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:04Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5465'
file_name: IST-2016-728-v1+1_main.pdf
file_size: 1014732
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '34'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '728'
status: public
title: Strong amplifiers of natural selection
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5806'
abstract:
- lang: eng
text: Although the concept of functional plane for naive plane is studied and reported
in the literature in great detail, no similar study is yet found for naive sphere.
This article exposes the first study in this line, opening up further prospects
of analyzing the topological properties of sphere in the discrete space. We show
that each quadraginta octant Q of a naive sphere forms a bijection with its projected
pixel set on a unique coordinate plane, which thereby serves as the functional
plane of Q, and hence gives rise to merely mono-jumps during back projection.
The other two coordinate planes serve as para-functional and dia-functional planes
for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds
neither of the two. Owing to this, the quadraginta octants form symmetry groups
and subgroups with equivalent jump conditions. We also show a potential application
in generating a special class of discrete 3D circles based on back projection
and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry,
uniqueness, and bounded distance from the underlying real sphere and real plane.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere
with application to circle drawing. In: Discrete Geometry for Computer Imagery.
Vol 9647. Cham: Springer Nature; 2016:256-267. doi:10.1007/978-3-319-32360-2_20'
apa: 'Biswas, R., & Bhowmick, P. (2016). On functionality of quadraginta octants
of naive sphere with application to circle drawing. In Discrete Geometry for
Computer Imagery (Vol. 9647, pp. 256–267). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-32360-2_20'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta
Octants of Naive Sphere with Application to Circle Drawing.” In Discrete Geometry
for Computer Imagery, 9647:256–67. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-32360-2_20.'
ieee: R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive
sphere with application to circle drawing,” in Discrete Geometry for Computer
Imagery, Nantes, France, 2016, vol. 9647, pp. 256–267.
ista: 'Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive
sphere with application to circle drawing. Discrete Geometry for Computer Imagery.
DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS,
vol. 9647, 256–267.'
mla: Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants
of Naive Sphere with Application to Circle Drawing.” Discrete Geometry for
Computer Imagery, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:10.1007/978-3-319-32360-2_20.
short: R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer
Nature, Cham, 2016, pp. 256–267.
conference:
end_date: 2016-04-20
location: Nantes, France
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2016-04-18
date_created: 2019-01-08T20:44:37Z
date_published: 2016-04-09T00:00:00Z
date_updated: 2022-01-28T08:10:11Z
day: '09'
department:
- _id: HeEd
doi: 10.1007/978-3-319-32360-2_20
extern: '1'
intvolume: ' 9647'
language:
- iso: eng
month: '04'
oa_version: None
page: 256-267
place: Cham
publication: Discrete Geometry for Computer Imagery
publication_identifier:
eisbn:
- 978-3-319-32360-2
isbn:
- 978-3-319-32359-6
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On functionality of quadraginta octants of naive sphere with application to
circle drawing
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9647
year: '2016'
...
---
_id: '5805'
abstract:
- lang: eng
text: Discretization of sphere in the integer space follows a particular discretization
scheme, which, in principle, conforms to some topological model. This eventually
gives rise to interesting topological properties of a discrete spherical surface,
which need to be investigated for its analytical characterization. This paper
presents some novel results on the local topological properties of the naive model
of discrete sphere. They follow from the bijection of each quadraginta octant
of naive sphere with its projection map called f -map on the corresponding functional
plane and from the characterization of certain jumps in the f-map. As an application,
we have shown how these properties can be used in designing an efficient reconstruction
algorithm for a naive spherical surface from an input voxel set when it is sparse
or noisy.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nabhasmita
full_name: Sen, Nabhasmita
last_name: Sen
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Sen N, Biswas R, Bhowmick P. On some local topological properties of naive
discrete sphere. In: Computational Topology in Image Context. Vol 9667.
Cham: Springer Nature; 2016:253-264. doi:10.1007/978-3-319-39441-1_23'
apa: 'Sen, N., Biswas, R., & Bhowmick, P. (2016). On some local topological
properties of naive discrete sphere. In Computational Topology in Image Context
(Vol. 9667, pp. 253–264). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-39441-1_23'
chicago: 'Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological
Properties of Naive Discrete Sphere.” In Computational Topology in Image Context,
9667:253–64. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-39441-1_23.'
ieee: 'N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties
of naive discrete sphere,” in Computational Topology in Image Context,
vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.'
ista: 'Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of
naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol.
9667, 253–264.'
mla: Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete
Sphere.” Computational Topology in Image Context, vol. 9667, Springer Nature,
2016, pp. 253–64, doi:10.1007/978-3-319-39441-1_23.
short: N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context,
Springer Nature, Cham, 2016, pp. 253–264.
conference:
end_date: 2016-06-17
location: Marseille, France
name: 'CTIC: Computational Topology in Image Context'
start_date: 2016-06-15
date_created: 2019-01-08T20:44:24Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2022-01-28T08:01:22Z
day: '02'
department:
- _id: HeEd
doi: 10.1007/978-3-319-39441-1_23
extern: '1'
intvolume: ' 9667'
language:
- iso: eng
month: '06'
oa_version: None
page: 253-264
place: Cham
publication: Computational Topology in Image Context
publication_identifier:
eisbn:
- 978-3-319-39441-1
eissn:
- 1611-3349
isbn:
- 978-3-319-39440-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On some local topological properties of naive discrete sphere
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9667
year: '2016'
...
---
_id: '5809'
abstract:
- lang: eng
text: A discrete spherical circle is a topologically well-connected 3D circle in
the integer space, which belongs to a discrete sphere as well as a discrete plane.
It is one of the most important 3D geometric primitives, but has not possibly
yet been studied up to its merit. This paper is a maiden exposition of some of
its elementary properties, which indicates a sense of its profound theoretical
prospects in the framework of digital geometry. We have shown how different types
of discretization can lead to forbidden and admissible classes, when one attempts
to define the discretization of a spherical circle in terms of intersection between
a discrete sphere and a discrete plane. Several fundamental theoretical results
have been presented, the algorithm for construction of discrete spherical circles
has been discussed, and some test results have been furnished to demonstrate its
practicality and usefulness.
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
- first_name: Valentin E.
full_name: Brimkov, Valentin E.
last_name: Brimkov
citation:
ama: 'Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete
spherical circles. In: Combinatorial Image Analysis. Vol 9448. Cham: Springer
Nature; 2016:86-100. doi:10.1007/978-3-319-26145-4_7'
apa: 'Biswas, R., Bhowmick, P., & Brimkov, V. E. (2016). On the connectivity
and smoothness of discrete spherical circles. In Combinatorial image analysis
(Vol. 9448, pp. 86–100). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-26145-4_7'
chicago: 'Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity
and Smoothness of Discrete Spherical Circles.” In Combinatorial Image Analysis,
9448:86–100. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-26145-4_7.'
ieee: 'R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness
of discrete spherical circles,” in Combinatorial image analysis, vol. 9448,
Cham: Springer Nature, 2016, pp. 86–100.'
ista: 'Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness
of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.'
mla: Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical
Circles.” Combinatorial Image Analysis, vol. 9448, Springer Nature, 2016,
pp. 86–100, doi:10.1007/978-3-319-26145-4_7.
short: R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis,
Springer Nature, Cham, 2016, pp. 86–100.
conference:
end_date: 2015-11-27
location: Kolkata, India
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2015-11-24
date_created: 2019-01-08T20:45:19Z
date_published: 2016-01-06T00:00:00Z
date_updated: 2022-01-28T08:13:03Z
day: '06'
department:
- _id: HeEd
doi: 10.1007/978-3-319-26145-4_7
extern: '1'
intvolume: ' 9448'
language:
- iso: eng
month: '01'
oa_version: None
page: 86-100
place: Cham
publication: Combinatorial image analysis
publication_identifier:
eisbn:
- 978-3-319-26145-4
eissn:
- 1611-3349
isbn:
- 978-3-319-26144-7
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On the connectivity and smoothness of discrete spherical circles
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9448
year: '2016'
...
---
_id: '8094'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. The idea is that the controller controls the world---the body plus
its environment---as reliably as possible. This paper focuses on new lines of
self-organization for developmental robotics. We apply the recently developed
differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder
system from the Myorobotics toolkit. In the experiments, we observe a vast variety
of self-organized behavior patterns: when left alone, the arm realizes pseudo-random
sequences of different poses. By applying physical forces, the system can be entrained
into definite motion patterns like wiping a table. Most interestingly, after attaching
an object, the controller gets in a functional resonance with the object''s internal
dynamics, starting to shake spontaneously bottles half-filled with water or sensitively
driving an attached pendulum into a circular mode. When attached to the crank
of a wheel the neural system independently discovers how to rotate it. In this
way, the robot discovers affordances of objects its body is interacting with.'
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Rafael
full_name: Hostettler, Rafael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon
driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial
Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized
control of an tendon driven arm by differential extrinsic plasticity. In Proceedings
of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico:
MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029'
chicago: Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized
Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings
of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.
ieee: G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control
of an tendon driven arm by differential extrinsic plasticity,” in Proceedings
of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp.
142–143.
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of
an tendon driven arm by differential extrinsic plasticity. Proceedings of the
Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on
the Synthesis and Simulation of Living Systems vol. 28, 142–143.'
mla: Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by
Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference
2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial
Life Conference 2016, MIT Press, 2016, pp. 142–143.
conference:
end_date: 2016-07-08
location: Cancun, Mexico
name: 'ALIFE 2016: 15th International Conference on the Synthesis and Simulation
of Living Systems'
start_date: 2016-07-04
date_created: 2020-07-05T22:00:47Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:16:53Z
day: '01'
ddc:
- '610'
department:
- _id: ChLa
- _id: GaTk
doi: 10.7551/978-0-262-33936-0-ch029
ec_funded: 1
file:
- access_level: open_access
checksum: cff63e7a4b8ac466ba51a9c84153a940
content_type: application/pdf
creator: cziletti
date_created: 2020-07-06T12:59:09Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8096'
file_name: 2016_ProcALIFE_Martius.pdf
file_size: 678670
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 28'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 142-143
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the Artificial Life Conference 2016
publication_identifier:
isbn:
- '9780262339360'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: 1
status: public
title: Self-organized control of an tendon driven arm by differential extrinsic plasticity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 28
year: '2016'
...
---
_id: '1197'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation
(http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation
(https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National
Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science
Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler
for helpful comments on the manuscript.
article_number: e1005855
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes
of the retinal population code. PLoS Computational Biology. 2016;12(11).
doi:10.1371/journal.pcbi.1005148
apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2016). Error-robust modes of the retinal population code. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148
chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS
Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust
modes of the retinal population code,” PLoS Computational Biology, vol.
12, no. 11. Public Library of Science, 2016.
ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust
modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.”
PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of
Science, 2016, doi:10.1371/journal.pcbi.1005148.
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational
Biology 12 (2016).
date_created: 2018-12-11T11:50:40Z
date_published: 2016-11-17T00:00:00Z
date_updated: 2023-02-23T14:05:40Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005148
file:
- access_level: open_access
checksum: 47b08cbd4dbf32b25ba161f5f4b262cc
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T10:35:00Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5884'
file_name: 2016_PLOS_Prentice.pdf
file_size: 4492021
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6153'
quality_controlled: '1'
related_material:
record:
- id: '9709'
relation: research_data
status: public
scopus_import: 1
status: public
title: Error-robust modes of the retinal population code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '9720'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A
sting in the spit: widespread cross-infection of multiple RNA viruses across wild
and managed bees. 2016. doi:10.5061/dryad.4b565'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple
RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees.” Dryad, 2016.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees, Dryad, 10.5061/dryad.4b565.'
mla: 'Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).
date_created: 2021-07-26T09:14:19Z
date_published: 2016-01-22T00:00:00Z
date_updated: 2023-02-23T10:17:25Z
day: '22'
department:
- _id: SyCr
doi: 10.5061/dryad.4b565
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.4b565
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1855'
relation: used_in_publication
status: public
status: public
title: 'Data from: A sting in the spit: widespread cross-infection of multiple RNA
viruses across wild and managed bees'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-02-23T14:11:16Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
related_material:
record:
- id: '9862'
relation: research_data
status: public
- id: '9863'
relation: research_data
status: public
scopus_import: 1
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1167'
abstract:
- lang: eng
text: Evolutionary pathways describe trajectories of biological evolution in the
space of different variants of organisms (genotypes). The probability of existence
and the number of evolutionary pathways that lead from a given genotype to a better-adapted
genotype are important measures of accessibility of local fitness optima and the
reproducibility of evolution. Both quantities have been studied in simple mathematical
models where genotypes are represented as binary sequences of two types of basic
units, and the network of permitted mutations between the genotypes is a hypercube
graph. However, it is unclear how these results translate to the biologically
relevant case in which genotypes are represented by sequences of more than two
units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the
mutational graph is not the hypercube. Here we investigate accessibility of the
best-adapted genotype in the general case of K > 2 units. Using computer generated
and experimental fitness landscapes we show that accessibility of the global fitness
maximum increases with K and can be much higher than for binary sequences. The
increase in accessibility comes from the increase in the number of indirect trajectories
exploited by evolution for higher K. As one of the consequences, the fraction
of genotypes that are accessible increases by three orders of magnitude when the
number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes.
This suggests that evolution can follow many different trajectories on such landscapes
and the reconstruction of evolutionary pathways from experimental data might be
an extremely difficult task.
acknowledgement: MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107.
BW was supported by the Scottish Government/Royal Society of Edinburgh Personal
Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading
the manuscript.
article_number: e1005218
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational
Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the
Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational
Networks.” PLoS Computational Biology. Public Library of Science, 2016.
https://doi.org/10.1371/journal.pcbi.1005218.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks,” PLoS
Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational Biology.
12(12), e1005218.
mla: Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility
of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational
Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.
short: M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-23T14:11:22Z
day: '09'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218
file:
- access_level: open_access
checksum: 84f44ae92866c52ff1ca8a574558dca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:08Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4926'
file_name: IST-2017-740-v1+1_journal.pcbi.1005218.pdf
file_size: 3822299
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6190'
pubrep_id: '740'
quality_controlled: '1'
related_material:
record:
- id: '9866'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Beyond the hypercube evolutionary accessibility of fitness landscapes with
realistic mutational networks
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 12
year: '2016'
...
---
_id: '9867'
abstract:
- lang: eng
text: In the beginning of our experiment, subjects were asked to read a few pages
on their computer screens that would explain the rules of the subsequent game.
Here, we provide these instructions, translated from German.
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Kristin
full_name: Hagel, Kristin
last_name: Hagel
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
citation:
ama: Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:10.1371/journal.pone.0163867.s008
apa: Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental game instructions.
Public Library of Science. https://doi.org/10.1371/journal.pone.0163867.s008
chicago: Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game
Instructions.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s008.
ieee: C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public
Library of Science, 2016.
ista: Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public
Library of Science, 10.1371/journal.pone.0163867.s008.
mla: Hilbe, Christian, et al. Experimental Game Instructions. Public Library
of Science, 2016, doi:10.1371/journal.pone.0163867.s008.
short: C. Hilbe, K. Hagel, M. Milinski, (2016).
date_created: 2021-08-10T08:42:00Z
date_updated: 2023-02-21T16:59:01Z
day: '04'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0163867.s008
month: '10'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1322'
relation: used_in_publication
status: public
status: public
title: Experimental game instructions
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9862'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation
study to test the robustness of ABC in face of recent times of divergence. 2016.
doi:10.1371/journal.pbio.2000234.s016
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Simulation study to test the robustness of ABC in face of recent times
of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness
of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016.
https://doi.org/10.1371/journal.pbio.2000234.s016.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Simulation study to test the robustness of ABC in face of recent times of divergence.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation
study to test the robustness of ABC in face of recent times of divergence, Public
Library of Science, 10.1371/journal.pbio.2000234.s016.
mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in
Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:20:17Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Simulation study to test the robustness of ABC in face of recent times of divergence
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9863'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions
of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Accessions of surveyed individuals, geographic locations and summary
statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic
Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Accessions of surveyed individuals, geographic locations and summary statistics.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions
of surveyed individuals, geographic locations and summary statistics, Public Library
of Science, 10.1371/journal.pbio.2000234.s017.
mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations
and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:22:52Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s017
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Accessions of surveyed individuals, geographic locations and summary statistics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9866'
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data
and computer programs. 2016. doi:10.1371/journal.pcbi.1005218.s009
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). ZIP-archived directory
containing all data and computer programs. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218.s009
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived
Directory Containing All Data and Computer Programs.” Public Library of Science,
2016. https://doi.org/10.1371/journal.pcbi.1005218.s009.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing
all data and computer programs.” Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all
data and computer programs, Public Library of Science, 10.1371/journal.pcbi.1005218.s009.
mla: Zagórski, Marcin P., et al. ZIP-Archived Directory Containing All Data and
Computer Programs. Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.s009.
short: M.P. Zagórski, Z. Burda, B. Wacław, (2016).
date_created: 2021-08-10T08:37:20Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-21T16:24:29Z
day: '09'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218.s009
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1167'
relation: used_in_publication
status: public
status: public
title: ZIP-archived directory containing all data and computer programs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9456'
abstract:
- lang: eng
text: The discovery of introns four decades ago was one of the most unexpected findings
in molecular biology. Introns are sequences interrupting genes that must be removed
as part of messenger RNA production. Genome sequencing projects have shown that
most eukaryotic genes contain at least one intron, and frequently many. Comparison
of these genomes reveals a history of long evolutionary periods during which few
introns were gained, punctuated by episodes of rapid, extensive gain. However,
although several detailed mechanisms for such episodic intron generation have
been proposed, none has been empirically supported on a genomic scale. Here we
show how short, non-autonomous DNA transposons independently generated hundreds
to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte
Aureococcus anophagefferens. Each transposon carries one splice site. The other
splice site is co-opted from the gene sequence that is duplicated upon transposon
insertion, allowing perfect splicing out of the RNA. The distributions of sequences
that can be co-opted are biased with respect to codons, and phasing of transposon-generated
introns is similarly biased. These transposons insert between pre-existing nucleosomes,
so that multiple nearby insertions generate nucleosome-sized intervening segments.
Thus, transposon insertion and sequence co-option may explain the intron phase
biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall,
the two independent examples of proliferating elements illustrate a general DNA
transposon mechanism that can plausibly account for episodes of rapid, extensive
intron gain during eukaryotic evolution.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Scott W.
full_name: Roy, Scott W.
last_name: Roy
citation:
ama: Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns
on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
apa: Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons
to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110
chicago: Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA
Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature
, 2016. https://doi.org/10.1038/nature20110.
ieee: J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to
generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer
Nature , pp. 533–536, 2016.
ista: Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate
introns on genomic scales. Nature. 538(7626), 533–536.
mla: Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on
Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp.
533–36, doi:10.1038/nature20110.
short: J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
date_created: 2021-06-04T11:34:55Z
date_published: 2016-10-27T00:00:00Z
date_updated: 2021-12-14T07:55:30Z
day: '27'
department:
- _id: DaZi
doi: 10.1038/nature20110
extern: '1'
external_id:
pmid:
- '27760113'
intvolume: ' 538'
issue: '7626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 533-536
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: 'Springer Nature '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism for DNA transposons to generate introns on genomic scales
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 538
year: '2016'
...
---
_id: '948'
abstract:
- lang: eng
text: Experience constantly shapes neural circuits through a variety of plasticity
mechanisms. While the functional roles of some plasticity mechanisms are well-understood,
it remains unclear how changes in neural excitability contribute to learning.
Here, we develop a normative interpretation of intrinsic plasticity (IP) as a
key component of unsupervised learning. We introduce a novel generative mixture
model that accounts for the class-specific statistics of stimulus intensities,
and we derive a neural circuit that learns the input classes and their intensities.
We will analytically show that inference and learning for our generative model
can be achieved by a neural circuit with intensity-sensitive neurons equipped
with a specific form of IP. Numerical experiments verify our analytical derivations
and show robust behavior for artificial and natural stimuli. Our results link
IP to non-trivial input statistics, in particular the statistics of stimulus intensities
for classes to which a neuron is sensitive. More generally, our work paves the
way toward new classification algorithms that are robust to intensity variations.
acknowledgement: DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1
(JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement
no. 291734 (CS)
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Travis
full_name: Monk, Travis
last_name: Monk
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Jörg
full_name: Lücke, Jörg
last_name: Lücke
citation:
ama: 'Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn
stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems;
2016:4285-4293.'
apa: 'Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic
plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented
at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural
Information Processing Systems.'
chicago: Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic
Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information
Processing Systems, 2016.
ieee: 'T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics,” presented at the NIPS: Neural Information
Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.'
ista: 'Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 4285–4293.'
mla: Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus
Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016,
pp. 4285–93.
short: T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems,
2016, pp. 4285–4293.
conference:
end_date: 2016-12-10
location: Barcelona, Spaine
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:49:21Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:08Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- url: https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics
month: '01'
oa_version: None
page: 4285 - 4293
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6469'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1262'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
acknowledgement: "This work was supported by the Federal Ministry of Food, Agriculture
and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10),
the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the
Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI
is funded jointly by the Biotechnology and Biological Sciences Research Council,
the Department for Environment, Food and Rural Affairs, the Natural Environment
Research Council, the Scottish Government and the Wellcome Trust, under the Living
with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A.
Soro\r\nfor support in obtaining\r\nV. destructor\r\n-free honeybees; and BBKA\r\nPresident
D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the
UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that
led to substantial\r\nimprovement of the manuscript."
article_number: '20160811'
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging
viral genotype as a driver of honeybee loss. Proceedings of the Royal Society
of London Series B Biological Sciences. 2016;283(1833). doi:10.1098/rspb.2016.0811
apa: Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver
of honeybee loss. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.0811
chicago: Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence
of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of
the Royal Society of London Series B Biological Sciences. Royal Society, The,
2016. https://doi.org/10.1098/rspb.2016.0811.
ieee: D. Mcmahon et al., “Elevated virulence of an emerging viral genotype
as a driver of honeybee loss,” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 283, no. 1833. Royal Society, The, 2016.
ista: Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver
of honeybee loss. Proceedings of the Royal Society of London Series B Biological
Sciences. 283(1833), 20160811.
mla: Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as
a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 283, no. 1833, 20160811, Royal Society, The, 2016,
doi:10.1098/rspb.2016.0811.
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological
Sciences 283 (2016).
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-29T00:00:00Z
date_updated: 2023-02-23T14:05:30Z
day: '29'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rspb.2016.0811
file:
- access_level: open_access
checksum: 0b0d1be38b497d004064650acb3baced
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:46Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4708'
file_name: IST-2016-701-v1+1_20160811.full.pdf
file_size: 796872
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 283'
issue: '1833'
language:
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month: '06'
oa: 1
oa_version: Published Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
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quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
scopus_import: 1
status: public
title: Elevated virulence of an emerging viral genotype as a driver of honeybee loss
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 283
year: '2016'
...
---
_id: '9704'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence
of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1'
apa: 'Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1'
chicago: 'Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated
Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad,
2016. https://doi.org/10.5061/dryad.cq7t1.'
ieee: 'D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral
genotype as a driver of honeybee loss.” Dryad, 2016.'
ista: 'Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.'
mla: 'Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral
Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.'
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, (2016).
date_created: 2021-07-23T08:30:38Z
date_published: 2016-05-06T00:00:00Z
date_updated: 2023-02-21T16:54:31Z
day: '06'
department:
- _id: SyCr
doi: 10.5061/dryad.cq7t1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.cq7t1
month: '05'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1262'
relation: used_in_publication
status: public
status: public
title: 'Data from: Elevated virulence of an emerging viral genotype as a driver of
honeybee loss'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1322'
abstract:
- lang: eng
text: Direct reciprocity is a major mechanism for the evolution of cooperation.
Several classical studies have suggested that humans should quickly learn to adopt
reciprocal strategies to establish mutual cooperation in repeated interactions.
On the other hand, the recently discovered theory of ZD strategies has found that
subjects who use extortionate strategies are able to exploit and subdue cooperators.
Although such extortioners have been predicted to succeed in any population of
adaptive opponents, theoretical follow-up studies questioned whether extortion
can evolve in reality. However, most of these studies presumed that individuals
have similar strategic possibilities and comparable outside options, whereas asymmetries
are ubiquitous in real world applications. Here we show with a model and an economic
experiment that extortionate strategies readily emerge once subjects differ in
their strategic power. Our experiment combines a repeated social dilemma with
asymmetric partner choice. In our main treatment there is one randomly chosen
group member who is unilaterally allowed to exchange one of the other group members
after every ten rounds of the social dilemma. We find that this asymmetric replacement
opportunity generally promotes cooperation, but often the resulting payoff distribution
reflects the underlying power structure. Almost half of the subjects in a better
strategic position turn into extortioners, who quickly proceed to exploit their
peers. By adapting their cooperation probabilities consistent with ZD theory,
extortioners force their co-players to cooperate without being similarly cooperative
themselves. Comparison to non-extortionate players under the same conditions indicates
a substantial net gain to extortion. Our results thus highlight how power asymmetries
can endanger mutually beneficial interactions, and transform them into exploitative
relationships. In particular, our results indicate that the extortionate strategies
predicted from ZD theory could play a more prominent role in our daily interactions
than previously thought.
acknowledgement: 'CH was funded by the Schrödinger program of the Austrian Science
Fund (FWF) J3475. '
article_number: e0163867
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Kristin
full_name: Hagel, Kristin
last_name: Hagel
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
citation:
ama: Hilbe C, Hagel K, Milinski M. Asymmetric power boosts extortion in an economic
experiment. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0163867
apa: Hilbe, C., Hagel, K., & Milinski, M. (2016). Asymmetric power boosts extortion
in an economic experiment. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867
chicago: Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Asymmetric Power
Boosts Extortion in an Economic Experiment.” PLoS One. Public Library of
Science, 2016. https://doi.org/10.1371/journal.pone.0163867.
ieee: C. Hilbe, K. Hagel, and M. Milinski, “Asymmetric power boosts extortion in
an economic experiment,” PLoS One, vol. 11, no. 10. Public Library of Science,
2016.
ista: Hilbe C, Hagel K, Milinski M. 2016. Asymmetric power boosts extortion in an
economic experiment. PLoS One. 11(10), e0163867.
mla: Hilbe, Christian, et al. “Asymmetric Power Boosts Extortion in an Economic
Experiment.” PLoS One, vol. 11, no. 10, e0163867, Public Library of Science,
2016, doi:10.1371/journal.pone.0163867.
short: C. Hilbe, K. Hagel, M. Milinski, PLoS One 11 (2016).
date_created: 2018-12-11T11:51:22Z
date_published: 2016-10-04T00:00:00Z
date_updated: 2023-02-23T14:11:27Z
day: '04'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0163867
file:
- access_level: open_access
checksum: 6b33e394003dfe8b4ca6be1858aaa8e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:08Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4668'
file_name: IST-2016-716-v1+1_journal.pone.0163867.PDF
file_size: 2077905
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5948'
pubrep_id: '716'
quality_controlled: '1'
related_material:
record:
- id: '9867'
relation: research_data
status: public
- id: '9868'
relation: research_data
status: public
scopus_import: 1
status: public
title: Asymmetric power boosts extortion in an economic experiment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1270'
abstract:
- lang: eng
text: A crucial step in the early development of multicellular organisms involves
the establishment of spatial patterns of gene expression which later direct proliferating
cells to take on different cell fates. These patterns enable the cells to infer
their global position within a tissue or an organism by reading out local gene
expression levels. The patterning system is thus said to encode positional information,
a concept that was formalized recently in the framework of information theory.
Here we introduce a toy model of patterning in one spatial dimension, which can
be seen as an extension of Wolpert's paradigmatic "French Flag" model,
to patterning by several interacting, spatially coupled genes subject to intrinsic
and extrinsic noise. Our model, a variant of an Ising spin system, allows us to
systematically explore expression patterns that optimally encode positional information.
We find that optimal patterning systems use positional cues, as in the French
Flag model, together with gene-gene interactions to generate combinatorial codes
for position which we call "Counter" patterns. Counter patterns can
also be stabilized against noise and variations in system size or morphogen dosage
by longer-range spatial interactions of the type invoked in the Turing model.
The simple setup proposed here qualitatively captures many of the experimentally
observed properties of biological patterning systems and allows them to be studied
in a single, theoretically consistent framework.
acknowledgement: The authors would like to thank Thomas Sokolowski and Filipe Tostevin
for helpful discussions. PH and UG were funded by the German Excellence Initiative
via the program "Nanosystems Initiative Munich" (https://www.nano-initiative-munich.de)
and the German Research Foundation via the SFB 1032 "Nanoagents for Spatiotemporal
Control of Molecular and Cellular Reactions" (http://www.sfb1032.physik.uni-muenchen.de).
GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).
article_number: e0163628
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting
spatial and gene regulatory interactions for positional information. PLoS One.
2016;11(9). doi:10.1371/journal.pone.0163628'
apa: 'Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag
model: Exploiting spatial and gene regulatory interactions for positional information.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628'
chicago: 'Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French
Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional
Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.'
ieee: 'P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model:
Exploiting spatial and gene regulatory interactions for positional information,”
PLoS One, vol. 11, no. 9. Public Library of Science, 2016.'
ista: 'Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting
spatial and gene regulatory interactions for positional information. PLoS One.
11(9), e0163628.'
mla: 'Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial
and Gene Regulatory Interactions for Positional Information.” PLoS One,
vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.'
short: P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
date_created: 2018-12-11T11:51:03Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-23T14:11:37Z
day: '27'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628
file:
- access_level: open_access
checksum: 3d0d55d373096a033bd9cf79288c8586
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:47Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4837'
file_name: IST-2016-696-v1+1_journal.pone.0163628.PDF
file_size: 4950415
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6050'
pubrep_id: '696'
quality_controlled: '1'
related_material:
record:
- id: '9869'
relation: research_data
status: public
- id: '9870'
relation: research_data
status: public
- id: '9871'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Beyond the French flag model: Exploiting spatial and gene regulatory interactions
for positional information'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1250'
abstract:
- lang: eng
text: In bacteria, replicative aging manifests as a difference in growth or survival
between the two cells emerging from division. One cell can be regarded as an aging
mother with a decreased potential for future survival and division, the other
as a rejuvenated daughter. Here, we aimed at investigating some of the processes
involved in aging in the bacterium Escherichia coli, where the two types of cells
can be distinguished by the age of their cell poles. We found that certain changes
in the regulation of the carbohydrate metabolism can affect aging. A mutation
in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative
lifespan; csrA mutants stop dividing once their pole exceeds an age of about five
divisions. These old-pole cells accumulate glycogen at their old cell poles; after
their last division, they do not contain a chromosome, presumably because of spatial
exclusion by the glycogen aggregates. The new-pole daughters produced by these
aging mothers are born young; they only express the deleterious phenotype once
their pole is old. These results demonstrate how manipulations of nutrient allocation
can lead to the exclusion of the chromosome and limit replicative lifespan in
E. coli, and illustrate how mutations can have phenotypic effects that are specific
for cells with old poles. This raises the question how bacteria can avoid the
accumulation of such mutations in their genomes over evolutionary times, and how
they can achieve the long replicative lifespans that have recently been reported.
acknowledgement: This manuscript is dedicated to the memory of Alex Böhm, who was
a great friend and a passionate biologist. Alex passed away after the initial submission
of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für
Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and
Nela Nikolic for helpful discussions. This work was supported by the Swiss National
Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).
article_number: e1005974
author:
- first_name: Alex
full_name: Boehm, Alex
last_name: Boehm
- first_name: Markus
full_name: Arnoldini, Markus
last_name: Arnoldini
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Thomas
full_name: Röösli, Thomas
last_name: Röösli
- first_name: Colette
full_name: Bigosch, Colette
last_name: Bigosch
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic
manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS
Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974
apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann,
M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan
in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974
chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects
Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science,
2016. https://doi.org/10.1371/journal.pgen.1005974.
ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
“Genetic manipulation of glycogen allocation affects replicative lifespan in E
coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.
ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
Genetic manipulation of glycogen allocation affects replicative lifespan in E
coli. PLoS Genetics. 12(4), e1005974.
mla: Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative
Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library
of Science, 2016, doi:10.1371/journal.pgen.1005974.
short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
PLoS Genetics 12 (2016).
date_created: 2018-12-11T11:50:56Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2023-02-23T14:11:39Z
day: '19'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974
file:
- access_level: open_access
checksum: 53d22b2b39e5adc243d34f18b2615a85
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:17Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5067'
file_name: IST-2016-705-v1+1_journal.pgen.1005974.PDF
file_size: 6273249
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6077'
pubrep_id: '705'
quality_controlled: '1'
related_material:
record:
- id: '9873'
relation: research_data
status: public
scopus_import: 1
status: public
title: Genetic manipulation of glycogen allocation affects replicative lifespan in
E coli
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '9870'
abstract:
- lang: eng
text: The effect of noise in the input field on an Ising model is approximated.
Furthermore, methods to compute positional information in an Ising model by transfer
matrices and Monte Carlo sampling are outlined.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in
an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional
information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of
Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information
in an Ising model.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information
in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002.
mla: Hillenbrand, Patrick, et al. Computation of Positional Information in an
Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T09:23:45Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s002
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Computation of positional information in an Ising model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9873'
article_processing_charge: No
author:
- first_name: Alex
full_name: Boehm, Alex
last_name: Boehm
- first_name: Markus
full_name: Arnoldini, Markus
last_name: Arnoldini
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Thomas
full_name: Röösli, Thomas
last_name: Röösli
- first_name: Colette
full_name: Bigosch, Colette
last_name: Bigosch
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification
of the growth rate reduction as a consequence of age-specific mortality. 2016.
doi:10.1371/journal.pgen.1005974.s015
apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann,
M. (2016). Quantification of the growth rate reduction as a consequence of age-specific
mortality. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974.s015
chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as
a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.s015.
ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
“Quantification of the growth rate reduction as a consequence of age-specific
mortality.” Public Library of Science, 2016.
ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
Quantification of the growth rate reduction as a consequence of age-specific mortality,
Public Library of Science, 10.1371/journal.pgen.1005974.s015.
mla: Boehm, Alex, et al. Quantification of the Growth Rate Reduction as a Consequence
of Age-Specific Mortality. Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.s015.
short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
(2016).
date_created: 2021-08-10T09:42:34Z
date_updated: 2023-02-21T16:50:13Z
day: '19'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974.s015
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1250'
relation: used_in_publication
status: public
status: public
title: Quantification of the growth rate reduction as a consequence of age-specific
mortality
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9869'
abstract:
- lang: eng
text: A lower bound on the error of a positional estimator with limited positional
information is derived.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position.
2016. doi:10.1371/journal.pone.0163628.s001
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator
of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on
an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of
position.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position,
Public Library of Science, 10.1371/journal.pone.0163628.s001.
mla: Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position.
Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T08:53:48Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Error bound on an estimator of position
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9871'
abstract:
- lang: eng
text: The positional information in a discrete morphogen field with Gaussian noise
is computed.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in
a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional
information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of
Positional Information in a Discrete Morphogen Field.” Public Library of Science,
2016. https://doi.org/10.1371/journal.pone.0163628.s003.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information
in a discrete morphogen field.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information
in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.
mla: Hillenbrand, Patrick, et al. Computation of Positional Information in a
Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T09:27:35Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s003
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Computation of positional information in a discrete morphogen field
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9868'
abstract:
- lang: eng
text: The raw data file containing the experimental decisions of all our study subjects.
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Kristin
full_name: Hagel, Kristin
last_name: Hagel
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
citation:
ama: Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:10.1371/journal.pone.0163867.s009
apa: Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental data. Public
Library of Science. https://doi.org/10.1371/journal.pone.0163867.s009
chicago: Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.”
Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s009.
ieee: C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of
Science, 2016.
ista: Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science,
10.1371/journal.pone.0163867.s009.
mla: Hilbe, Christian, et al. Experimental Data. Public Library of Science,
2016, doi:10.1371/journal.pone.0163867.s009.
short: C. Hilbe, K. Hagel, M. Milinski, (2016).
date_created: 2021-08-10T08:45:00Z
date_published: 2016-10-04T00:00:00Z
date_updated: 2023-02-21T16:59:01Z
day: '04'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0163867.s009
month: '10'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1322'
relation: used_in_publication
status: public
status: public
title: Experimental data
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1101'
abstract:
- lang: eng
text: Optical sensors based on the phenomenon of Förster resonance energy transfer
(FRET) are powerful tools that have advanced the study of small molecules in biological
systems. However, sensor construction is not trivial and often requires multiple
rounds of engineering or an ability to screen large numbers of variants. A method
that would allow the accurate rational design of FRET sensors would expedite the
production of biologically useful sensors. Here, we present Rangefinder, a computational
algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding
protein for the conjugation of a dye molecule to act as a Förster acceptor for
a fused fluorescent protein. We present three ratiometric fluorescent sensors
designed with Rangefinder, including a maltose sensor with a dynamic range of
>300% and the first sensors for the most abundant sialic acid in human cells,
N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation
that this model will facilitate the design of an optical sensor for any small
molecule of interest.
acknowledgement: "J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate
Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships.
C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator
Award and a Discovery Project and Future\r\nFellowship from the Australian Research
Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153)
and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure."
article_processing_charge: No
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET
sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576'
apa: 'Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L.,
O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor
design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576'
chicago: 'Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger,
Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic
FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society,
2016. https://doi.org/10.1021/acssensors.6b00576.'
ieee: 'J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design
algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp.
1286–1290, 2016.'
ista: 'Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS.
1(11), 1286–1290.'
mla: 'Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design
Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016,
pp. 1286–90, doi:10.1021/acssensors.6b00576.'
short: J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, ACS SENSORS 1 (2016) 1286–1290.
date_created: 2018-12-11T11:50:09Z
date_published: 2016-11-10T00:00:00Z
date_updated: 2023-03-30T11:32:33Z
day: '10'
department:
- _id: HaJa
doi: 10.1021/acssensors.6b00576
intvolume: ' 1'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1286 - 1290
publication: ACS SENSORS
publication_status: published
publisher: American Chemical Society
publist_id: '6274'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rangefinder: A semisynthetic FRET sensor design algorithm'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '12903'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling
the human hippocampus. In: AHPC16 - Austrian HPC Meeting 2016. VSC - Vienna
Scientific Cluster; 2016:37.'
apa: 'Schlögl, A., & Stadlbauer, S. (2016). High performance computing at IST
Austria: Modelling the human hippocampus. In AHPC16 - Austrian HPC Meeting
2016 (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.'
chicago: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at
IST Austria: Modelling the Human Hippocampus.” In AHPC16 - Austrian HPC Meeting
2016, 37. VSC - Vienna Scientific Cluster, 2016.'
ieee: 'A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria:
Modelling the human hippocampus,” in AHPC16 - Austrian HPC Meeting 2016,
Grundlsee, Austria, 2016, p. 37.'
ista: 'Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria:
Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian
HPC Meeting, 37.'
mla: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST
Austria: Modelling the Human Hippocampus.” AHPC16 - Austrian HPC Meeting 2016,
VSC - Vienna Scientific Cluster, 2016, p. 37.'
short: A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC -
Vienna Scientific Cluster, 2016, p. 37.
conference:
end_date: 2016-02-24
location: Grundlsee, Austria
name: 'AHPC: Austrian HPC Meeting'
start_date: 2016-02-22
date_created: 2023-05-05T12:54:47Z
date_published: 2016-02-24T00:00:00Z
date_updated: 2023-05-16T07:15:14Z
day: '24'
ddc:
- '000'
department:
- _id: ScienComp
- _id: PeJo
file:
- access_level: open_access
checksum: 4a7b00362e81358d568f5e216fa03c3e
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:03:56Z
date_updated: 2023-05-16T07:03:56Z
file_id: '12968'
file_name: 2016_AHPC_Schloegl.pdf
file_size: 1073523
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:03:56Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf
month: '02'
oa: 1
oa_version: Published Version
page: '37'
publication: AHPC16 - Austrian HPC Meeting 2016
publication_status: published
publisher: VSC - Vienna Scientific Cluster
quality_controlled: '1'
status: public
title: 'High performance computing at IST Austria: Modelling the human hippocampus'
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1341'
abstract:
- lang: eng
text: In resource allocation games, selfish players share resources that are needed
in order to fulfill their objectives. The cost of using a resource depends on
the load on it. In the traditional setting, the players make their choices concurrently
and in one-shot. That is, a strategy for a player is a subset of the resources.
We introduce and study dynamic resource allocation games. In this setting, the
game proceeds in phases. In each phase each player chooses one resource. A scheduler
dictates the order in which the players proceed in a phase, possibly scheduling
several players to proceed concurrently. The game ends when each player has collected
a set of resources that fulfills his objective. The cost for each player then
depends on this set as well as on the load on the resources in it – we consider
both congestion and cost-sharing games. We argue that the dynamic setting is the
suitable setting for many applications in practice. We study the stability of
dynamic resource allocation games, where the appropriate notion of stability is
that of subgame perfect equilibrium, study the inefficiency incurred due to selfish
behavior, and also study problems that are particular to the dynamic setting,
like constraints on the order in which resources can be chosen or the problem
of finding a scheduler that achieves stability.
acknowledgement: This research was supported in part by the European Research Council
(ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science
Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In:
Vol 9928. Springer; 2016:153-166. doi:10.1007/978-3-662-53354-3_13'
apa: 'Avni, G., Henzinger, T. A., & Kupferman, O. (2016). Dynamic resource allocation
games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic
Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_13'
chicago: Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation
Games,” 9928:153–66. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_13.
ieee: 'G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation
games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool,
United Kingdom, 2016, vol. 9928, pp. 153–166.'
ista: 'Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games.
SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.'
mla: Avni, Guy, et al. Dynamic Resource Allocation Games. Vol. 9928, Springer,
2016, pp. 153–66, doi:10.1007/978-3-662-53354-3_13.
short: G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.
conference:
end_date: 2016-09-21
location: Liverpool, United Kingdom
name: 'SAGT: Symposium on Algorithmic Game Theory'
start_date: 2016-09-19
date_created: 2018-12-11T11:51:28Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-08-17T13:52:49Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-53354-3_13
ec_funded: 1
file:
- access_level: open_access
checksum: 0825eefd4e22774f6f62cb7d7389b05a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:22Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5073'
file_name: IST-2016-645-v1+1_sagt-cr.pdf
file_size: 243458
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 9928'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 153 - 166
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5926'
pubrep_id: '645'
quality_controlled: '1'
related_material:
record:
- id: '6761'
relation: later_version
status: public
scopus_import: 1
status: public
title: Dynamic resource allocation games
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9928
year: '2016'
...
---
_id: '5749'
abstract:
- lang: eng
text: Parasitism creates selection for resistance mechanisms in host populations
and is hypothesized to promote increased host evolvability. However, the influence
of these traits on host evolution when parasites are no longer present is unclear.
We used experimental evolution and whole-genome sequencing of Escherichia coli
to determine the effects of past and present exposure to parasitic viruses (phages)
on the spread of mutator alleles, resistance, and bacterial competitive fitness.
We found that mutator alleles spread rapidly during adaptation to any of four
different phage species, and this pattern was even more pronounced with multiple
phages present simultaneously. However, hypermutability did not detectably accelerate
adaptation in the absence of phages and recovery of fitness costs associated with
resistance. Several lineages evolved phage resistance through elevated mucoidy,
and during subsequent evolution in phage-free conditions they rapidly reverted
to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this
phenotypic reversion was achieved by additional genetic changes rather than by
genotypic reversion of the initial resistance mutations. Insertion sequence (IS)
elements played a key role in both the acquisition of resistance and adaptation
in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions
were not more frequent in mutator lineages. Our results provide a genetic explanation
for rapid reversion of mucoidy, a phenotype observed in other bacterial species
including human pathogens. Moreover, this demonstrates that the types of genetic
change underlying adaptation to fitness costs, and consequently the impact of
evolvability mechanisms such as increased point-mutation rates, depend critically
on the mechanism of resistance.
acknowledgement: The authors thank three anonymous reviewers and the editor for helpful
comments on the manuscript, as well as Dominique Schneider for feedback on an earlier
draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was
supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an
EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824
to S.W.).
article_processing_charge: No
author:
- first_name: Sébastien
full_name: Wielgoss, Sébastien
last_name: Wielgoss
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M.
full_name: Bischofberger, Anna M.
last_name: Bischofberger
- first_name: Alex R.
full_name: Hall, Alex R.
last_name: Hall
citation:
ama: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites
and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
Biology and Evolution. 2016;33(3):770-782. doi:10.1093/molbev/msv270
apa: Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2016).
Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
bacteria. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv270
chicago: Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex
R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator
and Nonmutator Bacteria.” Molecular Biology and Evolution. Oxford University
Press, 2016. https://doi.org/10.1093/molbev/msv270.
ieee: S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation
to parasites and costs of parasite resistance in mutator and nonmutator bacteria,”
Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press,
pp. 770–782, 2016.
ista: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites
and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
Biology and Evolution. 33(3), 770–782.
mla: Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite
Resistance in Mutator and Nonmutator Bacteria.” Molecular Biology and Evolution,
vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:10.1093/molbev/msv270.
short: S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology
and Evolution 33 (2016) 770–782.
date_created: 2018-12-18T13:18:10Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-05T13:46:05Z
day: '01'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/molbev/msv270
external_id:
pmid:
- '26609077'
file:
- access_level: open_access
checksum: 47d9010690b6c5c17f2ac830cc63ac5c
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:21:45Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5750'
file_name: 2016_MolBiolEvol_Wielgoss.pdf
file_size: 634037
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 770-782
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
pubrep_id: '587'
quality_controlled: '1'
related_material:
record:
- id: '9719'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
bacteria
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 33
year: '2016'
...
---
_id: '1094'
abstract:
- lang: eng
text: Immunogold labeling of freeze-fracture replicas has recently been used for
high-resolution visualization of protein localization in electron microscopy.
This method has higher labeling efficiency than conventional immunogold methods
for membrane molecules allowing precise quantitative measurements. However, one
of the limitations of freeze-fracture replica immunolabeling is difficulty in
keeping structural orientation and identifying labeled profiles in complex tissues
like brain. The difficulty is partly due to fragmentation of freeze-fracture replica
preparations during labeling procedures and limited morphological clues on the
replica surface. To overcome these issues, we introduce here a grid-glued replica
method combined with SEM observation. This method allows histological staining
before dissolving the tissue and easy handling of replicas during immunogold labeling,
and keeps the whole replica surface intact without fragmentation. The procedure
described here is also useful for matched double-replica analysis allowing further
identification of labeled profiles in corresponding P-face and E-face.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body
used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron
microscope imaging. This work was supported by the European Union (HBP—Project Ref.
604102). '
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture
replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer;
2016:203-216. doi:10.1007/978-1-4939-6352-2_12'
apa: Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on
grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular
Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12
chicago: Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization
on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular
Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.
ieee: H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued
freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins,
vol. 1474, Springer, 2016, pp. 203–216.
ista: 'Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued
freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods
in Molecular Biology, vol. 1474, 203–216.'
mla: Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on
Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins,
vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12.
short: H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins,
Springer, 2016, pp. 203–216.
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-12T00:00:00Z
date_updated: 2023-09-05T14:09:01Z
day: '12'
department:
- _id: RySh
doi: 10.1007/978-1-4939-6352-2_12
ec_funded: 1
intvolume: ' 1474'
language:
- iso: eng
month: '08'
oa_version: None
page: 203 - 216
project:
- _id: 25CD3DD2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '604102'
name: Localization of ion channels and receptors by two and three-dimensional immunoelectron
microscopic approaches
publication: High-Resolution Imaging of Cellular Proteins
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6281'
quality_controlled: '1'
status: public
title: Immunogold protein localization on grid-glued freeze-fracture replicas
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1474
year: '2016'
...
---
_id: '1121'
abstract:
- lang: eng
text: "Horizontal gene transfer (HGT), the lateral acquisition of genes across existing
species\r\nboundaries, is a major evolutionary force shaping microbial genomes
that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial
drugs. As such,\r\nunderstanding the mechanisms and constraints that determine
the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and
to design better strategies to\r\novercome the challenges that originate from
it.\r\nFollowing the insertion and expression of a newly transferred gene, the
success of an\r\nHGT event will depend on the fitness effect it has on the recipient
(host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition
of a population critically\r\ndepends on the distribution of fitness effects (DFE)
of horizontally transferred genes.\r\nHowever, to date, we have little knowledge
of the DFE of newly transferred genes, and\r\nhence little is known about the
shape and scale of this distribution.\r\nIt is particularly important to better
understand the selective barriers that determine\r\nthe fitness effects of newly
transferred genes. In spite of substantial bioinformatics\r\nefforts to identify
horizontally transferred genes and selective barriers, a systematic\r\nexperimental
approach to elucidate the roles of different selective barriers in defining\r\nthe
fate of a transfer event has largely been absent. Similarly, although the fact
that\r\nenvironment might alter the fitness effect of a horizontally transferred
gene may seem\r\nobvious, little attention has been given to it in a systematic
experimental manner.\r\nIn this study, we developed a systematic experimental
approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium
orthologous genes into an\r\nEscherichia coli host, and estimating the fitness
effects of these transferred genes at a\r\nconstant expression level by performing
competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one
competition assays between a mutant strain\r\ncarrying a transferred gene and
the wild type strain. By using flow cytometry we\r\nestimated selection coefficients
for the transferred genes with a precision level of 10-3,and obtained the DFE
of horizontally transferred genes. We then investigated if these\r\nfitness effects
could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional
category, degree of complexity (protein-protein interactions), GC content,\r\ncodon
usage and length. Our analyses revealed that the functional category and length\r\nof
the genes act as potential selective barriers. Finally, using the same procedure
with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that
gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3,
using the same set of genes we investigated the role of environment on the\r\nsuccess
of HGT events. Under six different environments with different levels of stress\r\nwe
performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying
transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes
relative to wild type we used next generation sequencing. We found that the DFEs\r\nof
horizontally transferred genes are highly dependent on the environment, with\r\nabundant
gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship
between average fitness effect of a gene across all environments and its\r\nenvironmental
variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof
genes being highly environment-dependent, we still observed a common shape of\r\nDFEs
across all tested environments."
acknowledgement: "This study was supported by European Research Council ERC CoG 2014
– EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the
many people who made this thesis possible.\r\nI would like to first thank my advisor,
Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement,
sound advice, and good teaching over the last six\r\nyears.\r\nI would also like
to thank the members of my dissertation committee – Călin C. Guet\r\nand John F.
Baines – not only for their time and guidance, but for their intellectual\r\ncontributions
to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo
Redondo who have taught me all the\r\nskills in the laboratory with their graciousness
and friendship. Also special thanks to\r\nBollback group for their support and for
providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse,
Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant,
she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness
to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters
a lot."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
citation:
ama: Acar H. Selective barriers to horizontal gene transfer. 2016.
apa: Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute
of Science and Technology Austria.
chicago: Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute
of Science and Technology Austria, 2016.
ieee: H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science
and Technology Austria, 2016.
ista: Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of
Science and Technology Austria.
mla: Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute
of Science and Technology Austria, 2016.
short: H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science
and Technology Austria, 2016.
date_created: 2018-12-11T11:50:16Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2023-09-07T11:42:26Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoBo
ec_funded: 1
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language:
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month: '12'
oa: 1
oa_version: Published Version
page: '75'
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6239'
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
title: Selective barriers to horizontal gene transfer
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1662'
abstract:
- lang: eng
text: We introduce a modification of the classic notion of intrinsic volume using
persistence moments of height functions. Evaluating the modified first intrinsic
volume on digital approximations of a compact body with smoothly embedded boundary
in Rn, we prove convergence to the first intrinsic volume of the body as the resolution
of the approximation improves. We have weaker results for the other modified intrinsic
volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional
unit ball.
acknowledgement: "This research is partially supported by the Toposys project FP7-ICT-318493-STREP,
and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne
Marie Svane for her comments on an early version of this paper. The second author
wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for
enlightening discussions and their kind hospitality during a visit of their department
in 2014."
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic
volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004
apa: Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence
of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence
of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016.
https://doi.org/10.1016/j.aim.2015.10.004.
ieee: H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic
volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703,
2016.
ista: Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic
volume. Advances in Mathematics. 287, 674–703.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence
of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press,
2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004.
short: H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.
date_created: 2018-12-11T11:53:20Z
date_published: 2016-01-10T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '10'
ddc:
- '004'
department:
- _id: HeEd
doi: 10.1016/j.aim.2015.10.004
ec_funded: 1
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oa: 1
oa_version: Published Version
page: 674 - 703
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Advances in Mathematics
publication_status: published
publisher: Academic Press
publist_id: '5488'
pubrep_id: '774'
quality_controlled: '1'
related_material:
record:
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Approximation and convergence of the intrinsic volume
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 287
year: '2016'
...
---
_id: '1128'
abstract:
- lang: eng
text: "The process of gene expression is central to the modern understanding of
how cellular systems\r\nfunction. In this process, a special kind of regulatory
proteins, called transcription factors,\r\nare important to determine how much
protein is produced from a given gene. As biological\r\ninformation is transmitted
from transcription factor concentration to mRNA levels to amounts of\r\nprotein,
various sources of noise arise and pose limits to the fidelity of intracellular
signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene
expression: (i) the mathematical\r\ndescription of complex promoters responsible
for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information
processing the cell faces due to the interference from multiple\r\nfluctuating
signals, (iii) how the presence of gene expression noise influences the evolution\r\nof
regulatory sequences, (iv) and tools for the experimental study of origins and
consequences\r\nof cell-cell heterogeneity, including an application to bacterial
stress response systems."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
citation:
ama: Rieckh G. Studying the complexities of transcriptional regulation. 2016.
apa: Rieckh, G. (2016). Studying the complexities of transcriptional regulation.
Institute of Science and Technology Austria.
chicago: Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.”
Institute of Science and Technology Austria, 2016.
ieee: G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute
of Science and Technology Austria, 2016.
ista: Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute
of Science and Technology Austria.
mla: Rieckh, Georg. Studying the Complexities of Transcriptional Regulation.
Institute of Science and Technology Austria, 2016.
short: G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute
of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:18Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T11:44:34Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GaTk
file:
- access_level: closed
checksum: ec453918c3bf8e6f460fd1156ef7b493
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language:
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month: '08'
oa: 1
oa_version: Published Version
page: '114'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6232'
status: public
supervisor:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
title: Studying the complexities of transcriptional regulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1124'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maurizio
full_name: Morri, Maurizio
id: 4863116E-F248-11E8-B48F-1D18A9856A87
last_name: Morri
citation:
ama: Morri M. Optical functionalization of human class A orphan G-protein coupled
receptors. 2016.
apa: Morri, M. (2016). Optical functionalization of human class A orphan G-protein
coupled receptors. Institute of Science and Technology Austria.
chicago: Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein
Coupled Receptors.” Institute of Science and Technology Austria, 2016.
ieee: M. Morri, “Optical functionalization of human class A orphan G-protein coupled
receptors,” Institute of Science and Technology Austria, 2016.
ista: Morri M. 2016. Optical functionalization of human class A orphan G-protein
coupled receptors. Institute of Science and Technology Austria.
mla: Morri, Maurizio. Optical Functionalization of Human Class A Orphan G-Protein
Coupled Receptors. Institute of Science and Technology Austria, 2016.
short: M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled
Receptors, Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-07T11:43:03Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: HaJa
file:
- access_level: closed
checksum: b439803ac0827cdddd56562a54e3b53b
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T10:50:00Z
date_updated: 2019-08-13T10:50:00Z
file_id: '6812'
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creator: dernst
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date_updated: 2021-02-22T11:42:06Z
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file_name: 2016_MORRI_Thesis.pdf
file_size: 4495669
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:42:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '129'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6236'
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Optical functionalization of human class A orphan G-protein coupled receptors
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1129'
abstract:
- lang: eng
text: "Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms.
Despite its importance, basic questions regarding force transduction\r\nor directional
sensing are still heavily investigated. Directed migration of cells\r\nguided
by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as
embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al.,
2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise
adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009),
or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton
et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment
sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic
migration by inducing adhesion to adhesive ligands and directional\r\nguidance
(Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the
cellular response to immobilized guidance cues requires in vitro assays\r\nthat
foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular
scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration
of haptotactic cell migration through design and employment of such\r\nassays
represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes,
which after encountering danger\r\nsignals such as pathogens in peripheral organs
instruct naïve T-cells and\r\nconsequently the adaptive immune response in the
lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery,
DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber
et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients
have not yet been addressed. The main reason for this is the lack of\r\nan assay
that offers diverse haptotactic environments, hence allowing the study\r\nof DC
migration as a response to different signals of immobilized guidance cue.\r\nIn
this work, we developed an in vitro assay that enables us to\r\nquantitatively
assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning
with physically confining migration conditions. With this tool at hand, we studied
the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis.
We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration
in combination with the local\r\nsteepness of the gradient. Our analysis suggests
that the directionality of\r\nmigrating DCs is governed by the signal-to-noise
ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21
gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic
guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also
able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To
this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which
is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization
(Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial
for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm
those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic
guidance cues\r\noften coincide and compete with soluble chemotactic guidance
cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive
cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating
DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing
chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess
these complex coinciding immobilized and soluble\r\nguidance cues, we implemented
our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing
for chemotactic gradient generation. To validate\r\nthe assay, we observed DC
migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis
has been studied intensively over the\r\nlast century. However, quantitative studies
leading to conceptual models are\r\nlargely missing, again due to the lack of
a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro
assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished
by stable passivation of the surface. In\r\naddition, controlled adhesion must
be sustainable, quantifiable and dose\r\ndependent in order to create homogenous
gradients. Therefore, we developed a novel covalent photo-patterning technique
satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol
(PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to
direct cell migration. This\r\napproach allowed us to characterize the haptotactic
migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined
patterns of adhesive cue\r\nallowed us to control for cell shape and growth on
a subcellular scale."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
acknowledgement: "First, I would like to thank Michael Sixt for being a great supervisor,
mentor and\r\nscientist. I highly appreciate his guidance and continued support.
Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to
pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe
sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel
Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice
and encouragement during our regular progress meetings.\r\nI also want to thank
the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for
amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant
factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere
as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank
my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries,
Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf,
Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz,
Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing
time with many\r\nlegendary evenings and events. Along these lines I want to thank
the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions.
I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank
the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches.
In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens,
Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny,
Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful
after-lunch matches.\r\nI would not have been able to analyze the thousands of cell
trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration
with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings,
discussions and graphs and of course for proofreading and\r\nadvice for this thesis.
For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like
to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing
me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS
coated coverslips and help with anything\r\nmicro-fabrication related. And Maria
Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her
it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva,
Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility
as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for
excellent technical support. At this\r\npoint I especially want to thank Robert
for countless image analyses and\r\ntechnical ideas. Always interested and creative
he played an essential role in all\r\nof my projects.\r\nAdditionally I want to
thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for
scientific and especially mental support in all\r\nthose years, countless coffee
sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
citation:
ama: Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.
apa: Schwarz, J. (2016). Quantitative analysis of haptotactic cell migration.
Institute of Science and Technology Austria.
chicago: Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute
of Science and Technology Austria, 2016.
ieee: J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute
of Science and Technology Austria, 2016.
ista: Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute
of Science and Technology Austria.
mla: Schwarz, Jan. Quantitative Analysis of Haptotactic Cell Migration. Institute
of Science and Technology Austria, 2016.
short: J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute
of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:18Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T11:54:33Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
file:
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creator: dernst
date_created: 2019-08-13T10:55:35Z
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '178'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6231'
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: Quantitative analysis of haptotactic cell migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1126'
abstract:
- lang: eng
text: "Traditionally machine learning has been focusing on the problem of solving
a single\r\ntask in isolation. While being quite well understood, this approach
disregards an\r\nimportant aspect of human learning: when facing a new problem,
humans are able to\r\nexploit knowledge acquired from previously learned tasks.
Intuitively, access to several\r\nproblems simultaneously or sequentially could
also be advantageous for a machine\r\nlearning system, especially if these tasks
are closely related. Indeed, results of many\r\nempirical studies have provided
justification for this intuition. However, theoretical\r\njustifications of this
idea are rather limited.\r\nThe focus of this thesis is to expand the understanding
of potential benefits of information\r\ntransfer between several related learning
problems. We provide theoretical\r\nanalysis for three scenarios of multi-task
learning - multiple kernel learning, sequential\r\nlearning and active task selection.
We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate
how the task generation process influences the generalization\r\nguarantees in
this scenario. In addition, we show how some of the obtained\r\ntheoretical results
can be used to derive principled multi-task and lifelong learning\r\nalgorithms
and illustrate their performance on various synthetic and real-world datasets."
acknowledgement: "First and foremost I would like to express my gratitude to my supervisor,
Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of
doing research\r\n(including English grammar), for your trust in my capabilities
and endless support. Thank\r\nyou for granting me freedom in my research and, at
the same time, having time and\r\nhelping me cope with the consequences whenever
I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it
was a great pleasure and honor to be a part of\r\nit. There could not have been
a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming
me into his group at the University of Waterloo,\r\nfor inspiring discussions and
support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth
Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful
collaboration and for taking care of me during that not-so-sunny month of May.\r\nI
thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding
me with insightful comments.\r\nI would like to thank my colleagues for their support,
entertaining conversations and\r\nendless table soccer games we shared together:
Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas,
Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank
you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to
Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo.
Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring
and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST
administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost
of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible
without funding from the European\r\nResearch Council under the European Union's
Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
citation:
ama: Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:10.15479/AT:ISTA:TH_776
apa: Pentina, A. (2016). Theoretical foundations of multi-task lifelong learning.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_776
chicago: Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_776.
ieee: A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute
of Science and Technology Austria, 2016.
ista: Pentina A. 2016. Theoretical foundations of multi-task lifelong learning.
Institute of Science and Technology Austria.
mla: Pentina, Anastasia. Theoretical Foundations of Multi-Task Lifelong Learning.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_776.
short: A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute
of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-09-07T11:52:03Z
day: '01'
ddc:
- '006'
degree_awarded: PhD
department:
- _id: ChLa
doi: 10.15479/AT:ISTA:TH_776
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:07Z
date_updated: 2018-12-12T10:14:07Z
file_id: '5056'
file_name: IST-2017-776-v1+1_Pentina_Thesis_2016.pdf
file_size: 2140062
relation: main_file
file_date_updated: 2018-12-12T10:14:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '127'
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6234'
pubrep_id: '776'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Theoretical foundations of multi-task lifelong learning
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1397'
abstract:
- lang: eng
text: 'We study partially observable Markov decision processes (POMDPs) with objectives
used in verification and artificial intelligence. The qualitative analysis problem
given a POMDP and an objective asks whether there is a strategy (policy) to ensure
that the objective is satisfied almost surely (with probability 1), resp. with
positive probability (with probability greater than 0). For POMDPs with limit-average
payoff, where a reward value in the interval [0,1] is associated to every transition,
and the payoff of an infinite path is the long-run average of the rewards, we
consider two types of path constraints: (i) a quantitative limit-average constraint
defines the set of paths where the payoff is at least a given threshold L1 = 1.
Our main results for qualitative limit-average constraint under almost-sure winning
are as follows: (i) the problem of deciding the existence of a finite-memory controller
is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory
controller is undecidable. For quantitative limit-average constraints we show
that the problem of deciding the existence of a finite-memory controller is undecidable.
We present a prototype implementation of our EXPTIME algorithm. For POMDPs with
w-regular conditions specified as parity objectives, while the qualitative analysis
problems are known to be undecidable even for very special case of parity objectives,
we establish decidability (with optimal complexity) of the qualitative analysis
problems for POMDPs with parity objectives under finite-memory strategies. We
establish optimal (exponential) memory bounds and EXPTIME-completeness of the
qualitative analysis problems under finite-memory strategies for POMDPs with parity
objectives. Based on our theoretical algorithms we also present a practical approach,
where we design heuristics to deal with the exponential complexity, and have applied
our implementation on a number of well-known POMDP examples for robotics applications.
For POMDPs with a set of target states and an integer cost associated with every
transition, we study the optimization objective that asks to minimize the expected
total cost of reaching a state in the target set, while ensuring that the target
set is reached almost surely. We show that for general integer costs approximating
the optimal cost is undecidable. For positive costs, our results are as follows:
(i) we establish matching lower and upper bounds for the optimal cost, both double
and exponential in the POMDP state space size; (ii) we show that the problem of
approximating the optimal cost is decidable and present approximation algorithms
that extend existing algorithms for POMDPs with finite-horizon objectives. We
show experimentally that it performs well in many examples of interest. We study
more deeply the problem of almost-sure reachability, where given a set of target
states, the question is to decide whether there is a strategy to ensure that the
target set is reached almost surely. While in general the problem EXPTIME-complete,
in many practical cases strategies with a small amount of memory suffice. Moreover,
the existing solution to the problem is explicit, which first requires to construct
explicitly an exponential reduction to a belief-support MDP. We first study the
existence of observation-stationary strategies, which is NP-complete, and then
small-memory strategies. We present a symbolic algorithm by an efficient encoding
to SAT and using a SAT solver for the problem. We report experimental results
demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized
POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents
operate in an uncertain environment independently to achieve a joint objective.
In this work we consider Goal DEC-POMDPs, where given a set of target states,
the objective is to ensure that the target set is reached with minimal cost. We
consider the indefinite-horizon (infinite-horizon with either discounted-sum,
or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present
a new and novel method to solve the problem that extends methods for finite-horizon
DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present
experimental results on several examples, and show that our approach presents
promising results. In the end we present a short summary of a few other results
related to verification of MDPs and POMDPs.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chmelik M. Algorithms for partially observable markov decision processes. 2016.
apa: Chmelik, M. (2016). Algorithms for partially observable markov decision
processes. Institute of Science and Technology Austria.
chicago: Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.”
Institute of Science and Technology Austria, 2016.
ieee: M. Chmelik, “Algorithms for partially observable markov decision processes,”
Institute of Science and Technology Austria, 2016.
ista: Chmelik M. 2016. Algorithms for partially observable markov decision processes.
Institute of Science and Technology Austria.
mla: Chmelik, Martin. Algorithms for Partially Observable Markov Decision Processes.
Institute of Science and Technology Austria, 2016.
short: M. Chmelik, Algorithms for Partially Observable Markov Decision Processes,
Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2023-09-07T11:54:58Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
language:
- iso: eng
month: '02'
oa_version: None
page: '232'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5810'
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Algorithms for partially observable markov decision processes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1123'
abstract:
- lang: eng
text: "Motivated by topological Tverberg-type problems in topological combinatorics
and by classical\r\nresults about embeddings (maps without double points), we
study the question whether a finite\r\nsimplicial complex K can be mapped into
Rd without triple, quadruple, or, more generally, r-fold points (image points
with at least r distinct preimages), for a given multiplicity r ≤ 2. In particular,
we are interested in maps f : K → Rd that have no global r -fold intersection
points, i.e., no r -fold points with preimages in r pairwise disjoint simplices
of K , and we seek necessary and sufficient conditions for the existence of such
maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results
for embeddings, in particular of the completeness of the Van Kampen obstruction
\ for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically,
we show that under suitable restrictions on the dimensions(viz., if dimK = (r
≥ 1)k and d = rk \\ for some k ≥ 3), a well-known deleted product criterion
(DPC ) is not only necessary but also sufficient for the existence of maps without
global r -fold points. Our main technical tool is a higher-multiplicity version
of the classical Whitney trick , by which pairs of isolated r -fold points of
opposite sign can be eliminated by local modiffications of the map, assuming
codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that
suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence
of equivariant maps, might yield an approach to disproving the remaining open
cases of the the long-standing topological Tverberg conjecture , i.e., to construct
maps from the N -simplex σN to Rd without r-Tverberg points when r not a prime
power and\r\nN = (d + 1)(r – 1). Unfortunately, our proof of the sufficiency
of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K =
σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension
3 obstacle" and\r\nto construct the first counterexamples to the topological
Tverberg conjecture for all parameters(d; r ) with d ≥ 3r + 1 and r not a prime
power, by a reduction1 to a suitable lower-dimensional skeleton, for which the
codimension 3 restriction is satisfied and maps without r -Tverberg points exist
by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present
a different construction (which does not use the constraint method) that yields
counterexamples for d ≥ 3r , r not a prime power. "
acknowledgement: "Foremost, I would like to thank Uli Wagner for introducing me to
the exciting interface between\r\ntopology and combinatorics, and for our subsequent
years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection
points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy
Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and
IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril
Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek
Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand
Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner
and Roman Karasev\r\nfor their careful reading of the present manuscript and for
the many improvements they suggested."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
citation:
ama: 'Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney
trick for the topological Tverberg conjecture. 2016.'
apa: 'Mabillard, I. (2016). Eliminating higher-multiplicity intersections: an
r-fold Whitney trick for the topological Tverberg conjecture. Institute of
Science and Technology Austria.'
chicago: 'Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold
Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and
Technology Austria, 2016.'
ieee: 'I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney
trick for the topological Tverberg conjecture,” Institute of Science and Technology
Austria, 2016.'
ista: 'Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold
Whitney trick for the topological Tverberg conjecture. Institute of Science and
Technology Austria.'
mla: 'Mabillard, Isaac. Eliminating Higher-Multiplicity Intersections: An r-Fold
Whitney Trick for the Topological Tverberg Conjecture. Institute of Science
and Technology Austria, 2016.'
short: 'I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney
Trick for the Topological Tverberg Conjecture, Institute of Science and Technology
Austria, 2016.'
date_created: 2018-12-11T11:50:16Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T11:56:28Z
day: '01'
ddc:
- '500'
degree_awarded: PhD
department:
- _id: UlWa
file:
- access_level: closed
checksum: 2d140cc924cd1b764544906fc22684ef
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T08:45:27Z
date_updated: 2019-08-13T08:45:27Z
file_id: '6809'
file_name: Thesis_final version_Mabillard_w_signature_page.pdf
file_size: 2227916
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checksum: 2d140cc924cd1b764544906fc22684ef
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:36:34Z
date_updated: 2021-02-22T11:36:34Z
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file_date_updated: 2021-02-22T11:36:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '55'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6237'
related_material:
record:
- id: '2159'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: 'Eliminating higher-multiplicity intersections: an r-fold Whitney trick for
the topological Tverberg conjecture'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1432'
abstract:
- lang: eng
text: CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory
storage and pattern completion. Whether the plasticity properties of these synapses
are consistent with their proposed network functions remains unclear. Here, we
examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3
synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs)
and action potentials (APs) induces long-term potentiation (LTP), independent
of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms).
Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear
summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs)
following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and
EPSPs summate with dendritic ADPs. In autoassociative network models, storage
and recall are more robust with symmetric than with asymmetric STDP rules. Thus,
a specialized STDP induction rule allows reliable storage and recall of information
in the hippocampal CA3 network.
acknowledgement: 'We thank Jozsef Csicsvari and Nelson Spruston for critically reading
the manuscript. We also thank A. Schlögl for programming, F. Marr for technical
assistance and E. Kramberger for manuscript editing. '
article_number: '11552'
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity
at CA3–CA3 synapses optimizes storage and recall in autoassociative networks.
Nature Communications. 2016;7. doi:10.1038/ncomms11552
apa: Mishra, R. K., Kim, S., Guzmán, J., & Jonas, P. M. (2016). Symmetric spike
timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in
autoassociative networks. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/ncomms11552
chicago: Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric
Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall
in Autoassociative Networks.” Nature Communications. Nature Publishing
Group, 2016. https://doi.org/10.1038/ncomms11552.
ieee: R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks. Nature Communications. 7, 11552.
mla: Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at
CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” Nature
Communications, vol. 7, 11552, Nature Publishing Group, 2016, doi:10.1038/ncomms11552.
short: R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:59Z
date_published: 2016-05-13T00:00:00Z
date_updated: 2023-09-07T11:55:25Z
day: '13'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/ncomms11552
ec_funded: 1
file:
- access_level: open_access
checksum: 7e84d0392348c874d473b62f1042de22
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:33Z
date_updated: 2020-07-14T12:44:53Z
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file_name: IST-2016-582-v1+1_ncomms11552.pdf
file_size: 4510512
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5766'
pubrep_id: '582'
quality_controlled: '1'
related_material:
record:
- id: '1396'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage
and recall in autoassociative networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1396'
abstract:
- lang: eng
text: CA3 pyramidal neurons are thought to pay a key role in memory storage and
pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent
excitatory synapses. To examine the induction rules of synaptic plasticity at
CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal
slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory
postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum
oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced
N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although
LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel
blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute
to LTP induction without requirement of a somatic action potential (AP). We next
examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3
synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action
potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was
symmetric and broad, with a half-width of ~150 ms. Consistent with these specific
STDP induction properties, post-presynaptic sequences led to a supralinear summation
of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage
and recall was substantially more robust with symmetric than with asymmetric STDP
rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral
synapses with distinct induction rules. LTP induced by HFS may be associated with
dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic
activity induced LTP only if EPSP-AP were temporally very close. Together, these
induction mechanisms of synaptiic plasticity may contribute to memory storage
in the CA3-CA3 microcircuit at different ranges of activity.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
citation:
ama: Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus.
2016.
apa: Mishra, R. K. (2016). Synaptic plasticity rules at CA3-CA3 recurrent synapses
in hippocampus. Institute of Science and Technology Austria.
chicago: Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses
in Hippocampus.” Institute of Science and Technology Austria, 2016.
ieee: R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in
hippocampus,” Institute of Science and Technology Austria, 2016.
ista: Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in
hippocampus. Institute of Science and Technology Austria.
mla: Mishra, Rajiv Kumar. Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses
in Hippocampus. Institute of Science and Technology Austria, 2016.
short: R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus,
Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:46Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-07T11:55:26Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
file:
- access_level: closed
checksum: 5a010a838faf040f7064f3cfb802f743
content_type: application/pdf
creator: dernst
date_created: 2019-08-09T12:14:46Z
date_updated: 2020-07-14T12:44:48Z
file_id: '6782'
file_name: Thesis_Mishra_Rajiv (Final).pdf
file_size: 2407572
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date_created: 2021-02-22T11:48:44Z
date_updated: 2021-02-22T11:48:44Z
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language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5811'
related_material:
record:
- id: '1432'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1125'
abstract:
- lang: eng
text: "Natural environments are never constant but subject to spatial and temporal
change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial
to understand the\r\nimpact of environmental variation on evolutionary processes.
In this thesis, I present\r\nthree topics that share the common theme of environmental
variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst,
I show how a temporally fluctuating environment gives rise to second-order\r\nselection
on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations
are adapted to their environment, mutation rates are minimized. I argue\r\nthat
a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly
subjected to diverse environmental challenges, and I outline implications of\r\nthe
presented results to antibiotic treatment strategies.\r\nSecond, I discuss my
work on the evolution of dispersal. Besides reproducing\r\nknown results about
the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes
in dispersal type frequencies as a source for selection for increased\r\npropensities
to disperse. This concept contains effects of relatedness that are known\r\nto
promote dispersal, and I explain how it identifies other forces selecting for
dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances
of phenotypic traits under multivariate stabilizing\r\nselection. For the case
of constant environments, I generalize known formulae of\r\nequilibrium variances
to multiple traits and discuss how the genetic variance of a focal\r\ntrait is
influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary
work aiming at including environmental fluctuations in the form of moving\r\ntrait
optima into the model."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Evolutionary proccesses in variable emvironments. 2016.
apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments.
Institute of Science and Technology Austria.
chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute
of Science and Technology Austria, 2016.
ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of
Science and Technology Austria, 2016.
ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute
of Science and Technology Austria.
mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments.
Institute of Science and Technology Austria, 2016.
short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T09:01:00Z
date_updated: 2019-08-13T09:01:00Z
file_id: '6811'
file_name: Novak_thesis.pdf
file_size: 3564901
relation: main_file
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checksum: 30808d2f7ca920e09f63a95cdc49bffd
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T13:42:47Z
date_updated: 2021-02-22T13:42:47Z
file_id: '9186'
file_name: 2016_Novak_Thesis.pdf
file_size: 2814384
relation: main_file
success: 1
file_date_updated: 2021-02-22T13:42:47Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1130'
abstract:
- lang: eng
text: "In this thesis we present a computer-aided programming approach to concurrency.
Our approach helps the programmer by automatically fixing concurrency-related
bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive
scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are
program behaviours that are incorrect w.r.t. a specification. We consider both
user-provided explicit specifications in the form of assertion\r\nstatements in
the code as well as an implicit specification. The implicit specification is inferred
from the non-preemptive behaviour. Let us consider sequences of calls that the
program makes to an external interface. The implicit specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We consider several
semantics-preserving fixes that go beyond atomic sections typically explored in
the synchronisation synthesis literature. Our synthesis is able to place locks,
barriers and wait-signal statements and last, but not least reorder independent
statements. The latter may be useful if a thread is released to early, e.g., before
some initialisation is completed. We guarantee that our synthesis does not introduce
deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective
function. We dub our solution trace-based synchronisation synthesis and it is
loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis
works by discovering a trace that is incorrect w.r.t. the specification and identifying
ordering constraints crucial to trigger the specification violation. Synchronisation
may be placed immediately (greedy approach) or delayed until all incorrect traces
are found (non-greedy approach). For the non-greedy approach we construct a set
of global constraints over synchronisation placements. Each model of the global
constraints set corresponds to a correctness-ensuring synchronisation placement.
The placement that is optimal w.r.t. the given objective function is chosen as
the synchronisation solution. We evaluate our approach on a number of realistic
(albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions
of the drivers with known concurrency-related bugs. For the experiments with an
explicit specification we added assertions that would detect the bugs in the experiments.
Device drivers lend themselves to implicit specification, where the device and
the operating system are the external interfaces. Our experiments demonstrate
that our synthesis method is precise and efficient. We implemented objective functions
for coarse-grained and fine-grained locking and observed that different synchronisation
placements are produced for our experiments, favouring e.g. a minimal number of
synchronisation operations or maximum concurrency."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Tarrach T. Automatic synthesis of synchronisation primitives for concurrent
programs. 2016. doi:10.15479/at:ista:1130
apa: Tarrach, T. (2016). Automatic synthesis of synchronisation primitives for
concurrent programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1130
chicago: Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/at:ista:1130.
ieee: T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent
programs,” Institute of Science and Technology Austria, 2016.
ista: Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent
programs. Institute of Science and Technology Austria.
mla: Tarrach, Thorsten. Automatic Synthesis of Synchronisation Primitives for
Concurrent Programs. Institute of Science and Technology Austria, 2016, doi:10.15479/at:ista:1130.
short: T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent
Programs, Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-07T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '07'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1130
ec_funded: 1
file:
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checksum: 319a506831650327e85376db41fc1094
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creator: dernst
date_created: 2021-02-22T11:39:32Z
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file_name: 2016_Tarrach_Thesis.pdf
file_size: 1523935
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success: 1
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checksum: 39efcd789f0ad859ff15652cb7afc412
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:14:38Z
date_updated: 2021-11-17T13:46:55Z
file_id: '10296'
file_name: 2016_Tarrach_Thesispdfa.pdf
file_size: 1306068
relation: main_file
file_date_updated: 2021-11-17T13:46:55Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf
month: '07'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6230'
related_material:
record:
- id: '1729'
relation: part_of_dissertation
status: public
- id: '2218'
relation: part_of_dissertation
status: public
- id: '2445'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic synthesis of synchronisation primitives for concurrent programs
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1093'
abstract:
- lang: eng
text: 'We introduce a general class of distances (metrics) between Markov chains,
which are based on linear behaviour. This class encompasses distances given topologically
(such as the total variation distance or trace distance) as well as by temporal
logics or automata. We investigate which of the distances can be approximated
by observing the systems, i.e. by black-box testing or simulation, and we provide
both negative and positive results. '
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF)
under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award),
by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced
Postdoc. Mobility Fellowship – grant number P300P2_161067."
alternative_title:
- LIPIcs
article_number: '20'
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov
chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear
distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency
Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CONCUR.2016.20'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances
between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City;
Canada, 2016, vol. 59.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between
Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.'
mla: Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol.
59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City; Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
- _id: CaGu
doi: 10.4230/LIPIcs.CONCUR.2016.20
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:39Z
date_updated: 2018-12-12T10:11:39Z
file_id: '4895'
file_name: IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf
file_size: 501827
relation: main_file
file_date_updated: 2018-12-12T10:11:39Z
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6283'
pubrep_id: '794'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Linear distances between Markov chains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1234'
abstract:
- lang: eng
text: We present a new algorithm for the statistical model checking of Markov chains
with respect to unbounded temporal properties, including full linear temporal
logic. The main idea is that we monitor each simulation run on the fly, in order
to detect quickly if a bottom strongly connected component is entered with high
probability, in which case the simulation run can be terminated early. As a result,
our simulation runs are often much shorter than required by termination bounds
that are computed a priori for a desired level of confidence on a large state
space. In comparison to previous algorithms for statistical model checking our
method is not only faster in many cases but also requires less information about
the system, namely, only the minimum transition probability that occurs in the
Markov chain. In addition, our method can be generalised to unbounded quantitative
properties such as mean-payoff bounds.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under\r\ngrant agreement 267989 (QUAREM), the Austrian Science Fund
\ (FWF) under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh
Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility
Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation
under grant agreement P202/12/G061."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking
for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:10.1007/978-3-662-49674-9_7'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Faster
statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129).
Presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/978-3-662-49674-9_7'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29.
Springer, 2016. https://doi.org/10.1007/978-3-662-49674-9_7.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical
model checking for unbounded temporal properties,” presented at the TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands,
2016, vol. 9636, pp. 112–129.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model
checking for unbounded temporal properties. TACAS: Tools and Algorithms for the
Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.'
mla: Daca, Przemyslaw, et al. Faster Statistical Model Checking for Unbounded
Temporal Properties. Vol. 9636, Springer, 2016, pp. 112–29, doi:10.1007/978-3-662-49674-9_7.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp.
112–129.
conference:
end_date: 2016-04-08
location: Eindhoven, The Netherlands
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2016-04-02
date_created: 2018-12-11T11:50:51Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1007/978-3-662-49674-9_7
ec_funded: 1
intvolume: ' 9636'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.05739
month: '01'
oa: 1
oa_version: Preprint
page: 112 - 129
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6099'
quality_controlled: '1'
related_material:
record:
- id: '471'
relation: later_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster statistical model checking for unbounded temporal properties
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9636
year: '2016'
...
---
_id: '1230'
abstract:
- lang: eng
text: Concolic testing is a promising method for generating test suites for large
programs. However, it suffers from the path-explosion problem and often fails
to find tests that cover difficult-to-reach parts of programs. In contrast, model
checkers based on counterexample-guided abstraction refinement explore programs
exhaustively, while failing to scale on large programs with precision. In this
paper, we present a novel method that iteratively combines concolic testing and
model checking to find a test suite for a given coverage criterion. If concolic
testing fails to cover some test goals, then the model checker refines its program
abstraction to prove more paths infeasible, which reduces the search space for
concolic testing. We have implemented our method on top of the concolictesting
tool Crest and the model checker CpaChecker. We evaluated our tool on a collection
of programs and a category of SvComp benchmarks. In our experiments, we observed
an improvement in branch coverage compared to Crest from 48% to 63% in the best
case, and from 66% to 71% on average.
acknowledgement: "We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand
Michael Tautschnig for help with preparing the experiments. This research was supported
in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by
the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award)."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol
9583. Springer; 2016:328-347. doi:10.1007/978-3-662-49122-5_16'
apa: 'Daca, P., Gupta, A., & Henzinger, T. A. (2016). Abstraction-driven concolic
testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model
Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_16'
chicago: Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven
Concolic Testing,” 9583:328–47. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_16.
ieee: 'P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,”
presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.'
ista: 'Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583,
328–347.'
mla: Daca, Przemyslaw, et al. Abstraction-Driven Concolic Testing. Vol. 9583,
Springer, 2016, pp. 328–47, doi:10.1007/978-3-662-49122-5_16.
short: P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.
conference:
end_date: 2016-01-19
location: St. Petersburg, FL, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2016-01-17
date_created: 2018-12-11T11:50:50Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_16
ec_funded: 1
intvolume: ' 9583'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.02615
month: '01'
oa: 1
oa_version: Preprint
page: 328 - 347
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '6104'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Abstraction-driven concolic testing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9583
year: '2016'
...
---
_id: '1391'
abstract:
- lang: eng
text: "We present an extension to the quantifier-free theory of integer arrays which
allows us to express counting. The properties expressible in Array Folds Logic
(AFL) include statements such as "the first array cell contains the array
length," and "the array contains equally many minimal and maximal elements."
These properties cannot be expressed in quantified fragments of the theory of
arrays, nor in the theory of concatenation. Using reduction to counter machines,
we show that the satisfiability problem of AFL is PSPACE-complete, and with a
natural restriction the complexity decreases to NP. We also show that adding either
universal quantifiers or concatenation leads to undecidability.\r\nAFL contains
terms that fold a function over an array. We demonstrate that folding, a well-known
concept from functional languages, allows us to concisely summarize loops that
count over arrays, which occurs frequently in real-life programs. We provide a
tool that can discharge proof obligations in AFL, and we demonstrate on practical
examples that our decision procedure can solve a broad range of problems in symbolic
testing and program verification."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Andrey
full_name: Kupriyanov, Andrey
id: 2C311BF8-F248-11E8-B48F-1D18A9856A87
last_name: Kupriyanov
citation:
ama: 'Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer;
2016:230-248. doi:10.1007/978-3-319-41540-6_13'
apa: 'Daca, P., Henzinger, T. A., & Kupriyanov, A. (2016). Array folds logic
(Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto,
Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_13'
chicago: Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds
Logic,” 9780:230–48. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_13.
ieee: 'P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented
at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp.
230–248.'
ista: 'Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer
Aided Verification, LNCS, vol. 9780, 230–248.'
mla: Daca, Przemyslaw, et al. Array Folds Logic. Vol. 9780, Springer, 2016,
pp. 230–48, doi:10.1007/978-3-319-41540-6_13.
short: P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:51:45Z
date_published: 2016-07-13T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-319-41540-6_13
ec_funded: 1
intvolume: ' 9780'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1603.06850
month: '07'
oa: 1
oa_version: Preprint
page: 230 - 248
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5818'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Array folds logic
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9780
year: '2016'
...
---
_id: '1243'
abstract:
- lang: eng
text: Restriction-modification (RM) systems represent a minimal and ubiquitous biological
system of self/non-self discrimination in prokaryotes [1], which protects hosts
from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase
(M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by
methylating short specific DNA sequences called restriction sites, whereas R recognizes
unmethylated restriction sites as non-self and introduces a double-stranded DNA
break [3]. Restriction sites are significantly underrepresented in prokaryotic
genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally
leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore,
RM systems can promote DNA recombination [9] and contribute to genetic variation
in microbial populations, thus facilitating adaptive evolution [10]. However,
cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has
not been directly detected, and its cause, frequency, and outcome are unknown.
We quantify self-restriction caused by two RM systems of Escherichia coli and
find that, in agreement with levels of restriction site avoidance, EcoRI, but
not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic
process, which temporarily induces the SOS response, and is followed by DNA repair,
maintaining cell viability. We find that RM systems with higher restriction efficiency
against bacteriophage infections exhibit a higher rate of self-restriction, and
that this rate can be further increased by stochastic imbalance between R and
M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic
genomes.
acknowledgement: This work was funded by an HFSP Young Investigators’ grant. M.P.
is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute
of Science and Technology Austria. R.O. and Y.W. were supported by the Platform
for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi
for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing
us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G.
and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments
on an earlier version of the manuscript. We especially thank B.R. Levin for advice
and comments, and the anonymous reviewers for significantly improving the manuscript.
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Long
full_name: Qian, Long
last_name: Qian
- first_name: Reiko
full_name: Okura, Reiko
last_name: Okura
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Yuichi
full_name: Wakamoto, Yuichi
last_name: Wakamoto
- first_name: Edo
full_name: Kussell, Edo
last_name: Kussell
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification
system. Current Biology. 2016;26(3):404-409. doi:10.1016/j.cub.2015.12.041
apa: Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E.,
& Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification
system. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.12.041
chicago: Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto,
Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification
System.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2015.12.041.
ieee: M. Pleska et al., “Bacterial autoimmunity due to a restriction-modification
system,” Current Biology, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.
ista: Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016.
Bacterial autoimmunity due to a restriction-modification system. Current Biology.
26(3), 404–409.
mla: Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification
System.” Current Biology, vol. 26, no. 3, Cell Press, 2016, pp. 404–09,
doi:10.1016/j.cub.2015.12.041.
short: M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C.
Guet, Current Biology 26 (2016) 404–409.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-08T00:00:00Z
date_updated: 2023-09-07T11:59:32Z
day: '08'
department:
- _id: CaGu
doi: 10.1016/j.cub.2015.12.041
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 404 - 409
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '6087'
quality_controlled: '1'
related_material:
record:
- id: '202'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Bacterial autoimmunity due to a restriction-modification system
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1071'
abstract:
- lang: eng
text: 'We consider data-structures for answering reachability and distance queries
on constant-treewidth graphs with n nodes, on the standard RAM computational model
with wordsize W=Theta(log n). Our first contribution is a data-structure that
after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time;
and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically)
optimal and is faster than DFS/BFS when answering more than a constant number
of single-source queries. The data-structure uses at all times O(n) space. Our
second contribution is a space-time tradeoff data-structure for distance queries.
For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing
time that allows pair queries in O(n^{1-\epsilon} alpha(n)) time, where alpha
is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space.
The input graph G is not considered in the space complexity. '
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant
(279307: Graph Games).'
alternative_title:
- LIPIcs
article_number: '28'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space
time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ESA.2016.28'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs (Vol.
57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark:
Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ESA.2016.28'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant
Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016. https://doi.org/10.4230/LIPIcs.ESA.2016.28.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs,”
presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016,
vol. 57.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs. ESA:
European Symposium on Algorithms, LIPIcs, vol. 57, 28.'
mla: Chatterjee, Krishnendu, et al. Optimal Reachability and a Space Time Tradeoff
for Distance Queries in Constant Treewidth Graphs. Vol. 57, 28, Schloss Dagstuhl-
Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ESA.2016.28.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ESA.2016.28
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:31Z
date_updated: 2018-12-12T10:14:31Z
file_id: '5084'
file_name: IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf
file_size: 579225
relation: main_file
file_date_updated: 2018-12-12T10:14:31Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published 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: 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_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
publist_id: '6312'
pubrep_id: '777'
quality_controlled: '1'
related_material:
record:
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Optimal reachability and a space time tradeoff for distance queries in constant
treewidth graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '1362'
abstract:
- lang: eng
text: We present a boundary element based method for fast simulation of brittle
fracture. By introducing simplifying assumptions that allow us to quickly estimate
stress intensities and opening displacements during crack propagation, we build
a fracture algorithm where the cost of each time step scales linearly with the
length of the crackfront. The transition from a full boundary element method to
our faster variant is possible at the beginning of any time step. This allows
us to build a hybrid method, which uses the expensive but more accurate BEM while
the number of degrees of freedom is low, and uses the fast method once that number
exceeds a given threshold as the crack geometry becomes more complicated. Furthermore,
we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body
coupling solves a Neumann boundary value problem by carefully separating translational,
rotational and deformational components of the collision forces and then applying
a Tikhonov regularizer to the resulting linear system. We show that our method
produces physically reasonable results in standard test cases and is capable of
dealing with complex scenes faster than previous finite- or boundary element approaches.
alternative_title:
- ACM Transactions on Graphics
article_number: '104'
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture
simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925902'
apa: 'Hahn, D., & Wojtan, C. (2016). Fast approximations for boundary element
based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim,
CA, USA: ACM. https://doi.org/10.1145/2897824.2925902'
chicago: Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element
Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925902.
ieee: D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle
fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol.
35, no. 4.
ista: Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle
fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.
mla: Hahn, David, and Chris Wojtan. Fast Approximations for Boundary Element
Based Brittle Fracture Simulation. Vol. 35, no. 4, 104, ACM, 2016, doi:10.1145/2897824.2925902.
short: D. Hahn, C. Wojtan, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T12:02:56Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925902
ec_funded: 1
file:
- access_level: open_access
checksum: 943712d9c9dc8bb5048d4adc561d7d38
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:04Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5121'
file_name: IST-2016-632-v1+2_a104-hahn.pdf
file_size: 12453704
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5880'
pubrep_id: '632'
quality_controlled: '1'
related_material:
record:
- id: '839'
relation: dissertation_contains
status: public
status: public
title: Fast approximations for boundary element based brittle fracture simulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1229'
abstract:
- lang: eng
text: Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme
is defined for some NP language L and lets a sender encrypt messages relative
to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L,
but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps
and give another construction [GGH+13b] using indistinguishability obfuscation
(iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently
hardly be implemented on powerful hardware and will unlikely be realizable on
constrained devices like smart cards any time soon. We construct a WE scheme where
encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions
and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs
public parameters containing an obfuscated circuit (only required for decryption),
two encryption keys and a common reference string (used for encryption). This
setup need only be run once, and the parame- ters can be used for arbitrary many
encryptions. Our scheme can also be turned into a functional WE scheme, where
a message is encrypted w.r.t. a statement and a function f, and decryption with
a witness w yields f (m, w). Our construction is inspired by the functional encryption
scheme by Garg et al. and we prove (selective) security assuming iO and statistically
simulation-sound NIZK. We give a construction of the latter in bilinear groups
and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at
a 128-bit security level and can be computed on a smart card.
acknowledgement: Research supported by the European Research Council, ERC starting grant
(259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol
9696. Springer; 2016:285-303. doi:10.1007/978-3-319-39555-5_16'
apa: 'Abusalah, H. M., Fuchsbauer, G., & Pietrzak, K. Z. (2016). Offline witness
encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography
and Network Security, Guildford, UK: Springer. https://doi.org/10.1007/978-3-319-39555-5_16'
chicago: Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline
Witness Encryption,” 9696:285–303. Springer, 2016. https://doi.org/10.1007/978-3-319-39555-5_16.
ieee: 'H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,”
presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK,
2016, vol. 9696, pp. 285–303.'
ista: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption.
ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.'
mla: Abusalah, Hamza M., et al. Offline Witness Encryption. Vol. 9696, Springer,
2016, pp. 285–303, doi:10.1007/978-3-319-39555-5_16.
short: H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.
conference:
end_date: 2016-06-22
location: Guildford, UK
name: 'ACNS: Applied Cryptography and Network Security'
start_date: 2016-06-19
date_created: 2018-12-11T11:50:50Z
date_published: 2016-06-09T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '09'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_16
ec_funded: 1
file:
- access_level: open_access
checksum: 34fa9ce681da845a1ba945ba3dc57867
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:20Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5273'
file_name: IST-2017-765-v1+1_838.pdf
file_size: 515000
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9696'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 285 - 303
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6105'
pubrep_id: '765'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Offline witness encryption
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9696
year: '2016'
...
---
_id: '1236'
abstract:
- lang: eng
text: 'A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets
of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute
a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while
even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13
Boneh and Waters gave a construction which supports the most general set family
so far. Its keys kc are defined for sets decided by boolean circuits C and enable
evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF
input length and the size of the circuits C for which constrained keys can be
computed must be fixed beforehand during key generation. We construct a constrained
PRF that has an unbounded input length and whose constrained keys can be defined
for any set recognized by a Turing machine. The only a priori bound we make is
on the description size of the machines. We prove our construction secure assuming
publiccoin differing-input obfuscation. As applications of our constrained PRF
we build a broadcast encryption scheme where the number of potential receivers
need not be fixed at setup (in particular, the length of the keys is independent
of the number of parties) and the first identity-based non-interactive key exchange
protocol with no bound on the number of parties that can agree on a shared key.'
acknowledgement: Supported by the European Research Council, ERC Starting Grant (259668-PSPC).
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs.
In: Vol 9610. Springer; 2016:413-428. doi:10.1007/978-3-319-29485-8_24'
apa: 'Abusalah, H. M., Fuchsbauer, G., & Pietrzak, K. Z. (2016). Constrained
PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics
in Cryptology, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-29485-8_24'
chicago: Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained
PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. https://doi.org/10.1007/978-3-319-29485-8_24.
ieee: 'H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for
unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco,
CA, USA, 2016, vol. 9610, pp. 413–428.'
ista: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded
inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.'
mla: Abusalah, Hamza M., et al. Constrained PRFs for Unbounded Inputs. Vol.
9610, Springer, 2016, pp. 413–28, doi:10.1007/978-3-319-29485-8_24.
short: H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.
conference:
end_date: 2016-03-04
location: San Francisco, CA, USA
name: 'CT-RSA: Topics in Cryptology'
start_date: 2016-02-29
date_created: 2018-12-11T11:50:52Z
date_published: 2016-02-02T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '02'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-29485-8_24
ec_funded: 1
file:
- access_level: open_access
checksum: 3851cee49933ae13b1272e516f213e13
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:05Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4664'
file_name: IST-2017-764-v1+1_279.pdf
file_size: 495176
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 9610'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 413 - 428
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '6097'
pubrep_id: '764'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Constrained PRFs for unbounded inputs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9610
year: '2016'
...
---
_id: '1235'
abstract:
- lang: eng
text: 'A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets
of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute
a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈
S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah
et al. recently constructed the first constrained PRF for inputs of arbitrary
length whose sets S are decided by Turing machines. They use their CPRF to build
broadcast encryption and the first ID-based non-interactive key exchange for an
unbounded number of users. Their constrained keys are obfuscated circuits and
are therefore large. In this work we drastically reduce the key size and define
a constrained key for a Turing machine M as a short signature on M. For this,
we introduce a new signature primitive with constrained signing keys that let
one only sign certain messages, while forging a signature on others is hard even
when knowing the coins for key generation.'
acknowledgement: H. Abusalah—Research supported by the European Research Council,
ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
citation:
ama: 'Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short
keys. In: Vol 9696. Springer; 2016:445-463. doi:10.1007/978-3-319-39555-5_24'
apa: 'Abusalah, H. M., & Fuchsbauer, G. (2016). Constrained PRFs for unbounded
inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied
Cryptography and Network Security, Guildford, UK: Springer. https://doi.org/10.1007/978-3-319-39555-5_24'
chicago: Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded
Inputs with Short Keys,” 9696:445–63. Springer, 2016. https://doi.org/10.1007/978-3-319-39555-5_24.
ieee: 'H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs
with short keys,” presented at the ACNS: Applied Cryptography and Network Security,
Guildford, UK, 2016, vol. 9696, pp. 445–463.'
ista: 'Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with
short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696,
445–463.'
mla: Abusalah, Hamza M., and Georg Fuchsbauer. Constrained PRFs for Unbounded
Inputs with Short Keys. Vol. 9696, Springer, 2016, pp. 445–63, doi:10.1007/978-3-319-39555-5_24.
short: H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.
conference:
end_date: 2016-06-22
location: Guildford, UK
name: 'ACNS: Applied Cryptography and Network Security'
start_date: 2016-06-19
date_created: 2018-12-11T11:50:52Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_24
ec_funded: 1
intvolume: ' 9696'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/279.pdf
month: '01'
oa: 1
oa_version: Submitted Version
page: 445 - 463
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6098'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Constrained PRFs for unbounded inputs with short keys
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9696
year: '2016'
...
---
_id: '1441'
abstract:
- lang: eng
text: 'Optogenetics and photopharmacology enable the spatio-temporal control of
cell and animal behavior by light. Although red light offers deep-tissue penetration
and minimal phototoxicity, very few red-light-sensitive optogenetic methods are
currently available. We have now developed a red-light-induced homodimerization
domain. We first showed that an optimized sensory domain of the cyanobacterial
phytochrome 1 can be expressed robustly and without cytotoxicity in human cells.
We then applied this domain to induce the dimerization of two receptor tyrosine
kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor
trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway
non-invasively in mammalian tissue and in multicolor cell-signaling experiments.
The light-controlled dimerizer and red-light-activated receptor tyrosine kinases
will prove useful to regulate a variety of cellular processes with light. Go deep
with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was
repurposed to induce the homodimerization of proteins in living cells by red light.
By using this domain, light-activated protein kinases were engineered that can
be activated orthogonally from many fluorescent proteins and through mammalian
tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.'
acknowledgement: 'A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by
the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and
a FemTech fellowship (Austrian Research Promotion Agency: 3580812).'
author:
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Alexandra-Madelaine
full_name: Tichy, Alexandra-Madelaine
id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
last_name: Tichy
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL.
A phytochrome sensory domain permits receptor activation by red light. Angewandte
Chemie - International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736
apa: Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &
Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation
by red light. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.201601736
chicago: Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy,
Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits
Receptor Activation by Red Light.” Angewandte Chemie - International Edition.
Wiley, 2016. https://doi.org/10.1002/anie.201601736.
ieee: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H.
L. Janovjak, “A phytochrome sensory domain permits receptor activation by red
light,” Angewandte Chemie - International Edition, vol. 55, no. 21. Wiley,
pp. 6339–6342, 2016.
ista: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL.
2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte
Chemie - International Edition. 55(21), 6339–6342.
mla: Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor
Activation by Red Light.” Angewandte Chemie - International Edition, vol.
55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736.
short: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L.
Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.
date_created: 2018-12-11T11:52:02Z
date_published: 2016-05-17T00:00:00Z
date_updated: 2023-09-07T12:49:08Z
day: '17'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1002/anie.201601736
ec_funded: 1
file:
- access_level: open_access
checksum: 26da07960e57ac4750b54179197ce57f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:03Z
date_updated: 2020-07-14T12:44:55Z
file_id: '5255'
file_name: IST-2017-840-v1+1_reichhart.pdf
file_size: 1268662
relation: main_file
file_date_updated: 2020-07-14T12:44:55Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 6339 - 6342
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley
publist_id: '5755'
pubrep_id: '840'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: A phytochrome sensory domain permits receptor activation by red light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1358'
abstract:
- lang: eng
text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA
interactions. Limited specificity may lead to crosstalk: a regulatory state in
which a gene is either incorrectly activated due to noncognate TF–DNA interactions
or remains erroneously inactive. As each TF can have numerous interactions with
noncognate cis-regulatory elements, crosstalk is inherently a global problem,
yet has previously not been studied as such. We construct a theoretical framework
to analyse the effects of global crosstalk on gene regulation. We find that crosstalk
presents a significant challenge for organisms with low-specificity TFs, such
as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting
at equilibrium, including variants of cooperativity and combinatorial regulation.
Our results suggest that crosstalk imposes a previously unexplored global constraint
on the functioning and evolution of regulatory networks, which is qualitatively
distinct from the known constraints that act at the level of individual gene regulatory
elements.'
article_number: '12307'
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to
gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016).
Intrinsic limits to gene regulation by global crosstalk. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms12307
chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and
Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature
Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic
limits to gene regulation by global crosstalk,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits
to gene regulation by global crosstalk. Nature Communications. 7, 12307.
mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”
Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications
7 (2016).
date_created: 2018-12-11T11:51:34Z
date_published: 2016-08-04T00:00:00Z
date_updated: 2023-09-07T12:53:49Z
day: '04'
ddc:
- '576'
department:
- _id: GaTk
- _id: NiBa
- _id: CaGu
doi: 10.1038/ncomms12307
ec_funded: 1
file:
- access_level: open_access
checksum: fe3f3a1526d180b29fe691ab11435b78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4919'
file_name: IST-2016-627-v1+1_ncomms12307.pdf
file_size: 861805
relation: main_file
- access_level: open_access
checksum: 164864a1a675f3ad80e9917c27aba07f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:02Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4920'
file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf
file_size: 1084703
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5887'
pubrep_id: '627'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Intrinsic limits to gene regulation by global crosstalk
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1346'
abstract:
- lang: eng
text: ATP production requires the establishment of an electrochemical proton gradient
across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this
proton gradient and disrupt numerous cellular processes, including vesicular trafficking,
mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial
uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different
systems and that ES9 induces inhibition of CME not because of its effect on cellular
ATP, but rather due to its protonophore activity that leads to cytoplasm acidification.
We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely
used to block CME, displays similar properties, thus questioning its use as a
specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine
motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification
dramatically affects the dynamics and recruitment of clathrin and associated adaptors,
and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma
membrane.
acknowledgement: "We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi
Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen
Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing
S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys
for literature searches, VIB Bio Imaging Core for help with imaging conditions and
Martine De Cock for help in preparing the article. This work was supported by the
Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship
to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish
government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for
Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.);
the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.);
a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the
Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.),
the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated
by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet
grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral
fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R."
article_number: '11710'
author:
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Sabine
full_name: Kuenen, Sabine
last_name: Kuenen
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: Olivier
full_name: Keech, Olivier
last_name: Keech
- first_name: Corrado
full_name: Viotti, Corrado
last_name: Viotti
- first_name: Jef
full_name: Swerts, Jef
last_name: Swerts
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Fausto
full_name: Ortiz Morea, Fausto
last_name: Ortiz Morea
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Simon
full_name: Delang, Simon
last_name: Delang
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Xavier
full_name: Zarza, Xavier
last_name: Zarza
- first_name: Mareike
full_name: Heilmann, Mareike
last_name: Heilmann
- first_name: Jiorgos
full_name: Kourelis, Jiorgos
last_name: Kourelis
- first_name: Jaroslaw
full_name: Kasprowicz, Jaroslaw
last_name: Kasprowicz
- first_name: Le
full_name: Nguyen, Le
last_name: Nguyen
- first_name: Andrzej
full_name: Drozdzecki, Andrzej
last_name: Drozdzecki
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Anna
full_name: Szatmári, Anna
last_name: Szatmári
- first_name: Mateusz
full_name: Majda, Mateusz
last_name: Majda
- first_name: Gary
full_name: Baisa, Gary
last_name: Baisa
- first_name: Sebastian
full_name: Bednarek, Sebastian
last_name: Bednarek
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Dominique
full_name: Audenaert, Dominique
last_name: Audenaert
- first_name: Christa
full_name: Testerink, Christa
last_name: Testerink
- first_name: Teun
full_name: Munnik, Teun
last_name: Munnik
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Patrik
full_name: Verstreken, Patrik
last_name: Verstreken
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated
endocytosis largely through cytoplasmic acidification. Nature Communications.
2016;7. doi:10.1038/ncomms11710
apa: Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C.,
… Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis
largely through cytoplasmic acidification. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms11710
chicago: Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech,
Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated
Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications.
Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11710.
ieee: W. Dejonghe et al., “Mitochondrial uncouplers inhibit clathrin-mediated
endocytosis largely through cytoplasmic acidification,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych
M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis
J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa
G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann
I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial
uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification.
Nature Communications. 7, 11710.
mla: Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis
Largely through Cytoplasmic Acidification.” Nature Communications, vol.
7, 11710, Nature Publishing Group, 2016, doi:10.1038/ncomms11710.
short: W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J.
Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza,
M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte,
A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink,
T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken,
E. Russinova, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:30Z
date_published: 2016-06-08T00:00:00Z
date_updated: 2023-09-07T12:54:35Z
day: '08'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1038/ncomms11710
ec_funded: 1
file:
- access_level: open_access
checksum: e8dc81b3e44db5a7718d7f1501ce1aa7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:47Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5369'
file_name: IST-2016-653-v1+1_ncomms11710_1_.pdf
file_size: 3532505
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5906'
pubrep_id: '653'
quality_controlled: '1'
related_material:
record:
- id: '7172'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through
cytoplasmic acidification
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1096'
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- 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, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings
of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024
apa: Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P.
J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024
chicago: Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and
Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell.
Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024.
ieee: C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg,
“Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press,
pp. 493–506, 2016.
ista: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin
rings of power. Developmental Cell. 37(6), 493–506.
mla: Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell,
vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.
short: C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental
Cell 37 (2016) 493–506.
date_created: 2018-12-11T11:50:07Z
date_published: 2016-06-20T00:00:00Z
date_updated: 2023-09-07T12:56:41Z
day: '20'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2016.05.024
intvolume: ' 37'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 493 - 506
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6279'
quality_controlled: '1'
related_material:
record:
- id: '7186'
relation: part_of_dissertation
status: public
scopus_import: 1
status: public
title: Actin rings of power
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2016'
...
---
_id: '1328'
abstract:
- lang: eng
text: Hole spins have gained considerable interest in the past few years due to
their potential for fast electrically controlled qubits. Here, we study holes
confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature
magnetotransport measurements reveal a large anisotropy between the in-plane and
out-of-plane g-factors of up to 18. Numerical simulations verify that this large
anisotropy originates from a confined wave function of heavy-hole character. A
light-hole admixture of less than 1% is estimated for the states of lowest energy,
leading to a surprisingly large reduction of the out-of-plane g-factors compared
with those for pure heavy holes. Given this tiny light-hole contribution, the
spin lifetimes are expected to be very long, even in isotopically nonpurified
samples.
acknowledgement: 'The work was supported by the EC FP7 ICT project SiSPIN no. 323841,
the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20
project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions
related to the hut wire growth and for giving us access to the molecular beam epitaxy
system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko
for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous
support. '
author:
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Christoph
full_name: Kloeffel, Christoph
last_name: Kloeffel
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Marta
full_name: Rossell, Marta
last_name: Rossell
- first_name: Violetta
full_name: Sessi, Violetta
last_name: Sessi
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Raimund
full_name: Kirchschlager, Raimund
last_name: Kirchschlager
- first_name: Elisabeth
full_name: Lausecker, Elisabeth
id: 33662F76-F248-11E8-B48F-1D18A9856A87
last_name: Lausecker
- first_name: Alisha
full_name: Truhlar, Alisha
id: 49CBC780-F248-11E8-B48F-1D18A9856A87
last_name: Truhlar
- first_name: Martin
full_name: Glaser, Martin
last_name: Glaser
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Andreas
full_name: Fuhrer, Andreas
last_name: Fuhrer
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut
wires. Nano Letters. 2016;16(11):6879-6885. doi:10.1021/acs.nanolett.6b02715
apa: Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka,
J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. Nano Letters.
American Chemical Society. https://doi.org/10.1021/acs.nanolett.6b02715
chicago: Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta
Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium
Hut Wires.” Nano Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.nanolett.6b02715.
ieee: H. Watzinger et al., “Heavy-hole states in germanium hut wires,” Nano
Letters, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016.
ista: Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager
R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G.
2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.
mla: Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” Nano
Letters, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:10.1021/acs.nanolett.6b02715.
short: H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka,
R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer,
D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.
date_created: 2018-12-11T11:51:24Z
date_published: 2016-09-22T00:00:00Z
date_updated: 2023-09-07T13:15:02Z
day: '22'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.6b02715
ec_funded: 1
file:
- access_level: open_access
checksum: b63feece90d7b620ece49ca632e34ff3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:04Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5053'
file_name: IST-2016-664-v1+1_acs.nanolett.6b02715.pdf
file_size: 535121
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '11'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 6879 - 6885
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5941'
pubrep_id: '664'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
status: for_moderation
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Heavy-hole states in germanium hut wires
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1205'
abstract:
- lang: eng
text: In this paper, we present a formal model-driven engineering approach to establishing
a safety-assured implementation of Multifunction vehicle bus controller (MVBC)
based on the generic reference models and requirements described in the International
Electrotechnical Commission (IEC) standard IEC-61375. First, the generic models
described in IEC-61375 are translated into a network of timed automata, and some
safety requirements tested in IEC-61375 are formalized as timed computation tree
logic (TCTL) formulas. With the help of Uppaal, we check and debug whether the
timed automata satisfy the formulas or not. Within this step, several logic inconsistencies
in the original standard are detected and corrected. Then, we apply the tool Times
to generate C code from the verified model, which was later synthesized into a
real MVBC chip. Finally, the runtime verification tool RMOR is applied to verify
some safety requirements at the implementation level. We set up a real platform
with worldwide mostly used MVBC D113, and verify the correctness and the scalability
of the synthesized MVBC chip more comprehensively. The errors in the standard
has been confirmed and the resulted MVBC has been deployed in real train communication
network.
acknowledgement: "This research is sponsored in part by NSFC Program (No. 91218302,
No. 61527812), National Science and Technology Major Project (No. 2016ZX01038101),
Tsinghua University Initiative Scientific Research Program (20131089331), MIIT IT
funds (Research and application of TCN key technologies) of China, and the National
Key Technology R&D Program (No. 2015BAG14B01-02), Austrian Science Fund (FWF) under
grants S11402-N23 (RiSE/SHiNE) and Z211-N23.\r\n"
alternative_title:
- LNCS
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Houbing
full_name: Song, Houbing
last_name: Song
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ming
full_name: Gu, Ming
last_name: Gu
- first_name: Jiaguang
full_name: Sun, Jiaguang
last_name: Sun
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: 'Jiang Y, Liu H, Song H, et al. Safety assured formal model driven design of
the multifunction vehicle bus controller. In: Vol 9995. Springer; 2016:757-763.
doi:10.1007/978-3-319-48989-6_47'
apa: 'Jiang, Y., Liu, H., Song, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016).
Safety assured formal model driven design of the multifunction vehicle bus controller
(Vol. 9995, pp. 757–763). Presented at the FM: International Symposium on Formal
Methods, Limassol, Cyprus: Springer. https://doi.org/10.1007/978-3-319-48989-6_47'
chicago: Jiang, Yu, Han Liu, Houbing Song, Hui Kong, Ming Gu, Jiaguang Sun, and
Lui Sha. “Safety Assured Formal Model Driven Design of the Multifunction Vehicle
Bus Controller,” 9995:757–63. Springer, 2016. https://doi.org/10.1007/978-3-319-48989-6_47.
ieee: 'Y. Jiang et al., “Safety assured formal model driven design of the
multifunction vehicle bus controller,” presented at the FM: International Symposium
on Formal Methods, Limassol, Cyprus, 2016, vol. 9995, pp. 757–763.'
ista: 'Jiang Y, Liu H, Song H, Kong H, Gu M, Sun J, Sha L. 2016. Safety assured
formal model driven design of the multifunction vehicle bus controller. FM: International
Symposium on Formal Methods, LNCS, vol. 9995, 757–763.'
mla: Jiang, Yu, et al. Safety Assured Formal Model Driven Design of the Multifunction
Vehicle Bus Controller. Vol. 9995, Springer, 2016, pp. 757–63, doi:10.1007/978-3-319-48989-6_47.
short: Y. Jiang, H. Liu, H. Song, H. Kong, M. Gu, J. Sun, L. Sha, in:, Springer,
2016, pp. 757–763.
conference:
end_date: 2016-11-11
location: Limassol, Cyprus
name: 'FM: International Symposium on Formal Methods'
start_date: 2016-11-09
date_created: 2018-12-11T11:50:42Z
date_published: 2016-11-08T00:00:00Z
date_updated: 2023-09-18T08:12:48Z
day: '08'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-319-48989-6_47
file:
- access_level: open_access
checksum: fea0b3fae9a2a42e8bfec59840e30d8c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:13Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4673'
file_name: IST-2017-783-v1+1_FM-Safety-Assured-Development-of-MVBC.pdf
file_size: 281501
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9995'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 757 - 763
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '6144'
pubrep_id: '783'
quality_controlled: '1'
related_material:
record:
- id: '434'
relation: later_version
status: public
scopus_import: 1
status: public
title: Safety assured formal model driven design of the multifunction vehicle bus
controller
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9995
year: '2016'
...
---
_id: '1193'
abstract:
- lang: eng
text: We consider the recent formulation of the Algorithmic Lovász Local Lemma [1],
[2] for finding objects that avoid "bad features", or "flaws".
It extends the Moser-Tardos resampling algorithm [3] to more general discrete
spaces. At each step the method picks a flaw present in the current state and
"resamples" it using a "resampling oracle" provided by the
user. However, it is less flexible than the Moser-Tardos method since [1], [2]
require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and
thus can potentially be implemented more efficiently). We formulate a new "commutativity"
condition, and prove that it is sufficient for an arbitrary rule to work. It also
enables an efficient parallelization under an additional assumption. We then show
that existing resampling oracles for perfect matchings and permutations do satisfy
this condition. Finally, we generalize the precondition in [2] (in the case of
symmetric potential causality graphs). This unifies special cases that previously
were treated separately.
acknowledgement: European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no 616160
article_number: '7782993'
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings
- Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December.
IEEE; 2016. doi:10.1109/FOCS.2016.88'
apa: 'Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma.
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science
(Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88'
chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88.
ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings
- Annual IEEE Symposium on Foundations of Computer Science, New Brunswick,
NJ, USA , 2016, vol. 2016–December.
ista: 'Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma.
Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS:
Foundations of Computer Science vol. 2016–December, 7782993.'
mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.
short: V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of
Computer Science, IEEE, 2016.
conference:
end_date: 2016-09-11
location: 'New Brunswick, NJ, USA '
name: 'FOCS: Foundations of Computer Science'
start_date: 2016-09-09
date_created: 2018-12-11T11:50:38Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2023-09-19T14:24:57Z
day: '15'
department:
- _id: VlKo
doi: 10.1109/FOCS.2016.88
ec_funded: 1
external_id:
arxiv:
- '1506.08547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.08547v7
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings - Annual IEEE Symposium on Foundations of Computer Science
publication_status: published
publisher: IEEE
publist_id: '6158'
quality_controlled: '1'
related_material:
record:
- id: '5975'
relation: later_version
status: public
scopus_import: 1
status: public
title: Commutativity in the algorithmic Lovasz local lemma
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-December
year: '2016'
...
---
_id: '1438'
abstract:
- lang: eng
text: 'In this paper, we consider termination of probabilistic programs with real-valued
variables. The questions concerned are: (a) qualitative ones that ask (i) whether
the program terminates with probability 1 (almost-sure termination) and (ii) whether
the expected termination time is finite (finite termination); (b) quantitative
ones that ask (i) to approximate the expected termination time (expectation problem)
and (ii) to compute a bound B such that the probability to terminate after B steps
decreases exponentially (concentration problem). To solve these questions, we
utilize the notion of ranking supermartingales which is a powerful approach for
proving termination of probabilistic programs. In detail, we focus on algorithmic
synthesis of linear ranking-supermartingales over affine probabilistic programs
(APP''s) with both angelic and demonic non-determinism. An important subclass
of APP''s is LRAPP which is defined as the class of all APP''s over which a linear
ranking-supermartingale exists. Our main contributions are as follows. Firstly,
we show that the membership problem of LRAPP (i) can be decided in polynomial
time for APP''s with at most demonic non-determinism, and (ii) is NP-hard and
in PSPACE for APP''s with angelic non-determinism; moreover, the NP-hardness result
holds already for APP''s without probability and demonic non-determinism. Secondly,
we show that the concentration problem over LRAPP can be solved in the same complexity
as for the membership problem of LRAPP. Finally, we show that the expectation
problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP''s
without probability and non-determinism (i.e., deterministic programs). Our experimental
results demonstrate the effectiveness of our approach to answer the qualitative
and quantitative questions over APP''s with at most demonic non-determinism.'
acknowledgement: 'Supported by the Natural Science Foundation of China (NSFC) under
Grant No. 61532019 '
alternative_title:
- POPL
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
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Rouzbeh
full_name: Hasheminezhad, Rouzbeh
last_name: Hasheminezhad
citation:
ama: 'Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative
and quantitative termination problems for affine probabilistic programs. In: Vol
20-22. ACM; 2016:327-342. doi:10.1145/2837614.2837639'
apa: 'Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2016). Algorithmic
analysis of qualitative and quantitative termination problems for affine probabilistic
programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming
Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837639'
chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad.
“Algorithmic Analysis of Qualitative and Quantitative Termination Problems for
Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. https://doi.org/10.1145/2837614.2837639.
ieee: 'K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg,
FL, USA, 2016, vol. 20–22, pp. 327–342.'
ista: 'Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.'
mla: Chatterjee, Krishnendu, et al. Algorithmic Analysis of Qualitative and Quantitative
Termination Problems for Affine Probabilistic Programs. Vol. 20–22, ACM, 2016,
pp. 327–42, doi:10.1145/2837614.2837639.
short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2023-09-19T14:38:41Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/2837614.2837639
ec_funded: 1
external_id:
arxiv:
- '1510.08517'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.08517
month: '01'
oa: 1
oa_version: Preprint
page: 327 - 342
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: ACM
publist_id: '5760'
quality_controlled: '1'
related_material:
record:
- id: '5993'
relation: later_version
status: public
scopus_import: 1
status: public
title: Algorithmic analysis of qualitative and quantitative termination problems for
affine probabilistic programs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2023-09-20T11:56:33Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '1077'
relation: used_in_publication
status: public
status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
the coat protein of the ϕX174 phage family
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1165'
abstract:
- lang: eng
text: We show that c-planarity is solvable in quadratic time for flat clustered
graphs with three clusters if the combinatorial embedding of the underlying graph
is fixed. In simpler graph-theoretical terms our result can be viewed as follows.
Given a graph G with the vertex set partitioned into three parts embedded on a
2-sphere, our algorithm decides if we can augment G by adding edges without creating
an edge-crossing so that in the resulting spherical graph the vertices of each
part induce a connected sub-graph. We proceed by a reduction to the problem of
testing the existence of a perfect matching in planar bipartite graphs. We formulate
our result in a slightly more general setting of cyclic clustered graphs, i.e.,
the simple graph obtained by contracting each cluster, where we disregard loops
and multi-edges, is a cycle.
acknowledgement: "R. Fulek—The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI
would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions
that helped to improve the presentation of the result."
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
citation:
ama: 'Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer;
2016:94-106. doi:10.1007/978-3-319-50106-2_8'
apa: 'Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp.
94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens,
Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_8'
chicago: Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106.
Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.
ieee: 'R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD:
Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp.
94–106.'
ista: 'Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing
and Network Visualization, LNCS, vol. 9801, 94–106.'
mla: Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801,
Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8.
short: R. Fulek, in:, Springer, 2016, pp. 94–106.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-09-27T12:14:48Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_8
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.01346
month: '12'
oa: 1
oa_version: Preprint
page: 94 - 106
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6192'
quality_controlled: '1'
related_material:
record:
- id: '794'
relation: later_version
status: public
scopus_import: 1
status: public
title: C-planarity of embedded cyclic c-graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '9801 '
year: '2016'
...
---
_id: '1378'
abstract:
- lang: eng
text: 'We give a detailed and easily accessible proof of Gromov''s Topological Overlap
Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral
cell complex of dimension d. Informally, the theorem states that if X has sufficiently
strong higher-dimensional expansion properties (which generalize edge expansion
of graphs and are defined in terms of cellular cochains of X) then X has the following
topological overlap property: for every continuous map X → ℝd there exists a point
p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of
X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional
piecewise-linear (PL) manifold M, with a constant μ that depends only on d and
on the expansion properties of X, but not on M.'
alternative_title:
- LIPIcs
author:
- first_name: Dominic
full_name: Dotterrer, Dominic
last_name: Dotterrer
- first_name: Tali
full_name: Kaufman, Tali
last_name: Kaufman
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In:
Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing;
2016:35.1-35.10. doi:10.4230/LIPIcs.SoCG.2016.35'
apa: 'Dotterrer, D., Kaufman, T., & Wagner, U. (2016). On expansion and topological
overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational
Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH,
Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.35'
chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological
Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH,
Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.35.
ieee: 'D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,”
presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA,
2016, vol. 51, p. 35.1-35.10.'
ista: 'Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.'
mla: Dotterrer, Dominic, et al. On Expansion and Topological Overlap. Vol.
51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing,
2016, p. 35.1-35.10, doi:10.4230/LIPIcs.SoCG.2016.35.
short: D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-09-27T12:29:56Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.35
file:
- access_level: open_access
checksum: cee65b0e722d50f9d1cc70c90ec1d59b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:38Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4699'
file_name: IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf
file_size: 536923
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 35.1 - 35.10
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
publist_id: '5833'
pubrep_id: '623'
quality_controlled: '1'
related_material:
record:
- id: '742'
relation: later_version
status: public
scopus_import: 1
status: public
title: On expansion and topological overlap
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1616'
abstract:
- lang: eng
text: The hippocampus plays a key role in learning and memory. Previous studies
suggested that the main types of principal neurons, dentate gyrus granule cells
(GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity
pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal
neurons. It has been assumed but never shown that such different activity may
be caused by differential synaptic excitation. To test this hypothesis, we performed
high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo.
In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired
action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were
silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine
the underlying mechanisms, we quantitatively assessed the frequency of spontaneous
excitatory synaptic input, the passive membrane properties, and the active membrane
characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3
and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition.
Thus, differential synaptic excitation is not responsible for differences in firing.
Moreover, the three types of hippocampal neurons markedly differed in their passive
properties. While GCs showed the most negative membrane potential, CA3 pyramidal
neurons had the highest input resistance and the slowest membrane time constant.
The three types of neurons also differed in the active membrane characteristics.
GCs showed the highest action potential threshold, but displayed the largest gain
of the input-output curves. In conclusion, our results reveal that differential
firing of the three main types of hippocampal principal neurons in vivo is not
primarily caused by differences in the characteristics of the synaptic input,
but by the distinct properties of synaptic integration and input-output transformation.
acknowledgement: "The authors thank Jose Guzman for critically reading prior versions
of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices,
A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger
for manuscript editing."
article_processing_charge: No
author:
- first_name: Janina
full_name: Kowalski, Janina
id: 3F3CA136-F248-11E8-B48F-1D18A9856A87
last_name: Kowalski
- first_name: Jian
full_name: Gan, Jian
id: 3614E438-F248-11E8-B48F-1D18A9856A87
last_name: Gan
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
citation:
ama: Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties
determine hippocampal differential firing pattern in vivo in anesthetized rats.
Hippocampus. 2016;26(5):668-682. doi:10.1002/hipo.22550
apa: Kowalski, J., Gan, J., Jonas, P. M., & Pernia-Andrade, A. (2016). Intrinsic
membrane properties determine hippocampal differential firing pattern in vivo
in anesthetized rats. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22550
chicago: Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade.
“Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern
in Vivo in Anesthetized Rats.” Hippocampus. Wiley, 2016. https://doi.org/10.1002/hipo.22550.
ieee: J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane
properties determine hippocampal differential firing pattern in vivo in anesthetized
rats,” Hippocampus, vol. 26, no. 5. Wiley, pp. 668–682, 2016.
ista: Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties
determine hippocampal differential firing pattern in vivo in anesthetized rats.
Hippocampus. 26(5), 668–682.
mla: Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal
Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus,
vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:10.1002/hipo.22550.
short: J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016)
668–682.
date_created: 2018-12-11T11:53:03Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-10-17T10:02:02Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1002/hipo.22550
file:
- access_level: open_access
checksum: 284b72b12fbe15474833ed3d4549f86b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:47Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5033'
file_name: IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf
file_size: 905348
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 668 - 682
publication: Hippocampus
publication_identifier:
eissn:
- 1098-1063
issn:
- 1050-9631
publication_status: published
publisher: Wiley
publist_id: '5550'
pubrep_id: '469'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intrinsic membrane properties determine hippocampal differential firing pattern
in vivo in anesthetized rats
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: 26
year: '2016'
...
---
_id: '1794'
abstract:
- lang: eng
text: We consider Conditional random fields (CRFs) with pattern-based potentials
defined on a chain. In this model the energy of a string (labeling) (Formula presented.)
is the sum of terms over intervals [i, j] where each term is non-zero only if
the substring (Formula presented.) equals a prespecified pattern w. Such CRFs
can be naturally applied to many sequence tagging problems. We present efficient
algorithms for the three standard inference tasks in a CRF, namely computing (i)
the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities
are respectively (Formula presented.), (Formula presented.) and (Formula presented.)
where L is the combined length of input patterns, (Formula presented.) is the
maximum length of a pattern, and D is the input alphabet. This improves on the
previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively
(Formula presented.), (Formula presented.) and (Formula presented.), where (Formula
presented.) is the number of input patterns. In addition, we give an efficient
algorithm for sampling, and revisit the case of MAP with non-positive weights.
acknowledgement: This work has been partially supported by the European Research Council
under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no. 616160.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Rustem
full_name: Takhanov, Rustem
id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87
last_name: Takhanov
citation:
ama: Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence
data. Algorithmica. 2016;76(1):17-46. doi:10.1007/s00453-015-0017-7
apa: Kolmogorov, V., & Takhanov, R. (2016). Inference algorithms for pattern-based
CRFs on sequence data. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-0017-7
chicago: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based
CRFs on Sequence Data.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-0017-7.
ieee: V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs
on sequence data,” Algorithmica, vol. 76, no. 1. Springer, pp. 17–46, 2016.
ista: Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs
on sequence data. Algorithmica. 76(1), 17–46.
mla: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based
CRFs on Sequence Data.” Algorithmica, vol. 76, no. 1, Springer, 2016, pp.
17–46, doi:10.1007/s00453-015-0017-7.
short: V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46.
date_created: 2018-12-11T11:54:02Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-10-17T09:51:31Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00453-015-0017-7
ec_funded: 1
external_id:
arxiv:
- '1210.0508'
intvolume: ' 76'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1210.0508
month: '09'
oa: 1
oa_version: Preprint
page: 17 - 46
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '5316'
quality_controlled: '1'
related_material:
record:
- id: '2272'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Inference algorithms for pattern-based CRFs on sequence data
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2016'
...
---
_id: '510'
abstract:
- lang: eng
text: 'The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted
signaling peptides that are primarily involved in the regulation of stem cell
homeostasis in different plant meristems. Particularly, the characterization of
the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on
the potential roles of CLE peptides in vascular development and wood formation.
Nevertheless, our knowledge on this gene family in a tree species is limited.
In a recent study, we reported on a systematically investigation of the CLE gene
family in Populus trichocarpa . The potential roles of PtCLE genes were studied
by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members,
many PtCLE proteins share identical CLE motifs or contain the same CLE motif as
that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression
patterns comparing to their Arabidopsis counterparts. These fi ndings indicate
the existence of both functional conservation and functional divergence between
PtCLEs and their AtCLE orthologues. Our results provide valuable resources for
future functional investigations of these critical signaling molecules in woody
plants. '
acknowledgement: 'We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement
des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading
of the article. Work in our group is supported by the National Natural Science Foundation
of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ
ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of
Higher Education from the Ministry of Education of China (20120202120009), the Scientific
Research Foundation for the Returned Overseas Chinese Scholars, State Education
Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China
(2014JM3064). '
article_number: e1191734
article_processing_charge: No
author:
- first_name: Zhijun
full_name: Liu, Zhijun
last_name: Liu
- first_name: 'Nan'
full_name: Yang, Nan
last_name: Yang
- first_name: Yanting
full_name: Lv, Yanting
last_name: Lv
- first_name: Lixia
full_name: Pan, Lixia
last_name: Pan
- first_name: Shuo
full_name: Lv, Shuo
last_name: Lv
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Guodong
full_name: Wang, Guodong
last_name: Wang
citation:
ama: Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant
Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734
apa: Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016).
The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior.
Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734
chicago: Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and
Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling
& Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.
ieee: Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant
Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.
ista: Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family
in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734.
mla: Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant
Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis,
2016, doi:10.1080/15592324.2016.1191734.
short: Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling &
Behavior 11 (2016).
date_created: 2018-12-11T11:46:53Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2023-10-17T11:13:40Z
day: '02'
department:
- _id: JiFr
doi: 10.1080/15592324.2016.1191734
intvolume: ' 11'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/
month: '06'
oa: 1
oa_version: Submitted Version
publication: Plant Signaling & Behavior
publication_status: published
publisher: Taylor & Francis
publist_id: '7308'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The CLE gene family in Populus trichocarpa
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...