---
_id: '1976'
abstract:
- lang: eng
text: 'Complex I is a key enzyme of the respiratory chain in many organisms. This
multi-protein complex with an intricate evolutionary history originated from the
unification of prebuilt modules of hydrogenases and transporters. Using recently
determined crystallographic structures of complex I we reanalyzed evolutionarily
related complexes that couple oxidoreduction to trans-membrane ion translocation.
Our analysis points to the previously unnoticed structural homology of the electron
input module of formate dehydrogenlyases and subunit NuoG of complex I. We also
show that all related to complex I hydrogenases likely operate via a conformation
driven mechanism with structural changes generated in the conserved coupling site
located at the interface of subunits NuoB/D/H. The coupling apparently originated
once in evolutionary history, together with subunit NuoH joining hydrogenase and
transport modules. Analysis of quinone oxidoreduction properties and the structure
of complex I allows us to suggest a fully reversible coupling mechanism. Our model
predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously
controlled by the protein, 2) the negative electric charge of the anionic ubiquinol
head group is a major driving force for conformational changes.'
acknowledgement: The work in authors' laboratory was funded by the Medical Research
Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Efremov R, Sazanov LA. The coupling mechanism of respiratory complex i - A
structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics.
2012;1817(10):1785-1795. doi:10.1016/j.bbabio.2012.02.015
apa: Efremov, R., & Sazanov, L. A. (2012). The coupling mechanism of respiratory
complex i - A structural and evolutionary perspective. Biochimica et Biophysica
Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2012.02.015
chicago: Efremov, Rouslan, and Leonid A Sazanov. “The Coupling Mechanism of Respiratory
Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica
Acta - Bioenergetics. Elsevier, 2012. https://doi.org/10.1016/j.bbabio.2012.02.015.
ieee: R. Efremov and L. A. Sazanov, “The coupling mechanism of respiratory complex
i - A structural and evolutionary perspective,” Biochimica et Biophysica Acta
- Bioenergetics, vol. 1817, no. 10. Elsevier, pp. 1785–1795, 2012.
ista: Efremov R, Sazanov LA. 2012. The coupling mechanism of respiratory complex
i - A structural and evolutionary perspective. Biochimica et Biophysica Acta -
Bioenergetics. 1817(10), 1785–1795.
mla: Efremov, Rouslan, and Leonid A. Sazanov. “The Coupling Mechanism of Respiratory
Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica
Acta - Bioenergetics, vol. 1817, no. 10, Elsevier, 2012, pp. 1785–95, doi:10.1016/j.bbabio.2012.02.015.
short: R. Efremov, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1817
(2012) 1785–1795.
date_created: 2018-12-11T11:55:00Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2019-04-26T07:22:06Z
day: '01'
doi: 10.1016/j.bbabio.2012.02.015
extern: 1
intvolume: ' 1817'
issue: '10'
month: '10'
page: 1785 - 1795
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '5108'
quality_controlled: 0
status: public
title: The coupling mechanism of respiratory complex i - A structural and evolutionary
perspective
type: review
volume: 1817
year: '2012'
...
---
_id: '492'
abstract:
- lang: eng
text: 'Background: Characterizing root system architecture (RSA) is essential to
understanding the development and function of vascular plants. Identifying RSA-associated
genes also represents an underexplored opportunity for crop improvement. Software
tools are needed to accelerate the pace at which quantitative traits of RSA are
estimated from images of root networks.Results: We have developed GiA Roots (General
Image Analysis of Roots), a semi-automated software tool designed specifically
for the high-throughput analysis of root system images. GiA Roots includes user-assisted
algorithms to distinguish root from background and a fully automated pipeline
that extracts dozens of root system phenotypes. Quantitative information on each
phenotype, along with intermediate steps for full reproducibility, is returned
to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line
interface for interweaving the software into large-scale workflows. GiA Roots
can also be extended to estimate novel phenotypes specified by the end-user.Conclusions:
We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing
12 genotypes from the species Oryza sativa. We validate trait measurements against
prior analyses of this image set that demonstrated that RSA traits are likely
heritable and associated with genotypic differences. Moreover, we demonstrate
that GiA Roots is extensible and an end-user can add functionality so that GiA
Roots can estimate novel RSA traits. In summary, we show that the software can
function as an efficient tool as part of a workflow to move from large numbers
of root images to downstream analysis.'
article_number: '116'
article_processing_charge: No
author:
- first_name: Taras
full_name: Galkovskyi, Taras
last_name: Galkovskyi
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Alexander
full_name: Bucksch, Alexander
last_name: Bucksch
- first_name: Brad
full_name: Moore, Brad
last_name: Moore
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Charles
full_name: Price, Charles
last_name: Price
- first_name: Chrostopher
full_name: Topp, Chrostopher
last_name: Topp
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Paul
full_name: Zurek, Paul
last_name: Zurek
- first_name: Suqin
full_name: Fang, Suqin
last_name: Fang
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
citation:
ama: 'Galkovskyi T, Mileyko Y, Bucksch A, et al. GiA Roots: Software for the high
throughput analysis of plant root system architecture. BMC Plant Biology.
2012;12. doi:10.1186/1471-2229-12-116'
apa: 'Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price,
C., … Weitz, J. (2012). GiA Roots: Software for the high throughput analysis of
plant root system architecture. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-12-116'
chicago: 'Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga
Symonova, Charles Price, Chrostopher Topp, et al. “GiA Roots: Software for the
High Throughput Analysis of Plant Root System Architecture.” BMC Plant Biology.
BioMed Central, 2012. https://doi.org/10.1186/1471-2229-12-116.'
ieee: 'T. Galkovskyi et al., “GiA Roots: Software for the high throughput
analysis of plant root system architecture,” BMC Plant Biology, vol. 12.
BioMed Central, 2012.'
ista: 'Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C,
Iyer Pascuzzi A, Zurek P, Fang S, Harer J, Benfey P, Weitz J. 2012. GiA Roots:
Software for the high throughput analysis of plant root system architecture. BMC
Plant Biology. 12, 116.'
mla: 'Galkovskyi, Taras, et al. “GiA Roots: Software for the High Throughput Analysis
of Plant Root System Architecture.” BMC Plant Biology, vol. 12, 116, BioMed
Central, 2012, doi:10.1186/1471-2229-12-116.'
short: T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C.
Topp, A. Iyer Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey, J. Weitz, BMC
Plant Biology 12 (2012).
date_created: 2018-12-11T11:46:46Z
date_published: 2012-07-26T00:00:00Z
date_updated: 2025-09-30T08:36:34Z
day: '26'
ddc:
- '005'
- '514'
- '516'
doi: 10.1186/1471-2229-12-116
extern: '1'
external_id:
isi:
- '000309114300001'
file:
- access_level: open_access
checksum: 0c629e36acd5f2878ff7dd088d67d494
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:35Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4953'
file_name: IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf
file_size: 1691436
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
publication: BMC Plant Biology
publication_status: published
publisher: BioMed Central
publist_id: '7328'
pubrep_id: '946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'GiA Roots: Software for the high throughput analysis of plant root system
architecture'
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: 12
year: '2012'
...
---
_id: '493'
abstract:
- lang: eng
text: 'The BCI competition IV stands in the tradition of prior BCI competitions
that aim to provide high quality neuroscientific data for open access to the scientific
community. As experienced already in prior competitions not only scientists from
the narrow field of BCI compete, but scholars with a broad variety of backgrounds
and nationalities. They include high specialists as well as students.The goals
of all BCI competitions have always been to challenge with respect to novel paradigms
and complex data. We report on the following challenges: (1) asynchronous data,
(2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer,
(5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after
past competitions, our hope is that winning entries may enhance the analysis methods
of future BCIs.'
acknowledgement: "The studies were in part or completely supported by the Bundesministerium
für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science
Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631
and 216886, the World Class University Program through the National Research Foundation
of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008),
the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415
(Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk),
the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal
Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830,
German Research Foundation grants 550/B5 and C6, and by a scholarship from the German
National Academic Foundation. This paper only reflects the authors’ views and funding
agencies are not liable for any use that may be made of the information contained
herein.\r\n"
article_number: '55'
article_processing_charge: No
author:
- first_name: Michael
full_name: Tangermann, Michael
last_name: Tangermann
- first_name: Klaus
full_name: Müller, Klaus
last_name: Müller
- first_name: Ad
full_name: Aertsen, Ad
last_name: Aertsen
- first_name: Niels
full_name: Birbaumer, Niels
last_name: Birbaumer
- first_name: Christoph
full_name: Braun, Christoph
last_name: Braun
- first_name: Clemens
full_name: Brunner, Clemens
last_name: Brunner
- first_name: Robert
full_name: Leeb, Robert
last_name: Leeb
- first_name: Carsten
full_name: Mehring, Carsten
last_name: Mehring
- first_name: Kai
full_name: Miller, Kai
last_name: Miller
- first_name: Gernot
full_name: Müller Putz, Gernot
last_name: Müller Putz
- first_name: Guido
full_name: Nolte, Guido
last_name: Nolte
- first_name: Gert
full_name: Pfurtscheller, Gert
last_name: Pfurtscheller
- first_name: Hubert
full_name: Preissl, Hubert
last_name: Preissl
- first_name: Gerwin
full_name: Schalk, Gerwin
last_name: Schalk
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Carmen
full_name: Vidaurre, Carmen
last_name: Vidaurre
- first_name: Stephan
full_name: Waldert, Stephan
last_name: Waldert
- first_name: Benjamin
full_name: Blankertz, Benjamin
last_name: Blankertz
citation:
ama: Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV.
Frontiers in Neuroscience. 2012;6. doi:10.3389/fnins.2012.00055
apa: Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner,
C., … Blankertz, B. (2012). Review of the BCI competition IV. Frontiers in
Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnins.2012.00055
chicago: Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph
Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.”
Frontiers in Neuroscience. Frontiers Research Foundation, 2012. https://doi.org/10.3389/fnins.2012.00055.
ieee: M. Tangermann et al., “Review of the BCI competition IV,” Frontiers
in Neuroscience, vol. 6. Frontiers Research Foundation, 2012.
ista: Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R,
Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk
G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition
IV. Frontiers in Neuroscience. 6, 55.
mla: Tangermann, Michael, et al. “Review of the BCI Competition IV.” Frontiers
in Neuroscience, vol. 6, 55, Frontiers Research Foundation, 2012, doi:10.3389/fnins.2012.00055.
short: M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner,
R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H.
Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers
in Neuroscience 6 (2012).
date_created: 2018-12-11T11:46:46Z
date_published: 2012-07-13T00:00:00Z
date_updated: 2025-09-30T08:35:59Z
day: '13'
ddc:
- '004'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3389/fnins.2012.00055
external_id:
isi:
- '000209165300066'
file:
- access_level: open_access
checksum: 195238221c4b0b0f4035f6f6c16ea17c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:34Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5356'
file_name: IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf
file_size: 2693701
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7327'
pubrep_id: '945'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Review of the BCI competition IV
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: 6
year: '2012'
...
---
_id: '495'
abstract:
- lang: eng
text: An automaton with advice is a finite state automaton which has access to an
additional fixed infinite string called an advice tape. We refine the Myhill-Nerode
theorem to characterize the languages of finite strings that are accepted by automata
with advice. We do the same for tree automata with advice.
alternative_title:
- EPTCS
author:
- first_name: Alex
full_name: Kruckman, Alex
last_name: Kruckman
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
- first_name: John
full_name: Sheridan, John
last_name: Sheridan
- first_name: Ben
full_name: Zax, Ben
last_name: Zax
citation:
ama: 'Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata
with advice. In: Proceedings GandALF 2012. Vol 96. Open Publishing Association;
2012:238-246. doi:10.4204/EPTCS.96.18'
apa: 'Kruckman, A., Rubin, S., Sheridan, J., & Zax, B. (2012). A Myhill Nerode
theorem for automata with advice. In Proceedings GandALF 2012 (Vol. 96,
pp. 238–246). Napoli, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.96.18'
chicago: Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode
Theorem for Automata with Advice.” In Proceedings GandALF 2012, 96:238–46.
Open Publishing Association, 2012. https://doi.org/10.4204/EPTCS.96.18.
ieee: A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for
automata with advice,” in Proceedings GandALF 2012, Napoli, Italy, 2012,
vol. 96, pp. 238–246.
ista: 'Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for
automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics
and Formal Verification, EPTCS, vol. 96, 238–246.'
mla: Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.”
Proceedings GandALF 2012, vol. 96, Open Publishing Association, 2012, pp.
238–46, doi:10.4204/EPTCS.96.18.
short: A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012,
Open Publishing Association, 2012, pp. 238–246.
conference:
end_date: 2012-09-08
location: Napoli, Italy
name: 'GandALF: Games, Automata, Logics and Formal Verification'
start_date: 2012-09-06
corr_author: '1'
date_created: 2018-12-11T11:46:47Z
date_published: 2012-10-07T00:00:00Z
date_updated: 2024-10-09T20:55:00Z
day: '07'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4204/EPTCS.96.18
ec_funded: 1
file:
- access_level: open_access
checksum: 56277f95edc9d531fa3bdc5f9579fda8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:31Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5152'
file_name: IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf
file_size: 97736
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 96'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 238 - 246
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings GandALF 2012
publication_status: published
publisher: Open Publishing Association
publist_id: '7325'
pubrep_id: '944'
quality_controlled: '1'
scopus_import: 1
status: public
title: A Myhill Nerode theorem for automata with advice
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2012'
...
---
_id: '496'
abstract:
- lang: eng
text: 'We study the expressive power of logical interpretations on the class of
scattered trees, namely those with countably many infinite branches. Scattered
trees can be thought of as the tree analogue of scattered linear orders. Every
scattered tree has an ordinal rank that reflects the structure of its infinite
branches. We prove, roughly, that trees and orders of large rank cannot be interpreted
in scattered trees of small rank. We consider a quite general notion of interpretation:
each element of the interpreted structure is represented by a set of tuples of
subsets of the interpreting tree. Our trees are countable, not necessarily finitely
branching, and may have finitely many unary predicates as labellings. We also
show how to replace injective set-interpretations in (not necessarily scattered)
trees by ''finitary'' set-interpretations.'
alternative_title:
- LICS
article_number: '6280474'
article_processing_charge: No
author:
- first_name: Alexander
full_name: Rabinovich, Alexander
last_name: Rabinovich
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
citation:
ama: 'Rabinovich A, Rubin S. Interpretations in trees with countably many branches.
In: IEEE; 2012. doi:10.1109/LICS.2012.65'
apa: 'Rabinovich, A., & Rubin, S. (2012). Interpretations in trees with countably
many branches. Presented at the LICS: Logic in Computer Science, Dubrovnik, Croatia:
IEEE. https://doi.org/10.1109/LICS.2012.65'
chicago: Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with
Countably Many Branches.” IEEE, 2012. https://doi.org/10.1109/LICS.2012.65.
ieee: 'A. Rabinovich and S. Rubin, “Interpretations in trees with countably many
branches,” presented at the LICS: Logic in Computer Science, Dubrovnik, Croatia,
2012.'
ista: 'Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many
branches. LICS: Logic in Computer Science, LICS, , 6280474.'
mla: Rabinovich, Alexander, and Sasha Rubin. Interpretations in Trees with Countably
Many Branches. 6280474, IEEE, 2012, doi:10.1109/LICS.2012.65.
short: A. Rabinovich, S. Rubin, in:, IEEE, 2012.
conference:
end_date: 2012-06-28
location: Dubrovnik, Croatia
name: 'LICS: Logic in Computer Science'
start_date: 2012-06-25
date_created: 2018-12-11T11:46:47Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2025-09-30T08:34:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/LICS.2012.65
ec_funded: 1
external_id:
isi:
- '000309059900061'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: IEEE
publist_id: '7324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interpretations in trees with countably many branches
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2012'
...
---
_id: '497'
abstract:
- lang: eng
text: 'One central issue in the formal design and analysis of reactive systems is
the notion of refinement that asks whether all behaviors of the implementation
is allowed by the specification. The local interpretation of behavior leads to
the notion of simulation. Alternating transition systems (ATSs) provide a general
model for composite reactive systems, and the simulation relation for ATSs is
known as alternating simulation. The simulation relation for fair transition systems
is called fair simulation. In this work our main contributions are as follows:
(1) We present an improved algorithm for fair simulation with Büchi fairness constraints;
our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time
algorithm, where n is the number of states and m is the number of transitions.
(2) We present a game based algorithm for alternating simulation that requires
O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n
is the number of states and m is the size of transition relation. (3) We present
an iterative algorithm for alternating simulation that matches the time complexity
of the game based algorithm, but is more space efficient than the game based algorithm.
© Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.'
alternative_title:
- LIPIcs
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Siddhesh
full_name: Chaubal, Siddhesh
last_name: Chaubal
- first_name: Pritish
full_name: Kamath, Pritish
last_name: Kamath
citation:
ama: 'Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement
relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182.
doi:10.4230/LIPIcs.CSL.2012.167'
apa: 'Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms for
alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL:
European Association for Computer Science Logic, Fontainebleau, France: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2012.167'
chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms
for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2012. https://doi.org/10.4230/LIPIcs.CSL.2012.167.
ieee: 'K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating
refinement relations,” presented at the EACSL: European Association for Computer
Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.'
ista: 'Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating
refinement relations. EACSL: European Association for Computer Science Logic,
LIPIcs, vol. 16, 167–182.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement
Relations. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012,
pp. 167–82, doi:10.4230/LIPIcs.CSL.2012.167.
short: K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2012, pp. 167–182.
conference:
end_date: 2012-09-06
location: Fontainebleau, France
name: 'EACSL: European Association for Computer Science Logic'
start_date: 2012-09-03
date_created: 2018-12-11T11:46:48Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2025-01-14T12:24:50Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.CSL.2012.167
ec_funded: 1
file:
- access_level: open_access
checksum: f1b0dd99240800db2d7dbf9b5131fe5e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:50Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4712'
file_name: IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf
file_size: 471236
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 167 - 182
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7323'
pubrep_id: '943'
quality_controlled: '1'
related_material:
record:
- id: '5378'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Faster algorithms for alternating refinement relations
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2012'
...
---
_id: '498'
abstract:
- lang: eng
text: Understanding patterns and correlates of local adaptation in heterogeneous
landscapes can provide important information in the selection of appropriate seed
sources for restoration. We assessed the extent of local adaptation of fitness
components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides
(Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance,
quantitative (QST) and neutral (FST) genetic differentiation, and size of the
local and foreign populations could predict patterns of adaptive differentiation.
Local adaptation varied among populations and fitness components. Including all
population pairs, local adaptation was observed for seedling survival, but not
for biomass, while foreign genotype advantage was observed for reproduction (number
of inflorescences). Among population pairs, local adaptation increased with QST
and local population size for biomass. QST was associated with environmental distance,
suggesting ecological selection for phenotypic divergence. However, low FST and
variation in population structure in small populations demonstrates the interaction
of gene flow and drift in constraining local adaptation in R. leptorrhynchoides.
Our study indicates that for species in heterogeneous landscapes, collecting seed
from large populations from similar environments to candidate sites is likely
to provide the most appropriate seed sources for restoration.
acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and
Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment
and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability
and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer
C. H. Barrett for comments that improved the quality of the manuscript.\r\n"
article_processing_charge: No
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented
plant populations: Implications for restoration genetics. Evolutionary Applications.
2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x'
apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local
adaptation in fragmented plant populations: Implications for restoration genetics.
Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x'
chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting
Local Adaptation in Fragmented Plant Populations: Implications for Restoration
Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.'
ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation
in fragmented plant populations: Implications for restoration genetics,” Evolutionary
Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.'
ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in
fragmented plant populations: Implications for restoration genetics. Evolutionary
Applications. 5(8), 913–924.'
mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations:
Implications for Restoration Genetics.” Evolutionary Applications, vol.
5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.'
short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012)
913–924.
corr_author: '1'
date_created: 2018-12-11T11:46:48Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2025-09-30T08:33:55Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/j.1752-4571.2012.00284.x
external_id:
isi:
- '000312808900013'
file:
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date_updated: 2020-07-14T12:46:35Z
file_id: '4821'
file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf
file_size: 396136
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 913 - 924
publication: Evolutionary Applications
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7322'
pubrep_id: '942'
quality_controlled: '1'
status: public
title: 'Predicting local adaptation in fragmented plant populations: Implications
for restoration genetics'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2012'
...
---
_id: '5377'
abstract:
- lang: eng
text: 'Two-player games on graphs are central in many problems in formal verification
and program analysis such as synthesis and verification of open systems. In this
work we consider solving recursive game graphs (or pushdown game graphs) that
can model the control flow of sequential programs with recursion. While pushdown
games have been studied before with qualitative objectives, such as reachability
and ω-regular objectives, in this work we study for the first time such games
with the most well-studied quantitative objective, namely, mean-payoff objectives.
In pushdown games two types of strategies are relevant: (1) global strategies,
that depend on the entire global history; and (2) modular strategies, that have
only local memory and thus do not depend on the context of invocation, but only
on the history of the current invocation of the module. Our main results are as
follows: (1) One-player pushdown games with mean-payoff objectives under global
strategies are decidable in polynomial time. (2) Two- player pushdown games with
mean-payoff objectives under global strategies are undecidable. (3) One-player
pushdown games with mean-payoff objectives under modular strategies are NP- hard.
(4) Two-player pushdown games with mean-payoff objectives under modular strategies
can be solved in NP (i.e., both one-player and two-player pushdown games with
mean-payoff objectives under modular strategies are NP-complete). We also establish
the optimal strategy complexity showing that global strategies for mean-payoff
objectives require infinite memory even in one-player pushdown games; and memoryless
modular strategies are sufficient in two- player pushdown games. Finally we also
show that all the problems have the same complexity if the stack boundedness condition
is added, where along with the mean-payoff objective the player must also ensure
that the stack height is bounded.'
alternative_title:
- IST Austria Technical Report
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: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. Mean-Payoff Pushdown Games. IST Austria; 2012.
doi:10.15479/AT:IST-2012-0002
apa: Chatterjee, K., & Velner, Y. (2012). Mean-payoff pushdown games.
IST Austria. https://doi.org/10.15479/AT:IST-2012-0002
chicago: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games.
IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0002.
ieee: K. Chatterjee and Y. Velner, Mean-payoff pushdown games. IST Austria,
2012.
ista: Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p.
mla: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games.
IST Austria, 2012, doi:10.15479/AT:IST-2012-0002.
short: K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.
corr_author: '1'
date_created: 2018-12-12T11:38:59Z
date_published: 2012-07-02T00:00:00Z
date_updated: 2025-09-30T08:08:12Z
day: '02'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2012-0002
file:
- access_level: open_access
checksum: a03c08c1589dbb0c96183a8bcf3ab240
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:00Z
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file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
language:
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month: '07'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '10'
related_material:
record:
- id: '2956'
relation: later_version
status: public
status: public
title: Mean-payoff pushdown games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5378'
abstract:
- lang: eng
text: 'One central issue in the formal design and analysis of reactive systems is
the notion of refinement that asks whether all behaviors of the implementation
is allowed by the specification. The local interpretation of behavior leads to
the notion of simulation. Alternating transition systems (ATSs) provide a general
model for composite reactive systems, and the simulation relation for ATSs is
known as alternating simulation. The simulation relation for fair transition systems
is called fair simulation. In this work our main contributions are as follows:
(1) We present an improved algorithm for fair simulation with Büchi fairness constraints;
our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time
algorithm, where n is the number of states and m is the number of transitions.
(2) We present a game based algorithm for alternating simulation that requires
O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where
n is the number of states and m is the size of transition relation. (3) We present
an iterative algorithm for alternating simulation that matches the time complexity
of the game based algorithm, but is more space efficient than the game based algorithm.'
alternative_title:
- IST Austria Technical Report
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: Siddhesh
full_name: Chaubal, Siddhesh
last_name: Chaubal
- first_name: Pritish
full_name: Kamath, Pritish
last_name: Kamath
citation:
ama: Chatterjee K, Chaubal S, Kamath P. Faster Algorithms for Alternating Refinement
Relations. IST Austria; 2012. doi:10.15479/AT:IST-2012-0001
apa: Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms
for alternating refinement relations. IST Austria. https://doi.org/10.15479/AT:IST-2012-0001
chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. Faster
Algorithms for Alternating Refinement Relations. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0001.
ieee: K. Chatterjee, S. Chaubal, and P. Kamath, Faster algorithms for alternating
refinement relations. IST Austria, 2012.
ista: Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating
refinement relations, IST Austria, 21p.
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement
Relations. IST Austria, 2012, doi:10.15479/AT:IST-2012-0001.
short: K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement
Relations, IST Austria, 2012.
corr_author: '1'
date_created: 2018-12-12T11:38:59Z
date_published: 2012-07-04T00:00:00Z
date_updated: 2025-04-15T08:12:24Z
day: '04'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2012-0001
file:
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checksum: ec8d1857cc7095d3de5107a0162ced37
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '14'
related_material:
record:
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status: public
title: Faster algorithms for alternating refinement relations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5396'
abstract:
- lang: eng
text: We consider the problem of inference in agraphical model with binary variables.
While in theory it is arguably preferable to compute marginal probabilities, in
practice researchers often use MAP inference due to the availability of efficient
discrete optimization algorithms. We bridge the gap between the two approaches
by introducing the Discrete Marginals technique in which approximate marginals
are obtained by minimizing an objective function with unary and pair-wise terms
over a discretized domain. This allows the use of techniques originally devel-oped
for MAP-MRF inference and learning. We explore two ways to set up the objective
function - by discretizing the Bethe free energy and by learning it from training
data. Experimental results show that for certain types of graphs a learned function
can out-perform the Bethe approximation. We also establish a link between the
Bethe free energy and submodular functions.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Filip
full_name: Korc, Filip
id: 476A2FD6-F248-11E8-B48F-1D18A9856A87
last_name: Korc
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Korc F, Kolmogorov V, Lampert C. Approximating Marginals Using Discrete
Energy Minimization. IST Austria; 2012. doi:10.15479/AT:IST-2012-0003
apa: Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals
using discrete energy minimization. IST Austria. https://doi.org/10.15479/AT:IST-2012-0003
chicago: Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. Approximating
Marginals Using Discrete Energy Minimization. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0003.
ieee: F. Korc, V. Kolmogorov, and C. Lampert, Approximating marginals using discrete
energy minimization. IST Austria, 2012.
ista: Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete
energy minimization, IST Austria, 13p.
mla: Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization.
IST Austria, 2012, doi:10.15479/AT:IST-2012-0003.
short: F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete
Energy Minimization, IST Austria, 2012.
date_created: 2018-12-12T11:39:06Z
date_published: 2012-07-23T00:00:00Z
date_updated: 2024-10-09T20:54:48Z
day: '23'
ddc:
- '000'
department:
- _id: VlKo
- _id: ChLa
doi: 10.15479/AT:IST-2012-0003
file:
- access_level: open_access
checksum: 7e0ba85ad123b13223aaf6cdde2d288c
content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:46:44Z
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file_name: IST-2012-0003_IST-2012-0003.pdf
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '13'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '36'
related_material:
record:
- id: '3124'
relation: earlier_version
status: public
status: public
title: Approximating marginals using discrete energy minimization
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '5398'
abstract:
- lang: eng
text: This document is created as a part of the project “Repository for Research
Data on IST Austria”. It summarises the actual state of research data at IST Austria,
based on survey results. It supports the choice of appropriate software, which
would best fit the requirements of their users, the researchers.
author:
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: Porsche J. Actual State of Research Data @ ISTAustria. IST Austria;
2012.
apa: Porsche, J. (2012). Actual state of research data @ ISTAustria. IST
Austria.
chicago: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria,
2012.
ieee: J. Porsche, Actual state of research data @ ISTAustria. IST Austria,
2012.
ista: Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p.
mla: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria,
2012.
short: J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.
date_created: 2018-12-12T11:39:06Z
date_published: 2012-11-12T00:00:00Z
date_updated: 2020-07-14T23:04:49Z
day: '12'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: e0a7c041eea1ca4b70ab6f9ec5177f4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:11Z
date_updated: 2020-07-14T12:46:44Z
file_id: '5472'
file_name: IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf
file_size: 238544
relation: main_file
file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
pubrep_id: '103'
status: public
title: Actual state of research data @ ISTAustria
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
OA_place: repository
_id: '5745'
abstract:
- lang: eng
text: Unsatisfiability proofs find many applications in verification. Today, many
SAT solvers are capable of producing resolution proofs of unsatisfiability. For
efficiency smaller proofs are preferred over bigger ones. The solvers apply proof
reduction methods to remove redundant parts of the proofs while and after generating
the proofs. One method of reducing resolution proofs is redundant resolution reduction,
i.e., removing repeated pivots in the paths of resolution proofs (aka Pivot recycle).
The known single pass algorithm only tries to remove redundancies in the parts
of the proof that are trees. In this paper, we present three modifications to
improve the algorithm such that the redundancies can be found in the parts of
the proofs that are DAGs. The first modified algorithm covers greater number of
redundancies as compared to the known algorithm without incurring any additional
cost. The second modified algorithm covers even greater number of the redundancies
but it may have longer run times. Our third modified algorithm is parametrized
and can trade off between run times and the coverage of the redundancies. We have
implemented our algorithms in OpenSMT and applied them on unsatisfiability proofs
of 198 examples from plain MUS track of SAT11 competition. The first and second
algorithm additionally remove 0.89% and 10.57% of clauses respectively as compared
to the original algorithm. For certain value of the parameter, the third algorithm
removes almost as many clauses as the second algorithm but is significantly faster.
acknowledgement: "This work was supported by the ERC Advanced Investigator grant on
Quantitative\r\nReactive Modeling (QUAREM)."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
citation:
ama: 'Gupta A. Improved single pass algorithms for resolution proof reduction. In:
10th International Symposium on Automated Technology for Verification and Analysis.
Vol 7561. Springer Nature; 2012:107-121. doi:10.1007/978-3-642-33386-6_10'
apa: 'Gupta, A. (2012). Improved single pass algorithms for resolution proof reduction.
In 10th International Symposium on Automated Technology for Verification and
Analysis (Vol. 7561, pp. 107–121). Thiruvananthapuram, Kerala, India: Springer
Nature. https://doi.org/10.1007/978-3-642-33386-6_10'
chicago: Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof
Reduction.” In 10th International Symposium on Automated Technology for Verification
and Analysis, 7561:107–21. Springer Nature, 2012. https://doi.org/10.1007/978-3-642-33386-6_10.
ieee: A. Gupta, “Improved single pass algorithms for resolution proof reduction,”
in 10th International Symposium on Automated Technology for Verification and
Analysis, Thiruvananthapuram, Kerala, India, 2012, vol. 7561, pp. 107–121.
ista: 'Gupta A. 2012. Improved single pass algorithms for resolution proof reduction.
10th International Symposium on Automated Technology for Verification and Analysis.
ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 7561, 107–121.'
mla: Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.”
10th International Symposium on Automated Technology for Verification and Analysis,
vol. 7561, Springer Nature, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10.
short: A. Gupta, in:, 10th International Symposium on Automated Technology for Verification
and Analysis, Springer Nature, 2012, pp. 107–121.
conference:
end_date: 2012-10-06
location: Thiruvananthapuram, Kerala, India
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2012-10-03
corr_author: '1'
date_created: 2018-12-18T13:01:46Z
date_published: 2012-09-28T00:00:00Z
date_updated: 2025-04-15T07:56:27Z
day: '28'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-33386-6_10
ec_funded: 1
file:
- access_level: open_access
checksum: 68415837a315de3cc4d120f6019d752c
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:07:35Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5746'
file_name: 2012_ATVA_Gupta.pdf
file_size: 465502
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 7561'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 107-121
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: 10th International Symposium on Automated Technology for Verification
and Analysis
publication_identifier:
eisbn:
- '9783642333866'
eissn:
- 1611-3349
isbn:
- '9783642333859'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
pubrep_id: '180'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved single pass algorithms for resolution proof reduction
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7561
year: '2012'
...
---
_id: '5839'
abstract:
- lang: eng
text: "Canny's edge detection algorithm is a classical and robust method for edge
detection in gray-scale images. The two \r\nsignificant features of this method
are introduction of NMS (Non-Maximum Suppression) and double thresholding of \r\nthe
\ gradient image. Due to poor illumination, the region boundaries in
\ an image may become vague, creating \r\nuncertainties in the gradient
\ image. In this paper, we have proposed an algorithm based on the
\ concept of type-2 fuzzy sets to handle uncertainties that automatically
\ selects the threshold values needed to segment the gradient image using
classical Canny’s edge detection algorithm. The results show that our algorithm
works significantly well on different benchmark images as well as medical images
(hand radiography images). "
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Jaya
full_name: Sil, Jaya
last_name: Sil
citation:
ama: Biswas R, Sil J. An Improved Canny Edge Detection Algorithm Based on Type-2
Fuzzy Sets. Procedia Technology. 2012;4:820-824. doi:10.1016/j.protcy.2012.05.134
apa: Biswas, R., & Sil, J. (2012). An Improved Canny Edge Detection Algorithm
Based on Type-2 Fuzzy Sets. Procedia Technology. Elsevier. https://doi.org/10.1016/j.protcy.2012.05.134
chicago: Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm
Based on Type-2 Fuzzy Sets.” Procedia Technology. Elsevier, 2012. https://doi.org/10.1016/j.protcy.2012.05.134.
ieee: R. Biswas and J. Sil, “An Improved Canny Edge Detection Algorithm Based on
Type-2 Fuzzy Sets,” Procedia Technology, vol. 4. Elsevier, pp. 820–824,
2012.
ista: Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on
Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824.
mla: Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based
on Type-2 Fuzzy Sets.” Procedia Technology, vol. 4, Elsevier, 2012, pp.
820–24, doi:10.1016/j.protcy.2012.05.134.
short: R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824.
date_created: 2019-01-17T11:54:21Z
date_published: 2012-05-01T00:00:00Z
date_updated: 2021-01-12T08:03:43Z
day: '01'
ddc:
- '000'
doi: 10.1016/j.protcy.2012.05.134
extern: '1'
file:
- access_level: open_access
checksum: ba0185986b151d8c11201f48cd505ceb
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T07:28:06Z
date_updated: 2020-07-14T12:47:12Z
file_id: '5863'
file_name: 2012_Procedia_Biswas.pdf
file_size: 305426
relation: main_file
file_date_updated: 2020-07-14T12:47:12Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 820-824
publication: Procedia Technology
publication_identifier:
issn:
- 2212-0173
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2012'
...
---
_id: '596'
abstract:
- lang: eng
text: The human Mediator complex controls RNA polymerase II (pol II) function in
ways that remain incompletely understood. Activator-Mediator binding alters Mediator
structure, and these activator-induced structural shifts appear to play key roles
in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed
that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly
in which Mediator was bound to the activation domain of viral protein 16 (VP16).
Whereas TFIIF was shown to be important for orienting pol II within this assembly,
the potential role of the activator was not assessed. To determine how activator
binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF
complexes in which Mediator was not bound to an activator. Cryo-EM analysis of
this assembly, coupled with pol II crystal structure docking, revealed that pol
II binds Mediator at the same general location; however, in contrast to VP16-bound
Mediator, pol II does not appear to stably orient in the absence of an activator.
Variability in pol II orientation might be important mechanistically, perhaps
to enable sense and antisense transcription at human promoters. Because Mediator
interacts extensively with pol II, these results suggest that Mediator structural
shifts induced by activator binding help stably orient pol II prior to transcription
initiation.
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Dylan
full_name: Taatjes, Dylan
last_name: Taatjes
citation:
ama: Bernecky C, Taatjes D. Activator-mediator binding stabilizes RNA polymerase
II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal
of Molecular Biology. 2012;417(5):387-394. doi:10.1016/j.jmb.2012.02.014
apa: Bernecky, C., & Taatjes, D. (2012). Activator-mediator binding stabilizes
RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF
assembly. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2012.02.014
chicago: Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes
RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF
Assembly.” Journal of Molecular Biology. Elsevier, 2012. https://doi.org/10.1016/j.jmb.2012.02.014.
ieee: C. Bernecky and D. Taatjes, “Activator-mediator binding stabilizes RNA polymerase
II orientation within the human mediator-RNA polymerase II-TFIIF assembly,” Journal
of Molecular Biology, vol. 417, no. 5. Elsevier, pp. 387–394, 2012.
ista: Bernecky C, Taatjes D. 2012. Activator-mediator binding stabilizes RNA polymerase
II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal
of Molecular Biology. 417(5), 387–394.
mla: Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes
RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF
Assembly.” Journal of Molecular Biology, vol. 417, no. 5, Elsevier, 2012,
pp. 387–94, doi:10.1016/j.jmb.2012.02.014.
short: C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394.
date_created: 2018-12-11T11:47:24Z
date_published: 2012-04-13T00:00:00Z
date_updated: 2021-01-12T08:05:21Z
day: '13'
doi: 10.1016/j.jmb.2012.02.014
extern: '1'
intvolume: ' 417'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/
month: '04'
oa: 1
oa_version: None
page: 387 - 394
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '7208'
status: public
title: Activator-mediator binding stabilizes RNA polymerase II orientation within
the human mediator-RNA polymerase II-TFIIF assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 417
year: '2012'
...
---
_id: '6136'
abstract:
- lang: eng
text: Tonic receptors convey stimulus duration and intensity and are implicated
in homeostatic control. However, how tonic homeostatic signals are generated and
how they reconfigure neural circuits and modify animal behavior is poorly understood.
Here we show that Caenorhabditis elegans O2-sensing neurons are tonic receptors
that continuously signal ambient [O2] to set the animal's behavioral state. Sustained
signaling relied on a Ca2+ relay involving L-type voltage-gated Ca2+ channels,
the ryanodine and the inositol-1,4,5-trisphosphate receptors. Tonic activity evoked
continuous neuropeptide release, which helps elicit the enduring behavioral state
associated with high [O2]. Sustained O2 receptor signaling was propagated to downstream
neural circuits, including the hub interneuron RMG. O2 receptors evoked similar
locomotory states at particular O2 concentrations, regardless of previous d[O2]/dt.
However, a phasic component of the URX receptors' response to high d[O2]/dt, as
well as tonic-to-phasic transformations in downstream interneurons, enabled transient
reorientation movements shaped by d[O2]/dt. Our results highlight how tonic homeostatic
signals can generate both transient and enduring behavioral change.
author:
- first_name: Karl Emanuel
full_name: Busch, Karl Emanuel
last_name: Busch
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Zoltan
full_name: Soltesz, Zoltan
last_name: Soltesz
- first_name: Robin Joseph
full_name: Murphy, Robin Joseph
last_name: Murphy
- first_name: Olivier
full_name: Faivre, Olivier
last_name: Faivre
- first_name: Berthold
full_name: Hedwig, Berthold
last_name: Hedwig
- first_name: Martin
full_name: Thomas, Martin
last_name: Thomas
- first_name: Heather L
full_name: Smith, Heather L
last_name: Smith
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Busch KE, Laurent P, Soltesz Z, et al. Tonic signaling from O2 sensors sets
neural circuit activity and behavioral state. Nature Neuroscience. 2012;15(4):581-591.
doi:10.1038/nn.3061
apa: Busch, K. E., Laurent, P., Soltesz, Z., Murphy, R. J., Faivre, O., Hedwig,
B., … de Bono, M. (2012). Tonic signaling from O2 sensors sets neural circuit
activity and behavioral state. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn.3061
chicago: Busch, Karl Emanuel, Patrick Laurent, Zoltan Soltesz, Robin Joseph Murphy,
Olivier Faivre, Berthold Hedwig, Martin Thomas, Heather L Smith, and Mario de
Bono. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral
State.” Nature Neuroscience. Springer Nature, 2012. https://doi.org/10.1038/nn.3061.
ieee: K. E. Busch et al., “Tonic signaling from O2 sensors sets neural circuit
activity and behavioral state,” Nature Neuroscience, vol. 15, no. 4. Springer
Nature, pp. 581–591, 2012.
ista: Busch KE, Laurent P, Soltesz Z, Murphy RJ, Faivre O, Hedwig B, Thomas M, Smith
HL, de Bono M. 2012. Tonic signaling from O2 sensors sets neural circuit activity
and behavioral state. Nature Neuroscience. 15(4), 581–591.
mla: Busch, Karl Emanuel, et al. “Tonic Signaling from O2 Sensors Sets Neural Circuit
Activity and Behavioral State.” Nature Neuroscience, vol. 15, no. 4, Springer
Nature, 2012, pp. 581–91, doi:10.1038/nn.3061.
short: K.E. Busch, P. Laurent, Z. Soltesz, R.J. Murphy, O. Faivre, B. Hedwig, M.
Thomas, H.L. Smith, M. de Bono, Nature Neuroscience 15 (2012) 581–591.
date_created: 2019-03-20T14:23:30Z
date_published: 2012-03-04T00:00:00Z
date_updated: 2021-01-12T08:06:17Z
day: '04'
doi: 10.1038/nn.3061
extern: '1'
external_id:
pmid:
- '22388961'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/
month: '03'
oa: 1
oa_version: Submitted Version
page: 581-591
pmid: 1
publication: Nature Neuroscience
publication_identifier:
issn:
- 1097-6256
- 1546-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Tonic signaling from O2 sensors sets neural circuit activity and behavioral
state
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2012'
...
---
_id: '1987'
abstract:
- lang: eng
text: |
In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction-diffusion system.
acknowledgement: 'This work was supported by the Max-Planck-Society (P.S. and M.L.)
and by the German Research Foundation as part of the Research Training Group “Nano-
and Biotechnologies for Electronic Device Packaging” (GRK 1401) (J.S.) and by the
Leibniz-Award (P.S.). '
author:
- first_name: Jakob
full_name: Schweizer, Jakob
last_name: Schweizer
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Mike
full_name: 'Bonny, Mike '
last_name: Bonny
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Ingolf
full_name: Mönch, Ingolf
last_name: Mönch
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
citation:
ama: Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, Schwille P. Geometry sensing
by self-organized protein patterns. PNAS. 2012;109(38):15283-15288. doi:10.1073/pnas.1206953109
apa: Schweizer, J., Loose, M., Bonny, M., Kruse, K., Mönch, I., & Schwille,
P. (2012). Geometry sensing by self-organized protein patterns. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1206953109
chicago: Schweizer, Jakob, Martin Loose, Mike Bonny, Karsten Kruse, Ingolf Mönch,
and Petra Schwille. “Geometry Sensing by Self-Organized Protein Patterns.” PNAS.
National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1206953109.
ieee: J. Schweizer, M. Loose, M. Bonny, K. Kruse, I. Mönch, and P. Schwille, “Geometry
sensing by self-organized protein patterns,” PNAS, vol. 109, no. 38. National
Academy of Sciences, pp. 15283–15288, 2012.
ista: Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, Schwille P. 2012. Geometry
sensing by self-organized protein patterns. PNAS. 109(38), 15283–15288.
mla: Schweizer, Jakob, et al. “Geometry Sensing by Self-Organized Protein Patterns.”
PNAS, vol. 109, no. 38, National Academy of Sciences, 2012, pp. 15283–88,
doi:10.1073/pnas.1206953109.
short: J. Schweizer, M. Loose, M. Bonny, K. Kruse, I. Mönch, P. Schwille, PNAS 109
(2012) 15283–15288.
date_created: 2018-12-11T11:55:04Z
date_published: 2012-09-18T00:00:00Z
date_updated: 2021-01-12T06:54:31Z
day: '18'
doi: 10.1073/pnas.1206953109
extern: 1
intvolume: ' 109'
issue: '38'
month: '09'
page: 15283 - 15288
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5096'
quality_controlled: 0
status: public
title: Geometry sensing by self-organized protein patterns
type: journal_article
volume: 109
year: '2012'
...
---
_id: '2073'
abstract:
- lang: eng
text: 'Background: Drosophila albomicans is a unique model organism for studying
both sex chromosome and B chromosome evolution. A pair of its autosomes comprising
roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only
about 0.12 million years ago, thereby creating the youngest and most gene-rich
neo-sex system reported to date. This species also possesses recently derived
B chromosomes that show non-Mendelian inheritance and significantly influence
fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome
coverage using next-generation sequencing. To characterize neo-Y specific changes
and B chromosome sequences, we also sequenced inbred female flies derived from
the same strain but without B''s at 28.5-fold.Results: We assembled a female genome
and placed 53% of the sequence and 85% of the annotated proteins into specific
chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent
origin, the non-recombining neo-Y chromosome shows various signs of degeneration,
including a significant enrichment of non-functional genes compared to the neo-X,
and an excess of tandem duplications relative to other chromosomes. We also characterized
a B-chromosome linked scaffold that contains an actively transcribed unit and
shows sequence similarity to the subcentromeric regions of both the ancient X
and the neo-X chromosome.Conclusions: Our results provide novel insights into
the very early stages of sex chromosome evolution and B chromosome origination,
and suggest an unprecedented connection between the births of these two systems
in D. albomicans.'
author:
- first_name: Qi
full_name: Zhou, Qi
last_name: Zhou
- first_name: Hongmei
full_name: Zhu, Hongmei
last_name: Zhu
- first_name: Quanfei
full_name: Huang, Quanfei
last_name: Huang
- first_name: Li
full_name: Zhao, Li
last_name: Zhao
- first_name: Guo
full_name: Zhang, Guo J
last_name: Zhang
- first_name: Scott
full_name: Roy, Scott W
last_name: Roy
- first_name: Beatriz
full_name: Beatriz Vicoso
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Zhaolin
full_name: Xuan, Zhaolin
last_name: Xuan
- first_name: Jue
full_name: Ruan, Jue
last_name: Ruan
- first_name: Yue
full_name: Zhang, Yue
last_name: Zhang
- first_name: Ruoping
full_name: Zhao, Ruoping
last_name: Zhao
- first_name: Chen
full_name: Ye, Chen
last_name: Ye
- first_name: Xiuqing
full_name: Zhang, Xiuqing
last_name: Zhang
- first_name: Jùn
full_name: Wang, Jùn
last_name: Wang
- first_name: Wen
full_name: Wang, Wen
last_name: Wang
- first_name: Doris
full_name: Bachtrog, Doris
last_name: Bachtrog
citation:
ama: Zhou Q, Zhu H, Huang Q, et al. Deciphering neo-sex and B chromosome evolution
by the draft genome of Drosophila albomicans. BMC Genomics. 2012;13(1).
doi:10.1186/1471-2164-13-109
apa: Zhou, Q., Zhu, H., Huang, Q., Zhao, L., Zhang, G., Roy, S., … Bachtrog, D.
(2012). Deciphering neo-sex and B chromosome evolution by the draft genome of
Drosophila albomicans. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-13-109
chicago: Zhou, Qi, Hongmei Zhu, Quanfei Huang, Li Zhao, Guo Zhang, Scott Roy, Beatriz
Vicoso, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome
of Drosophila Albomicans.” BMC Genomics. BioMed Central, 2012. https://doi.org/10.1186/1471-2164-13-109.
ieee: Q. Zhou et al., “Deciphering neo-sex and B chromosome evolution by
the draft genome of Drosophila albomicans,” BMC Genomics, vol. 13, no.
1. BioMed Central, 2012.
ista: Zhou Q, Zhu H, Huang Q, Zhao L, Zhang G, Roy S, Vicoso B, Xuan Z, Ruan J,
Zhang Y, Zhao R, Ye C, Zhang X, Wang J, Wang W, Bachtrog D. 2012. Deciphering
neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans.
BMC Genomics. 13(1).
mla: Zhou, Qi, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft
Genome of Drosophila Albomicans.” BMC Genomics, vol. 13, no. 1, BioMed
Central, 2012, doi:10.1186/1471-2164-13-109.
short: Q. Zhou, H. Zhu, Q. Huang, L. Zhao, G. Zhang, S. Roy, B. Vicoso, Z. Xuan,
J. Ruan, Y. Zhang, R. Zhao, C. Ye, X. Zhang, J. Wang, W. Wang, D. Bachtrog, BMC
Genomics 13 (2012).
date_created: 2018-12-11T11:55:33Z
date_published: 2012-03-22T00:00:00Z
date_updated: 2021-01-12T06:55:08Z
day: '22'
doi: 10.1186/1471-2164-13-109
extern: 1
intvolume: ' 13'
issue: '1'
month: '03'
publication: BMC Genomics
publication_status: published
publisher: BioMed Central
publist_id: '4965'
quality_controlled: 0
status: public
title: Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila
albomicans
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
volume: 13
year: '2012'
...
---
_id: '2079'
abstract:
- lang: eng
text: We introduce an algorithm and representation for fabricating 3D shape abstractions
using mutually intersecting planar cut-outs. The planes have prefabricated slits
at their intersections and are assembled by sliding them together. Often such
abstractions are used as a sculptural art form or in architecture and are colloquially
called ‘cardboard sculptures’. Based on an analysis of construction rules, we
propose an extended binary space partitioning tree as an efficient representation
of such cardboard models which allows us to quickly evaluate the feasibility of
newly added planar elements. The complexity of insertion order quickly increases
with the number of planar elements and manual analysis becomes intractable. We
provide tools for generating cardboard sculptures with guaranteed constructibility.
In combination with a simple optimization and sampling strategy for new elements,
planar shape abstraction models can be designed by iteratively adding elements.
As an output, we obtain a fabrication plan that can be printed or sent to a laser
cutter. We demonstrate the complete process by designing and fabricating cardboard
models of various well-known 3D shapes.
author:
- first_name: Kristian
full_name: Hildebrand, Kristian
last_name: Hildebrand
- first_name: Bernd
full_name: Bernd Bickel
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Marc
full_name: Alexa, Marc
last_name: Alexa
citation:
ama: 'Hildebrand K, Bickel B, Alexa M. crdbrd: Shape fabrication by sliding planar
slices. Computer Graphics Forum. 2012;31(2pt3):583-592. doi:10.1111/j.1467-8659.2012.03037.x'
apa: 'Hildebrand, K., Bickel, B., & Alexa, M. (2012). crdbrd: Shape fabrication
by sliding planar slices. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2012.03037.x'
chicago: 'Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Crdbrd: Shape Fabrication
by Sliding Planar Slices.” Computer Graphics Forum. Wiley-Blackwell, 2012.
https://doi.org/10.1111/j.1467-8659.2012.03037.x.'
ieee: 'K. Hildebrand, B. Bickel, and M. Alexa, “crdbrd: Shape fabrication by sliding
planar slices,” Computer Graphics Forum, vol. 31, no. 2pt3. Wiley-Blackwell,
pp. 583–592, 2012.'
ista: 'Hildebrand K, Bickel B, Alexa M. 2012. crdbrd: Shape fabrication by sliding
planar slices. Computer Graphics Forum. 31(2pt3), 583–592.'
mla: 'Hildebrand, Kristian, et al. “Crdbrd: Shape Fabrication by Sliding Planar
Slices.” Computer Graphics Forum, vol. 31, no. 2pt3, Wiley-Blackwell, 2012,
pp. 583–92, doi:10.1111/j.1467-8659.2012.03037.x.'
short: K. Hildebrand, B. Bickel, M. Alexa, Computer Graphics Forum 31 (2012) 583–592.
date_created: 2018-12-11T11:55:35Z
date_published: 2012-05-01T00:00:00Z
date_updated: 2021-01-12T06:55:10Z
day: '01'
doi: 10.1111/j.1467-8659.2012.03037.x
extern: 1
intvolume: ' 31'
issue: 2pt3
month: '05'
page: 583 - 592
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4959'
quality_controlled: 0
status: public
title: 'crdbrd: Shape fabrication by sliding planar slices'
type: journal_article
volume: 31
year: '2012'
...
---
_id: '10387'
abstract:
- lang: eng
text: We report numerical simulations of membrane tubulation driven by large colloidal
particles. Using Monte Carlo simulations we study how the process depends on particle
size and binding strength, and present accurate free energy calculations to sort
out how tube formation compares with the competing budding process. We find that
tube formation is a result of the collective behavior of the particles adhering
on the surface, and it occurs for binding strengths that are smaller than those
required for budding. We also find that long linear aggregates of particles forming
on the membrane surface act as nucleation seeds for tubulation by lowering the
free energy barrier associated to the process.
article_number: '188101'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive
nanocomponents. Physical Review Letters. 2012;109(18). doi:10.1103/physrevlett.109.188101
apa: Šarić, A., & Cacciuto, A. (2012). Mechanism of membrane tube formation
induced by adhesive nanocomponents. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/physrevlett.109.188101
chicago: Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation
Induced by Adhesive Nanocomponents.” Physical Review Letters. American
Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.188101.
ieee: A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by
adhesive nanocomponents,” Physical Review Letters, vol. 109, no. 18. American
Physical Society, 2012.
ista: Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by
adhesive nanocomponents. Physical Review Letters. 109(18), 188101.
mla: Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced
by Adhesive Nanocomponents.” Physical Review Letters, vol. 109, no. 18,
188101, American Physical Society, 2012, doi:10.1103/physrevlett.109.188101.
short: A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012).
date_created: 2021-11-29T14:08:00Z
date_published: 2012-10-31T00:00:00Z
date_updated: 2021-11-29T14:29:25Z
day: '31'
doi: 10.1103/physrevlett.109.188101
extern: '1'
external_id:
arxiv:
- '1206.3528'
pmid:
- '23215334'
intvolume: ' 109'
issue: '18'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1206.3528
month: '10'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of membrane tube formation induced by adhesive nanocomponents
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 109
year: '2012'
...
---
_id: '10388'
abstract:
- lang: eng
text: Using computer simulations, we show that lipid membranes can mediate linear
aggregation of spherical nanoparticles binding to it for a wide range of biologically
relevant bending rigidities. This result is in net contrast with the isotropic
aggregation of nanoparticles on fluid interfaces or the expected clustering of
isotropic insertions in biological membranes. We present a phase diagram indicating
where linear aggregation is expected and compute explicitly the free-energy barriers
associated with linear and isotropic aggregation. Finally, we provide simple scaling
arguments to explain this phenomenology.
acknowledgement: "This work was supported by the National Science Foundation under
Career Grant No. DMR-0846426.\r\n"
article_number: '118101'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed
spherical nanoparticles. Physical Review Letters. 2012;108(11). doi:10.1103/physrevlett.108.118101
apa: Šarić, A., & Cacciuto, A. (2012). Fluid membranes can drive linear aggregation
of adsorbed spherical nanoparticles. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.108.118101
chicago: Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation
of Adsorbed Spherical Nanoparticles.” Physical Review Letters. American
Physical Society, 2012. https://doi.org/10.1103/physrevlett.108.118101.
ieee: A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of
adsorbed spherical nanoparticles,” Physical Review Letters, vol. 108, no.
11. American Physical Society, 2012.
ista: Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of
adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101.
mla: Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation
of Adsorbed Spherical Nanoparticles.” Physical Review Letters, vol. 108,
no. 11, 118101, American Physical Society, 2012, doi:10.1103/physrevlett.108.118101.
short: A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).
date_created: 2021-11-29T14:30:05Z
date_published: 2012-03-14T00:00:00Z
date_updated: 2021-11-29T15:12:13Z
day: '14'
doi: 10.1103/physrevlett.108.118101
extern: '1'
external_id:
arxiv:
- '1201.0036'
pmid:
- '22540513'
intvolume: ' 108'
issue: '11'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1201.0036
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 108
year: '2012'
...