---
_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'
article_processing_charge: No
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).
corr_author: '1'
date_created: 2018-12-11T11:51:34Z
date_published: 2016-08-04T00:00:00Z
date_updated: 2026-04-08T13:54:24Z
day: '04'
ddc:
- '576'
department:
- _id: GaTk
- _id: NiBa
- _id: CaGu
doi: 10.1038/ncomms12307
ec_funded: 1
external_id:
isi:
- '000380858400001'
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'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2016'
...
---
_id: '1096'
article_processing_charge: No
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: 2026-04-08T13:55:28Z
day: '20'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2016.05.024
external_id:
isi:
- '000378204200005'
intvolume: ' 37'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
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
article_processing_charge: No
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: 2026-04-08T14:10:21Z
day: '09'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_16
ec_funded: 1
external_id:
isi:
- '000386324500016'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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: 2026-04-08T14:10:21Z
day: '02'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-29485-8_24
ec_funded: 1
external_id:
isi:
- '000374102500024'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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: 2026-04-08T14:10:21Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_24
ec_funded: 1
external_id:
isi:
- '000386324500024'
intvolume: ' 9696'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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).'
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T11:52:02Z
date_published: 2016-05-17T00:00:00Z
date_updated: 2026-04-08T14:11:53Z
day: '17'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1002/anie.201601736
ec_funded: 1
external_id:
isi:
- '000377918400039'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 55
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'
article_processing_charge: No
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
corr_author: '1'
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2026-04-08T14:20:15Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925902
ec_funded: 1
external_id:
isi:
- '000380112400074'
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'
isi: 1
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: 'Big Splash: 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
scopus_import: '1'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
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.
article_processing_charge: No
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: 2026-04-08T14:19:43Z
day: '08'
department:
- _id: CaGu
doi: 10.1016/j.cub.2015.12.041
external_id:
isi:
- '000369502900034'
intvolume: ' 26'
isi: 1
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
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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'
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: 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 für 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 für 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 für 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 für Informatik, 2016, doi:10.4230/LIPIcs.ESA.2016.28.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl -
Leibniz-Zentrum für 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: 2026-04-08T14:22:16Z
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 für 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2026-04-08T14:23:19Z
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:50:18Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2026-04-08T14:28:53Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
file:
- access_level: closed
checksum: e3cd6b28f9c5cccb8891855565a2dade
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T10:55:35Z
date_updated: 2019-08-13T10:55:35Z
file_id: '6813'
file_name: Thesis_JSchwarz_final.pdf
file_size: 32044069
relation: main_file
- access_level: open_access
checksum: c3dbe219acf87eed2f46d21d5cca00de
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:43:14Z
date_updated: 2021-02-22T11:43:14Z
file_id: '9181'
file_name: 2016_Thesis_JSchwarz.pdf
file_size: 8396717
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:43:14Z
has_accepted_license: '1'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_id: '1122'
abstract:
- lang: eng
text: "Computer graphics is an extremely exciting field for two reasons. On the
one hand,\r\nthere is a healthy injection of pragmatism coming from the visual
effects industry\r\nthat want robust algorithms that work so they can produce
results at an increasingly\r\nfrantic pace. On the other hand, they must always
try to push the envelope and\r\nachieve the impossible to wow their audiences
in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism,
and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance
that it will pan into something\r\nuseful.\r\nWater simulation has been in visual
effects for decades, however it still remains\r\nextremely challenging because
of its high computational cost and difficult artdirectability.\r\nThe work in
this thesis tries to address some of these difficulties.\r\nSpecifically, we make
the following three novel contributions to the state-of-the-art\r\nin water simulation
for visual effects.\r\nFirst, we develop the first algorithm that can convert
any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art
methods at the time\r\ncould only handle surfaces with fixed connectivity, but
we are the first to be able to\r\nhandle surfaces that merge and split apart.
This is important for water simulation\r\npractitioners, because it allows them
to convert splashy water surfaces extracted\r\nfrom particles or simulated using
grid-based level sets into triangle meshes that can\r\nbe either textured and
enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm
to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions
of human performances.\r\nSecond, we formulate a surface-based energy that measures
the deviation of a\r\nwater surface froma physically valid state. Such discrepancies
arise when there is a\r\nmismatch in the degrees of freedom between the water
surface and the underlying\r\nphysics solver. This commonly happens when practitioners
use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution
grid-based surfaces\r\nare combined with low-resolution physics. Following the
direction of steepest\r\ndescent on our surface-based energy, we can either smooth
these artifacts or turn\r\nthem into high-resolution waves by interpreting the
energy as a physical potential.\r\nThird, we extend state-of-the-art techniques
in non-reflecting boundaries to handle spatially and time-varying background flows.
This allows a novel new\r\nworkflow where practitioners can re-simulate part of
an existing simulation, such\r\nas removing a solid obstacle, adding a new splash
or locally changing the resolution.\r\nSuch changes can easily lead to new waves
in the re-simulated region that would\r\nreflect off of the new simulation boundary,
effectively ruining the illusion of a\r\nseamless simulation boundary between
the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure
that such waves are absorbed."
acknowledgement: "First and foremost I would like to thank Chris. I have been incredibly
lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right
thing in all walks of\r\nlife is something I admire and aspire to. I also really
appreciate the fact that when\r\nworking with you it felt like we were equals. I
think we had a very synergetic work\r\nrelationship: I learned immensely from you,
but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would
like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working
with you. You showed me how to persevere and keep morale\r\nhigh when things were
looking the most bleak before the deadline. You are an\r\nincredible motivator and
super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker
games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing
you by asking about your guitar playing that one\r\ntime. You really are quite awesome!
Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch
researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also
like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have
learned so much. The excellent discussions we had in reading\r\ngroups and research
meetings really helped me become a better researcher!\r\nNext, I would like to thank
all the amazing people that I met during my PhD\r\nstudies, both at IST Austria,
in Vienna and elsewhere. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
citation:
ama: Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016.
doi:10.15479/AT:ISTA:th_640
apa: Bojsen-Hansen, M. (2016). Tracking, correcting and absorbing water surface
waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_640
chicago: Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface
Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:th_640.
ieee: M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,”
Institute of Science and Technology Austria, 2016.
ista: Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves.
Institute of Science and Technology Austria.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:th_640.
short: M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:50:16Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2026-04-08T14:24:06Z
day: '15'
ddc:
- '004'
- '005'
- '006'
- '532'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_640
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:02Z
date_updated: 2018-12-12T10:13:02Z
file_id: '4982'
file_name: IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf
file_size: 13869345
relation: main_file
file_date_updated: 2018-12-12T10:13:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
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: '6238'
related_material:
record:
- id: '5558'
relation: other
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Tracking, correcting and absorbing water surface waves
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_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.'
corr_author: '1'
date_created: 2018-12-11T11:50:16Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2026-04-08T14:24:23Z
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
relation: main_file
- access_level: open_access
checksum: 2d140cc924cd1b764544906fc22684ef
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:36:34Z
date_updated: 2021-02-22T11:36:34Z
file_id: '9178'
file_name: 2016_Mabillard_Thesis.pdf
file_size: 2227916
relation: main_file
success: 1
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:50:18Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2026-04-08T14:24:58Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GaTk
file:
- access_level: closed
checksum: ec453918c3bf8e6f460fd1156ef7b493
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T11:46:25Z
date_updated: 2019-08-13T11:46:25Z
file_id: '6815'
file_name: Thesis_Georg_Rieckh_w_signature_page.pdf
file_size: 2614660
relation: main_file
- access_level: open_access
checksum: 51ae398166370d18fd22478b6365c4da
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T11:30:40Z
date_updated: 2020-09-21T11:30:40Z
file_id: '8542'
file_name: Thesis_Georg_Rieckh.pdf
file_size: 6096178
relation: main_file
success: 1
file_date_updated: 2020-09-21T11:30:40Z
has_accepted_license: '1'
language:
- iso: eng
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:50:17Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2026-04-08T14:26:54Z
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'
file_name: MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf
file_size: 4785167
relation: main_file
- access_level: open_access
checksum: dd4136247fe472e7d47880ec68ac8de0
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:42:06Z
date_updated: 2021-02-22T11:42:06Z
file_id: '9180'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
_id: '5558'
abstract:
- lang: eng
text: PhD thesis LaTeX source code
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
citation:
ama: Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016.
doi:10.15479/AT:ISTA:48
apa: Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48
chicago: Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface
Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.
ieee: M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.”
Institute of Science and Technology Austria, 2016.
ista: Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.
short: M. Bojsen-Hansen, (2016).
datarep_id: '48'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2026-04-08T14:24:05Z
day: '23'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:48
file:
- access_level: open_access
checksum: 5b1b256ad796fbddb4b7729f5e45e444
content_type: application/x-bzip2
creator: system
date_created: 2018-12-12T13:02:18Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5589'
file_name: IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2
file_size: 55237885
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
month: '09'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '6238'
pubrep_id: '640'
related_material:
record:
- id: '1122'
relation: other
status: public
status: public
title: Tracking, Correcting and Absorbing Water Surface Waves
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:50:17Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2026-04-09T10:49:34Z
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:50:16Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2026-04-09T10:51:38Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoBo
ec_funded: 1
file:
- access_level: closed
checksum: 94bbbc754c36115bf37f8fc11fad43c4
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T11:17:50Z
date_updated: 2019-08-13T11:17:50Z
file_id: '6814'
file_name: PhDThesis_HandeAcar_1230.pdf
file_size: 3682711
relation: main_file
- access_level: open_access
checksum: 94bbbc754c36115bf37f8fc11fad43c4
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:51:13Z
date_updated: 2021-02-22T11:51:13Z
file_id: '9184'
file_name: 2016_Thesis_HandeAcar.pdf
file_size: 3682711
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:51:13Z
has_accepted_license: '1'
language:
- iso: eng
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_place: publisher
_id: '1398'
abstract:
- lang: eng
text: Hybrid zones represent evolutionary laboratories, where recombination brings
together alleles in combinations which have not previously been tested by selection.
This provides an excellent opportunity to test the effect of molecular variation
on fitness, and how this variation is able to spread through populations in a
natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for
two loci controlling the distribution of yellow and magenta floral pigments. Where
the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley
in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine
to give striking transgressive variation for flower colour. The sharp transition
in phenotype over ~1km implies strong selection maintaining the hybrid zone. An
indirect assay of pollinator visitation in the field found that pollinators forage
in a positive-frequency dependent manner on Antirrhinum, matching previous data
on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds
demonstrated assortative mating for pigmentation alleles, and that pollinator
behaviour alone is sufficient to explain this pattern. Selection by pollinators
should be sufficiently strong to maintain the hybrid zone, although other mechanisms
may be at work. At a broader scale I examined evolutionary transitions between
yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection
has acted strate that pollinators are a major determinant of reproductive success
and mating patterns in wild Antirrhinum.
acknowledgement: "I am indebted to many people for their support during my PhD, but
I particularly wish to thank Nick Barton for his guidance and intuition, and for
encouraging me to take the time to look beyond the immediate topic of my PhD to
understand the broader context. I am also especially grateful to David Field his
bottomless patience, invaluable advice on experimental design, analysis and scientific
writing, and for tireless work on the population surveys and genomic work without
most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work
with the combined strengths of the groups at The John Innes Centre, University of
Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in
Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank
David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections,
as well as Monique Burrus and Christophe Andalo and a large number of volunteers
for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski
for providing seeds and for her input into the design of the experimental arrays,
and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those
mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous
reviewers for their insightful comments on sections of this manuscript. I also thank
Jana Porsche for her e ff orts in tracking down the more obscure references for
chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted
to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer
and Magnus Nordborg for taking the time to read and evaluate the thesis given a
shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been
the supportive atmosphere of IST. In particular, I have come to appreciate the enormous
support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann
and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for
their enthusiasm and readiness to help where possible in setting up our greenhouse
and experiments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a
flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526
apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526
chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute
of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .
ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of
a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of
Science and Technology Austria, 2016.
ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria.
mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute
of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .
short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of
a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of
Science and Technology Austria, 2016.
corr_author: '1'
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2026-04-09T10:52:07Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
- _id: GradSch
doi: '10.15479/AT:ISTA:TH_526 '
file:
- access_level: open_access
checksum: f0f7c260e19ec1416824b165afe2d5fd
content_type: application/pdf
creator: dernst
date_created: 2025-07-03T06:24:17Z
date_updated: 2025-07-03T06:24:17Z
file_id: '19957'
file_name: 2016_Thesis_Ellis_noSignatures.pdf
file_size: 7590862
relation: main_file
- access_level: closed
checksum: a89b17ff27cf92c9a15f6b3d46bd7e53
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:51Z
date_updated: 2025-07-03T06:24:39Z
file_id: '5106'
file_name: IST-2016-526-v1+1_Ellis_signed_thesis.pdf
file_size: 11928241
relation: main_file
file_date_updated: 2025-07-03T06:24:39Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '130'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5809'
pubrep_id: '526'
related_material:
record:
- id: '5553'
relation: dissertation_contains
status: public
- id: '5551'
relation: dissertation_contains
status: public
- id: '5552'
relation: dissertation_contains
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: The role of pollinator-mediated selection in the maintenance of a flower color
polymorphism in an Antirrhinum majus hybrid zone
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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'
article_processing_charge: No
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).
corr_author: '1'
date_created: 2018-12-11T11:51:59Z
date_published: 2016-05-13T00:00:00Z
date_updated: 2026-04-09T10:52:26Z
day: '13'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/ncomms11552
ec_funded: 1
external_id:
isi:
- '000375938200001'
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
file_id: '5355'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2016'
...