---
_id: '5441'
abstract:
- lang: eng
text: We study algorithmic questions for concurrent systems where the transitions
are labeled from a complete, closed semiring, and path properties are algebraic
with semiring operations. The algebraic path properties can model dataflow analysis
problems, the shortest path problem, and many other natural problems that arise
in program analysis. We consider that each component of the concurrent system
is a graph with constant treewidth, a property satisfied by the controlflow graphs
of most programs. We allow for multiple possible queries, which arise naturally
in demand driven dataflow analysis. The study of multiple queries allows us to
consider the tradeoff between the resource usage of the one-time preprocessing
and for each individual query. The traditional approach constructs the product
graph of all components and applies the best-known graph algorithm on the product.
In this approach, even the answer to a single query requires the transitive closure
(i.e., the results of all possible queries), which provides no room for tradeoff
between preprocessing and query time. Our main contributions are algorithms that
significantly improve the worst-case running time of the traditional approach,
and provide various tradeoffs depending on the number of queries. For example,
in a concurrent system of two components, the traditional approach requires hexic
time in the worst case for answering one query as well as computing the transitive
closure, whereas we show that with one-time preprocessing in almost cubic time,
each subsequent query can be answered in at most linear time, and even the transitive
closure can be computed in almost quartic time. Furthermore, we establish conditional
optimality results showing that the worst-case running time of our algorithms
cannot be improved without achieving major breakthroughs in graph algorithms (i.e.,
improving the worst-case bound for the shortest path problem in general graphs).
Preliminary experimental results show that our algorithms perform favorably on
several benchmarks.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- 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, Goharshady AK, Pavlogiannis A. Algorithms
for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.
IST Austria; 2015. doi:10.15479/AT:IST-2015-340-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A.
(2015). Algorithms for algebraic path properties in concurrent systems of constant
treewidth components. IST Austria. https://doi.org/10.15479/AT:IST-2015-340-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady,
and Andreas Pavlogiannis. Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-340-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms
for algebraic path properties in concurrent systems of constant treewidth components,
IST Austria, 24p.
mla: Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties
in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015,
doi:10.15479/AT:IST-2015-340-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms
for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,
IST Austria, 2015.
date_created: 2018-12-12T11:39:21Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2025-04-15T08:11:48Z
day: '11'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-340-v1-1
file:
- access_level: open_access
checksum: df383dc62c94d7b2ea639aba088a76c6
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:09Z
date_updated: 2020-07-14T12:46:56Z
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '340'
related_material:
record:
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relation: earlier_version
status: public
- id: '6009'
relation: later_version
status: public
- id: '1437'
relation: later_version
status: public
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5442'
abstract:
- lang: eng
text: "We study algorithmic questions for concurrent systems where the transitions
are labeled from a complete, closed semiring, and path properties are algebraic
with semiring operations. The algebraic path properties can model dataflow analysis
problems, the shortest path problem, and many other natural properties that arise
in program analysis.\r\nWe consider that each component of the concurrent system
is a graph with constant treewidth, and it is known that the controlflow graphs
of most programs have constant treewidth. We allow for multiple possible queries,
which arise naturally in demand driven dataflow analysis problems (e.g., alias
analysis). The study of multiple queries allows us to consider the tradeoff between
the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual}
query. The traditional approaches construct the product graph of all components
and apply the best-known graph algorithm on the product. In the traditional approach,
even the answer to a single query requires the transitive closure computation
(i.e., the results of all possible queries), which provides no room for tradeoff
between preprocessing and query time.\r\n\r\nOur main contributions are algorithms
that significantly improve the worst-case running time of the traditional approach,
and provide various tradeoffs depending on the number of queries. For example,
in a concurrent system of two components, the traditional approach requires hexic
time in the worst case for answering one query as well as computing the transitive
closure, whereas we show that with one-time preprocessing in almost cubic time,
\r\neach subsequent query can be answered in at most linear time, and even the
transitive closure can be computed in almost quartic time. Furthermore, we establish
conditional optimality results that show that the worst-case running times of
our algorithms cannot be improved without achieving major breakthroughs in graph
algorithms (such as improving \r\nthe worst-case bounds for the shortest path
problem in general graphs whose current best-known bound has not been improved
in five decades). Finally, we provide a prototype implementation of our algorithms
which significantly outperforms the existing algorithmic methods on several benchmarks."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic
Path Properties in Concurrent Systems of Constant Treewidth Components. IST
Austria; 2015.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms
for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.
IST Austria, 2015.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for
algebraic path properties in concurrent systems of constant treewidth components.
IST Austria, 2015.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic
path properties in concurrent systems of constant treewidth components, IST Austria,
22p.
mla: Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components. IST Austria, 2015.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic
Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria,
2015.
date_created: 2018-12-12T11:39:21Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2025-04-15T08:11:49Z
day: '14'
ddc:
- '000'
file:
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checksum: 98fd936102f3e057fc321ef6d316001d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:37Z
date_updated: 2020-07-14T12:46:57Z
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date_updated: 2020-07-14T12:46:57Z
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file_size: 139
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '344'
related_material:
record:
- id: '5441'
relation: later_version
status: public
- id: '6009'
relation: later_version
status: public
- id: '1437'
relation: later_version
status: public
scopus_import: 1
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5443'
abstract:
- lang: eng
text: POMDPs are standard models for probabilistic planning problems, where an agent
interacts with an uncertain environment. We study the problem of almost-sure reachability,
where given a set of target states, the question is to decide whether there is
a policy to ensure that the target set is reached with probability 1 (almost-surely).
While in general the problem is EXPTIME-complete, in many practical cases policies
with a small amount of memory suffice. Moreover, the existing solution to the
problem is explicit, which first requires to construct explicitly an exponential
reduction to a belief-support MDP. In this work, we first study the existence
of observation-stationary strategies, which is NP-complete, and then small-memory
strategies. We present a symbolic algorithm by an efficient encoding to SAT and
using a SAT solver for the problem. We report experimental results demonstrating
the scalability of our symbolic (SAT-based) approach.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Jessica
full_name: Davies, Jessica
id: 378E0060-F248-11E8-B48F-1D18A9856A87
last_name: Davies
citation:
ama: Chatterjee K, Chmelik M, Davies J. A Symbolic SAT-Based Algorithm for Almost-Sure
Reachability with Small Strategies in POMDPs. IST Austria; 2015. doi:10.15479/AT:IST-2015-325-v2-1
apa: Chatterjee, K., Chmelik, M., & Davies, J. (2015). A symbolic SAT-based
algorithm for almost-sure reachability with small strategies in POMDPs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-325-v2-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. A Symbolic
SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-325-v2-1.
ieee: K. Chatterjee, M. Chmelik, and J. Davies, A symbolic SAT-based algorithm
for almost-sure reachability with small strategies in POMDPs. IST Austria,
2015.
ista: Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for
almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.
mla: Chatterjee, Krishnendu, et al. A Symbolic SAT-Based Algorithm for Almost-Sure
Reachability with Small Strategies in POMDPs. IST Austria, 2015, doi:10.15479/AT:IST-2015-325-v2-1.
short: K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for
Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.
date_created: 2018-12-12T11:39:22Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2025-06-25T11:52:13Z
day: '06'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-325-v2-1
file:
- access_level: open_access
checksum: f0fa31ad8161ed655137e94012123ef9
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:05Z
date_updated: 2020-07-14T12:46:57Z
file_id: '5466'
file_name: IST-2015-325-v2+1_main.pdf
file_size: 412379
relation: main_file
file_date_updated: 2020-07-14T12:46:57Z
fulldoi: https://doi.org/10.15479/AT:IST-2015-325-v2-1
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '23'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '362'
related_material:
record:
- id: '1166'
relation: later_version
status: public
status: public
title: A symbolic SAT-based algorithm for almost-sure reachability with small strategies
in POMDPs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5444'
abstract:
- lang: eng
text: A comprehensive understanding of the clonal evolution of cancer is critical
for understanding neoplasia. Genome-wide sequencing data enables evolutionary
studies at unprecedented depth. However, classical phylogenetic methods often
struggle with noisy sequencing data of impure DNA samples and fail to detect subclones
that have different evolutionary trajectories. We have developed a tool, called
Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly
available sequencing technologies. Using Bayesian inference and Integer Linear
Programming, robust phylogenies consistent with the biological processes underlying
cancer evolution were obtained for pancreatic, ovarian, and prostate cancers.
Furthermore, Treeomics correctly identified sequencing artifacts such as those
resulting from low statistical power; nearly 7% of variants were misclassified
by conventional statistical methods. These artifacts can skew phylogenies by creating
illusory tumor heterogeneity among distinct samples. Importantly, we show that
the evolutionary trees generated with Treeomics are mathematically optimal.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Alvin
full_name: Makohon-Moore, Alvin
last_name: Makohon-Moore
- first_name: Jeffrey
full_name: Gerold, Jeffrey
last_name: Gerold
- first_name: Ivana
full_name: Bozic, Ivana
last_name: Bozic
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christine
full_name: Iacobuzio-Donahue, Christine
last_name: Iacobuzio-Donahue
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies
of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1
apa: Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue,
C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers.
IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1
chicago: Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu
Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing
Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1.
ieee: J. Reiter et al., Reconstructing robust phylogenies of metastatic
cancers. IST Austria, 2015.
ista: Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue
C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic
cancers, IST Austria, 25p.
mla: Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic
Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1.
short: J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue,
B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers,
IST Austria, 2015.
date_created: 2018-12-12T11:39:22Z
date_published: 2015-12-30T00:00:00Z
date_updated: 2020-07-14T23:05:07Z
day: '30'
ddc:
- '000'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-399-v1-1
file:
- access_level: open_access
checksum: c47d33bdda06181753c0af36f16e7b5d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:24Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5485'
file_name: IST-2015-399-v1+1_treeomics.pdf
file_size: 3533200
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
fulldoi: https://doi.org/10.15479/AT:IST-2015-399-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '25'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '399'
status: public
title: Reconstructing robust phylogenies of metastatic cancers
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5549'
abstract:
- lang: eng
text: "This repository contains the experimental part of the CAV 2015 publication
Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe
extended the probabilistic model checker PRISM to represent strategies of Markov
Decision Processes as Decision Trees.\r\nThe archive contains a java executable
version of the extended tool (prism_dectree.jar) together with a few examples
of the PRISM benchmark library.\r\nTo execute the program, please have a look
at the README.txt, which provides instructions and further information on the
archive.\r\nThe archive contains scripts that (if run often enough) reproduces
the data presented in the publication."
article_processing_charge: No
author:
- first_name: Andreas
full_name: Fellner, Andreas
id: 42BABFB4-F248-11E8-B48F-1D18A9856A87
last_name: Fellner
citation:
ama: 'Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation
by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28'
apa: 'Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28'
chicago: 'Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes.” Institute
of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28.'
ieee: 'A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation
by Learning Small Strategies in Markov Decision Processes.” Institute of Science
and Technology Austria, 2015.'
ista: 'Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:28.'
mla: 'Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample
Explanation by Learning Small Strategies in Markov Decision Processes. Institute
of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.'
short: A. Fellner, (2015).
contributor:
- first_name: Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
datarep_id: '28'
date_created: 2018-12-12T12:31:29Z
date_published: 2015-08-13T00:00:00Z
date_updated: 2025-09-23T08:23:15Z
day: '13'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:ISTA:28
ec_funded: 1
file:
- access_level: open_access
checksum: b8bcb43c0893023cda66c1b69c16ac62
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:31Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5597'
file_name: IST-2015-28-v1+2_Fellner_DataRep.zip
file_size: 49557109
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
fulldoi: https://doi.org/10.15479/AT:ISTA:28
has_accepted_license: '1'
keyword:
- Markov Decision Process
- Decision Tree
- Probabilistic Verification
- Counterexample Explanation
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '08'
oa: 1
oa_version: Published Version
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
publisher: Institute of Science and Technology Austria
publist_id: '5564'
related_material:
record:
- id: '1603'
relation: popular_science
status: public
status: public
title: 'Experimental part of CAV 2015 publication: Counterexample Explanation by Learning
Small Strategies in Markov Decision Processes'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5804'
abstract:
- lang: eng
text: We present here the first integer-based algorithm for constructing a well-defined
lattice sphere specified by integer radius and integer center. The algorithm evolves
from a unique correspondence between the lattice points comprising the sphere
and the distribution of sum of three square numbers in integer intervals. We characterize
these intervals to derive a useful set of recurrences, which, in turn, aids in
efficient computation. Each point of the lattice sphere is determined by resorting
to only a few primitive operations in the integer domain. The symmetry of its
quadraginta octants provides an added advantage by confining the computation to
its prima quadraginta octant. Detailed theoretical analysis and experimental results
have been furnished to demonstrate its simplicity and elegance.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. From prima quadraginta octant to lattice sphere through
primitive integer operations. Theoretical Computer Science. 2015;624(4):56-72.
doi:10.1016/j.tcs.2015.11.018
apa: Biswas, R., & Bhowmick, P. (2015). From prima quadraginta octant to lattice
sphere through primitive integer operations. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2015.11.018
chicago: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to
Lattice Sphere through Primitive Integer Operations.” Theoretical Computer
Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.11.018.
ieee: R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere
through primitive integer operations,” Theoretical Computer Science, vol.
624, no. 4. Elsevier, pp. 56–72, 2015.
ista: Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere
through primitive integer operations. Theoretical Computer Science. 624(4), 56–72.
mla: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice
Sphere through Primitive Integer Operations.” Theoretical Computer Science,
vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:10.1016/j.tcs.2015.11.018.
short: R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72.
date_created: 2019-01-08T20:44:06Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2021-01-12T08:03:36Z
day: '18'
doi: 10.1016/j.tcs.2015.11.018
extern: '1'
fulldoi: https://doi.org/10.1016/j.tcs.2015.11.018
intvolume: ' 624'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 56-72
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: From prima quadraginta octant to lattice sphere through primitive integer operations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 624
year: '2015'
...
---
_id: '5807'
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On different topological classes of spherical geodesic
paths and circles inZ3. Theoretical Computer Science. 2015;605(11):146-163.
doi:10.1016/j.tcs.2015.09.003
apa: Biswas, R., & Bhowmick, P. (2015). On different topological classes of
spherical geodesic paths and circles inZ3. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2015.09.003
chicago: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes
of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science.
Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.09.003.
ieee: R. Biswas and P. Bhowmick, “On different topological classes of spherical
geodesic paths and circles inZ3,” Theoretical Computer Science, vol. 605,
no. 11. Elsevier, pp. 146–163, 2015.
ista: Biswas R, Bhowmick P. 2015. On different topological classes of spherical
geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163.
mla: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical
Geodesic Paths and Circles InZ3.” Theoretical Computer Science, vol. 605,
no. 11, Elsevier, 2015, pp. 146–63, doi:10.1016/j.tcs.2015.09.003.
short: R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163.
date_created: 2019-01-08T20:44:52Z
date_published: 2015-11-09T00:00:00Z
date_updated: 2021-01-12T08:03:37Z
day: '09'
doi: 10.1016/j.tcs.2015.09.003
extern: '1'
fulldoi: https://doi.org/10.1016/j.tcs.2015.09.003
intvolume: ' 605'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 146-163
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On different topological classes of spherical geodesic paths and circles inZ3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 605
year: '2015'
...
---
_id: '5808'
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797.
doi:10.1007/s00371-015-1101-3
apa: Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer.
Springer Nature. https://doi.org/10.1007/s00371-015-1101-3
chicago: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual
Computer. Springer Nature, 2015. https://doi.org/10.1007/s00371-015-1101-3.
ieee: R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer,
vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.
ista: Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8),
787–797.
mla: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer,
vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:10.1007/s00371-015-1101-3.
short: R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.
date_created: 2019-01-08T20:45:05Z
date_published: 2015-05-08T00:00:00Z
date_updated: 2021-01-12T08:03:37Z
day: '08'
doi: 10.1007/s00371-015-1101-3
extern: '1'
fulldoi: https://doi.org/10.1007/s00371-015-1101-3
intvolume: ' 31'
issue: 6-8
language:
- iso: eng
month: '05'
oa_version: None
page: 787-797
publication: The Visual Computer
publication_identifier:
issn:
- 0178-2789
- 1432-2315
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Layer the sphere
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
OA_type: closed access
_id: '594'
abstract:
- lang: eng
text: Transcription of eukaryotic protein-coding genes commences with the assembly
of a conserved initiation complex, which consists of RNA polymerase II (Pol II)
and the general transcription factors, at promoter DNA. After two decades of research,
the structural basis of transcription initiation is emerging. Crystal structures
of many components of the initiation complex have been resolved, and structural
information on Pol II complexes with general transcription factors has recently
been obtained. Although mechanistic details await elucidation, available data
outline how Pol II cooperates with the general transcription factors to bind to
and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the
promoter.
article_processing_charge: No
article_type: review
author:
- first_name: Sarah
full_name: Sainsbury, Sarah
last_name: Sainsbury
- 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: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation
by RNA polymerase II. Nature Reviews Molecular Cell Biology. 2015;16(3):129-143.
doi:10.1038/nrm3952
apa: Sainsbury, S., Bernecky, C., & Cramer, P. (2015). Structural basis of transcription
initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology.
Springer Nature. https://doi.org/10.1038/nrm3952
chicago: Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis
of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular
Cell Biology. Springer Nature, 2015. https://doi.org/10.1038/nrm3952.
ieee: S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription
initiation by RNA polymerase II,” Nature Reviews Molecular Cell Biology,
vol. 16, no. 3. Springer Nature, pp. 129–143, 2015.
ista: Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription
initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3),
129–143.
mla: Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA
Polymerase II.” Nature Reviews Molecular Cell Biology, vol. 16, no. 3,
Springer Nature, 2015, pp. 129–43, doi:10.1038/nrm3952.
short: S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology
16 (2015) 129–143.
date_created: 2018-12-11T11:47:23Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2026-05-19T08:24:08Z
day: '01'
doi: 10.1038/nrm3952
extern: '1'
external_id:
pmid:
- '25693126'
fulldoi: https://doi.org/10.1038/nrm3952
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 129 - 143
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
eissn:
- 1471-0080
issn:
- 1471-0072
publication_status: published
publisher: Springer Nature
publist_id: '7206'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of transcription initiation by RNA polymerase II
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 16
year: '2015'
...
---
_id: '6118'
abstract:
- lang: eng
text: 'Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information
about their environment, such as the potential presence of prey or predators.
The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified
three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli.
Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can
detect CO2 independently of these sensory pathways. Many of the C. elegans sensory
neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory
neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise
in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’
major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response
to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore
may couple detection of CO2 to that of other cues at the earliest stages of sensory
processing. We show that C. elegans persistently suppresses oviposition at high
CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying,
are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system
partly through the AWC olfactory neurons: High CO2 tonically activates AWC by
a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that
CO2 is a more complex sensory cue for C. elegans than previously thought, both
in terms of behavior and neural circuitry.'
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- 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: Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying
by modulating olfactory neurons and evokes widespread changes in neural activity.
Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534.
doi:10.1073/pnas.1423808112
apa: Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis
elegans egg-laying by modulating olfactory neurons and evokes widespread changes
in neural activity. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.1423808112
chicago: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112.
ieee: L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity,” Proceedings of the National Academy of Sciences, vol. 112, no.
27. National Academy of Sciences, pp. E3525–E3534, 2015.
ista: Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.
mla: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences, vol.
112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112
(2015) E3525–E3534.
date_created: 2019-03-19T14:15:50Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:06:12Z
day: '07'
ddc:
- '570'
doi: 10.1073/pnas.1423808112
extern: '1'
external_id:
pmid:
- '26100886'
file:
- access_level: open_access
checksum: 3d2da5af8d72467e382a565abc2e003d
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:21:07Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6119'
file_name: 2015_PNAS_Fenk.pdf
file_size: 2822681
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
fulldoi: https://doi.org/10.1073/pnas.1423808112
has_accepted_license: '1'
intvolume: ' 112'
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E3525-E3534
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating
olfactory neurons and evokes widespread changes in neural activity
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '6120'
abstract:
- lang: eng
text: Brains organize behavior and physiology to optimize the response to threats
or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms
C. elegans' global state, inducing sustained locomotory arousal and altering expression
of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing
neurons drive arousal at 21% O2 by tonically activating the RMG interneurons.
Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL,
or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal.
However, disrupting cation currents in these neurons curtails RMG neurosecretion
and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters
reveal neural circuit state, as neurosecretion stimulates neuropeptide expression.
Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration
rather than behavior, while the activity of downstream interneurons such as AVB
and AIY reflect both O2 levels and the behavior being executed.
article_number: e04241
author:
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Zoltan
full_name: Soltesz, Zoltan
last_name: Soltesz
- first_name: Geoffrey M
full_name: Nelson, Geoffrey M
last_name: Nelson
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Emmanuel
full_name: Levy, Emmanuel
last_name: Levy
- 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: Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling
global animal state in C. elegans. eLife. 2015;4. doi:10.7554/elife.04241
apa: Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy,
E., & de Bono, M. (2015). Decoding a neural circuit controlling global animal
state in C. elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.04241
chicago: Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto
Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit
Controlling Global Animal State in C. Elegans.” ELife. eLife Sciences Publications,
2015. https://doi.org/10.7554/elife.04241.
ieee: P. Laurent et al., “Decoding a neural circuit controlling global animal
state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015.
ista: Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono
M. 2015. Decoding a neural circuit controlling global animal state in C. elegans.
eLife. 4, e04241.
mla: Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal
State in C. Elegans.” ELife, vol. 4, e04241, eLife Sciences Publications,
2015, doi:10.7554/elife.04241.
short: P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy,
M. de Bono, ELife 4 (2015).
date_created: 2019-03-19T14:23:51Z
date_published: 2015-03-11T00:00:00Z
date_updated: 2021-01-12T08:06:13Z
day: '11'
ddc:
- '570'
doi: 10.7554/elife.04241
extern: '1'
external_id:
pmid:
- '25760081'
file:
- access_level: open_access
checksum: cf641b7a363aecd0a101755d23dee7e0
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:29:43Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6121'
file_name: 2015_elife_Laurent.pdf
file_size: 6723528
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
fulldoi: https://doi.org/10.7554/elife.04241
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Decoding a neural circuit controlling global animal state in C. elegans
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19805'
abstract:
- lang: eng
text: Understanding the role of electron correlations in strong spin-orbit transition-metal
oxides is key to the realization of numerous exotic phases including spin-orbit–assisted
Mott insulators, correlated topological solids, and prospective new high-temperature
superconductors. To date, most attention has been focused on the 5d iridium-based
oxides. We instead consider the Pt-based delafossite oxide PtCoO2. Our transport
measurements, performed on single-crystal samples etched to well-defined geometries
using focused ion beam techniques, yield a room temperature resistivity of only
2.1 microhm·cm (μΩ-cm), establishing PtCoO2 as the most conductive oxide known.
From angle-resolved photoemission and density functional theory, we show that
the underlying Fermi surface is a single cylinder of nearly hexagonal cross-section,
with very weak dispersion along kz. Despite being predominantly composed of d-orbital
character, the conduction band is remarkably steep, with an average effective
mass of only 1.14me. Moreover, the sharp spectral features observed in photoemission
remain well defined with little additional broadening for more than 500 meV below
EF, pointing to suppressed electron-electron scattering. Together, our findings
establish PtCoO2 as a model nearly-free–electron system in a 5d delafossite transition-metal
oxide.
article_number: '1500692'
article_processing_charge: No
article_type: original
author:
- first_name: Pallavi
full_name: Kushwaha, Pallavi
last_name: Kushwaha
- first_name: Veronika
full_name: Sunko, Veronika
id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3
last_name: Sunko
orcid: 0000-0003-2724-3523
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
- first_name: Lewis
full_name: Bawden, Lewis
last_name: Bawden
- first_name: Jonathon M.
full_name: Riley, Jonathon M.
last_name: Riley
- first_name: Nabhanila
full_name: Nandi, Nabhanila
last_name: Nandi
- first_name: Helge
full_name: Rosner, Helge
last_name: Rosner
- first_name: Marcus P.
full_name: Schmidt, Marcus P.
last_name: Schmidt
- first_name: Frank
full_name: Arnold, Frank
last_name: Arnold
- first_name: Elena
full_name: Hassinger, Elena
last_name: Hassinger
- first_name: Timur K.
full_name: Kim, Timur K.
last_name: Kim
- first_name: Moritz
full_name: Hoesch, Moritz
last_name: Hoesch
- first_name: Andrew P.
full_name: Mackenzie, Andrew P.
last_name: Mackenzie
- first_name: Phil D. C.
full_name: King, Phil D. C.
last_name: King
citation:
ama: Kushwaha P, Sunko V, Moll PJW, et al. Nearly free electrons in a 5d delafossite
oxide metal. Science Advances. 2015;1(9). doi:10.1126/sciadv.1500692
apa: Kushwaha, P., Sunko, V., Moll, P. J. W., Bawden, L., Riley, J. M., Nandi, N.,
… King, P. D. C. (2015). Nearly free electrons in a 5d delafossite oxide metal.
Science Advances. American Association for the Advancement of Science.
https://doi.org/10.1126/sciadv.1500692
chicago: Kushwaha, Pallavi, Veronika Sunko, Philip J. W. Moll, Lewis Bawden, Jonathon
M. Riley, Nabhanila Nandi, Helge Rosner, et al. “Nearly Free Electrons in a 5d
Delafossite Oxide Metal.” Science Advances. American Association for the
Advancement of Science, 2015. https://doi.org/10.1126/sciadv.1500692.
ieee: P. Kushwaha et al., “Nearly free electrons in a 5d delafossite oxide
metal,” Science Advances, vol. 1, no. 9. American Association for the Advancement
of Science, 2015.
ista: Kushwaha P, Sunko V, Moll PJW, Bawden L, Riley JM, Nandi N, Rosner H, Schmidt
MP, Arnold F, Hassinger E, Kim TK, Hoesch M, Mackenzie AP, King PDC. 2015. Nearly
free electrons in a 5d delafossite oxide metal. Science Advances. 1(9), 1500692.
mla: Kushwaha, Pallavi, et al. “Nearly Free Electrons in a 5d Delafossite Oxide
Metal.” Science Advances, vol. 1, no. 9, 1500692, American Association
for the Advancement of Science, 2015, doi:10.1126/sciadv.1500692.
short: P. Kushwaha, V. Sunko, P.J.W. Moll, L. Bawden, J.M. Riley, N. Nandi, H. Rosner,
M.P. Schmidt, F. Arnold, E. Hassinger, T.K. Kim, M. Hoesch, A.P. Mackenzie, P.D.C.
King, Science Advances 1 (2015).
date_created: 2025-06-10T09:09:54Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2025-06-10T13:09:49Z
day: '01'
ddc:
- '530'
doi: 10.1126/sciadv.1500692
extern: '1'
fulldoi: https://doi.org/10.1126/sciadv.1500692
intvolume: ' 1'
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/sciadv.1500692
month: '10'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nearly free electrons in a 5d delafossite oxide metal
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '1981'
abstract:
- lang: eng
text: Variation in mitochondrial DNA is often assumed to be neutral and is used
to construct the genealogical relationships among populations and species. However,
if extant variation is the result of episodes of positive selection, these genealogies
may be incorrect, although this information itself may pro-vide biologically and
evolutionary meaningful information. In fact, positive Darwinian selection has
been detected in the mitochondrial-encoded subunits that comprise complex I from
diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional
implications of the selected sites are unknown. Complex I produces roughly 40%
of the proton flux that is used to synthesize ATP from ADP, and a functional model
based on the high-resolution structure of complex I described a unique biomechanical
apparatus for proton translocation. We reported positive selection at sites in
this apparatus during the evolution of Pacific salmon, and it appeared this was
also the case in published reports from other taxa, but a comparison among studies
was difficult because different statistical tests were used to detect selection
and oftentimes, specific sites were not reported. Here we review the literature
of positive selection in mitochondrial genomes, the statistical tests used to
detect selection, and the structural and functional models that are currently
available to study the physiological implications of selection. We then search
for signatures of positive selection among the coding mitochondrial genomes of
237 species with a common set of tests and verify that the ND5 subunit of complex
I is a repeated target of positive Darwinian selection in diverse taxa. We propose
a novel hypothesis to explain the results based on their bioenergetic life histories
and provide a guide for laboratory and field studies to test this hypothesis.
acknowledgement: Funded by University of Alaska Center for Global Change Student
Research Cooperative Institute for Alaska Research and the Rasmuson Foundation
article_processing_charge: No
article_type: review
author:
- first_name: Michael
full_name: Garvin, Michael
last_name: Garvin
- first_name: Joseph
full_name: Bielawski, Joseph
last_name: Bielawski
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Anthony
full_name: Gharrett, Anthony
last_name: Gharrett
citation:
ama: Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of
natural selection in mitochondrial complex I in metazoans. Journal of Zoological
Systematics and Evolutionary Research. 2015;53(1):1-17. doi:10.1111/jzs.12079
apa: Garvin, M., Bielawski, J., Sazanov, L. A., & Gharrett, A. (2015). Review
and meta-analysis of natural selection in mitochondrial complex I in metazoans.
Journal of Zoological Systematics and Evolutionary Research. Wiley. https://doi.org/10.1111/jzs.12079
chicago: Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett.
“Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.”
Journal of Zoological Systematics and Evolutionary Research. Wiley, 2015.
https://doi.org/10.1111/jzs.12079.
ieee: M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis
of natural selection in mitochondrial complex I in metazoans,” Journal of Zoological
Systematics and Evolutionary Research, vol. 53, no. 1. Wiley, pp. 1–17, 2015.
ista: Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2015. Review and meta-analysis
of natural selection in mitochondrial complex I in metazoans. Journal of Zoological
Systematics and Evolutionary Research. 53(1), 1–17.
mla: Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial
Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary
Research, vol. 53, no. 1, Wiley, 2015, pp. 1–17, doi:10.1111/jzs.12079.
short: M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological
Systematics and Evolutionary Research 53 (2015) 1–17.
date_created: 2018-12-11T11:55:02Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2025-08-05T14:47:50Z
day: '01'
doi: 10.1111/jzs.12079
extern: '1'
fulldoi: https://doi.org/10.1111/jzs.12079
intvolume: ' 53'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 17
publication: Journal of Zoological Systematics and Evolutionary Research
publication_status: published
publisher: Wiley
publist_id: '5102'
status: public
title: Review and meta-analysis of natural selection in mitochondrial complex I in
metazoans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2015'
...
---
_id: '1992'
abstract:
- lang: eng
text: "We present a method and a tool for generating succinct representations of
sets of concurrent traces. We focus on trace sets that contain all correct or
all incorrect permutations of events from a given trace. We represent trace sets
as HB-Formulas that are Boolean combinations of happens-before constraints between
events. To generate a representation of incorrect interleavings, our method iteratively
explores interleavings that violate the specification and gathers generalizations
of the discovered interleavings into an HB-Formula; its complement yields a representation
of correct interleavings.\r\n\r\nWe claim that our trace set representations can
drive diverse verification, fault localization, repair, and synthesis techniques
for concurrent programs. We demonstrate this by using our tool in three case studies
involving synchronization synthesis, bug summarization, and abstraction refinement
based verification. In each case study, our initial experimental results have
been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring
missing synchronization from an HB-Formula representing correct interleavings
of a given trace. The algorithm applies rules to rewrite specific patterns in
the HB-Formula into locks, barriers, and wait-notify constructs. In the second
case study, we use an HB-Formula representing incorrect interleavings for bug
summarization. While the HB-Formula itself is a concise counterexample summary,
we present additional inference rules to help identify specific concurrency bugs
such as data races, define-use order violations, and two-stage access bugs. In
the final case study, we present a novel predicate learning procedure that uses
HB-Formulas representing abstract counterexamples to accelerate counterexample-guided
abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure
refines the abstraction to eliminate multiple spurious abstract counterexamples
drawn from the HB-Formula."
article_processing_charge: No
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation
of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008'
apa: 'Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach,
T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented
at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta,
and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44.
ACM, 2015. https://doi.org/10.1145/2676726.2677008.
ieee: 'A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct
representation of concurrent trace sets,” presented at the POPL: Principles of
Programming Languages, Mumbai, India, 2015, pp. 433–444.'
ista: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct
representation of concurrent trace sets. POPL: Principles of Programming Languages,
433–444.'
mla: Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets.
ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.
short: A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM,
2015, pp. 433–444.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'POPL: Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:55:05Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2025-03-07T08:44:29Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/2676726.2677008
file:
- access_level: open_access
checksum: f0d4395b600f410a191256ac0b73af32
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:56Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5314'
file_name: IST-2015-317-v1+1_author_version.pdf
file_size: 399462
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
fulldoi: https://doi.org/10.1145/2676726.2677008
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 433 - 444
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5091'
pubrep_id: '317'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Succinct representation of concurrent trace sets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1993'
abstract:
- lang: eng
text: 'The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens. '
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2)
and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank
Line V. Ugelvig for help with ant collection and statistical discussion, Xavier
Espadaler for detailed information on the ant collection site, Birgit Lautenschläger
for the electron microscopy images and Eva Sixt for ant drawings. We further thank
Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization
and immune gene primer development, Paul Schmid-Hempel for discussion, and Line
V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript.
S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments;
M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with
intense contributions of A.V.G. and S.T.; all authors approved the manuscript."
article_number: '20141976'
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival
costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal
Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976
apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.1976
chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen
Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.
ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1799. The Royal Society, 2015.
ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus
survival costs mediated by an ectosymbiont in an ant host. Proceedings of the
Royal Society of London Series B Biological Sciences. 282(1799), 20141976.
mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated
by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society,
2015, doi:10.1098/rspb.2014.1976.
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society
of London Series B Biological Sciences 282 (2015).
corr_author: '1'
date_created: 2018-12-11T11:55:06Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2025-09-23T07:55:03Z
day: '22'
department:
- _id: SyCr
doi: 10.1098/rspb.2014.1976
ec_funded: 1
external_id:
isi:
- '000345624600008'
pmid:
- '25473011'
fulldoi: https://doi.org/10.1098/rspb.2014.1976
intvolume: ' 282'
isi: 1
issue: '1799'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
publist_id: '5090'
quality_controlled: '1'
related_material:
record:
- id: '9740'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 282
year: '2015'
...
---
_id: '1997'
abstract:
- lang: eng
text: We prove that the three-state toric homogeneous Markov chain model has Markov
degree two. In algebraic terminology this means, that a certain class of toric
ideals is generated by quadratic binomials. This was conjectured by Haws, Martin
del Campo, Takemura and Yoshida, who proved that they are generated by degree
six binomials.
article_processing_charge: No
arxiv: 1
author:
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Noren P. The three-state toric homogeneous Markov chain model has Markov degree
two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296.
doi:10.1016/j.jsc.2014.09.014
apa: Noren, P. (2015). The three-state toric homogeneous Markov chain model has
Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014
chicago: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has
Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.
ieee: P. Noren, “The three-state toric homogeneous Markov chain model has Markov
degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June.
Elsevier, pp. 285–296, 2015.
ista: Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov
degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.
mla: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov
Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June,
Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.
short: P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.
corr_author: '1'
date_created: 2018-12-11T11:55:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2025-09-23T14:17:34Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jsc.2014.09.014
external_id:
arxiv:
- '1207.0077'
isi:
- '000347767600016'
fulldoi: https://doi.org/10.1016/j.jsc.2014.09.014
isi: 1
issue: May-June
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0077
month: '05'
oa: 1
oa_version: Preprint
page: 285 - 296
publication: Journal of Symbolic Computation
publication_status: published
publisher: Elsevier
publist_id: '5082'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The three-state toric homogeneous Markov chain model has Markov degree two
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 68/Part 2
year: '2015'
...
---
_id: '2006'
abstract:
- lang: eng
text: 'The monotone secant conjecture posits a rich class of polynomial systems,
all of whose solutions are real. These systems come from the Schubert calculus
on flag manifolds, and the monotone secant conjecture is a compelling generalization
of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko).
We present some theoretical evidence for this conjecture, as well as computational
evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of
the phenomena we observed in our data. '
article_processing_charge: No
arxiv: 1
author:
- first_name: Nicolas
full_name: Hein, Nicolas
last_name: Hein
- first_name: Christopher
full_name: Hillar, Christopher
last_name: Hillar
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
- first_name: Zach
full_name: Teitler, Zach
last_name: Teitler
citation:
ama: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone
secant conjecture in the real Schubert calculus. Experimental Mathematics.
2015;24(3):261-269. doi:10.1080/10586458.2014.980044
apa: Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler,
Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental
Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044
chicago: Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank
Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.
ieee: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler,
“The monotone secant conjecture in the real Schubert calculus,” Experimental
Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.
ista: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015.
The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics.
24(3), 261–269.
mla: Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis,
2015, pp. 261–69, doi:10.1080/10586458.2014.980044.
short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler,
Experimental Mathematics 24 (2015) 261–269.
date_created: 2018-12-11T11:55:10Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2025-09-23T14:07:49Z
day: '23'
department:
- _id: CaUh
doi: 10.1080/10586458.2014.980044
external_id:
arxiv:
- '1109.3436'
isi:
- '000356873900001'
fulldoi: https://doi.org/10.1080/10586458.2014.980044
intvolume: ' 24'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.3436
month: '06'
oa: 1
oa_version: Preprint
page: 261 - 269
publication: Experimental Mathematics
publication_status: published
publisher: Taylor & Francis
publist_id: '5070'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The monotone secant conjecture in the real Schubert calculus
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 24
year: '2015'
...
---
_id: '2008'
abstract:
- lang: eng
text: The paper describes a generalized iterative proportional fitting procedure
that can be used for maximum likelihood estimation in a special class of the general
log-linear model. The models in this class, called relational, apply to multivariate
discrete sample spaces that do not necessarily have a Cartesian product structure
and may not contain an overall effect. When applied to the cell probabilities,
the models without the overall effect are curved exponential families and the
values of the sufficient statistics are reproduced by the MLE only up to a constant
of proportionality. The paper shows that Iterative Proportional Fitting, Generalized
Iterative Scaling, and Improved Iterative Scaling fail to work for such models.
The algorithm proposed here is based on iterated Bregman projections. As a by-product,
estimates of the multiplicative parameters are also obtained. An implementation
of the algorithm is available as an R-package.
acknowledgement: Part of the material presented here was contained in the PhD thesis
of the first author to which the second author and Thomas Richardson were advisers.
The authors wish to thank him for several comments and suggestions. We also thank
the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1
uses the idea of Olga Klimova, to whom the authors are also indebted. The second
author was supported in part by Grant K-106154 from the Hungarian National Scientific
Research Fund (OTKA).
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian
Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139
apa: Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential
families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139
chicago: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential
Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.
ieee: A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,”
Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847,
2015.
ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families.
Scandinavian Journal of Statistics. 42(3), 832–847.
mla: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.”
Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47,
doi:10.1111/sjos.12139.
short: A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.
date_created: 2018-12-11T11:55:11Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2025-09-23T09:25:01Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/sjos.12139
external_id:
arxiv:
- '1307.3282'
isi:
- '000360077100012'
fulldoi: https://doi.org/10.1111/sjos.12139
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3282
month: '09'
oa: 1
oa_version: Preprint
page: 832 - 847
publication: Scandinavian Journal of Statistics
publication_status: published
publisher: Wiley
publist_id: '5068'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterative scaling in curved exponential families
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
year: '2015'
...
---
_id: '2014'
abstract:
- lang: eng
text: The concepts of faithfulness and strong-faithfulness are important for statistical
learning of graphical models. Graphs are not sufficient for describing the association
structure of a discrete distribution. Hypergraphs representing hierarchical log-linear
models are considered instead, and the concept of parametric (strong-) faithfulness
with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence
of uniformly consistent parameter estimators and enables building uniformly consistent
procedures for a hypergraph search. The strength of association in a discrete
distribution can be quantified with various measures, leading to different concepts
of strong-faithfulness. Lower and upper bounds for the proportions of distributions
that do not satisfy strong-faithfulness are computed for different parameterizations
and measures of association.
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete
distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72.
doi:10.1016/j.csda.2015.01.017
apa: Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs
from discrete distributions. Computational Statistics & Data Analysis.
Elsevier. https://doi.org/10.1016/j.csda.2015.01.017
chicago: Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning
Hypergraphs from Discrete Distributions.” Computational Statistics & Data
Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.
ieee: A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs
from discrete distributions,” Computational Statistics & Data Analysis,
vol. 87, no. 7. Elsevier, pp. 57–72, 2015.
ista: Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from
discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.
mla: Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete
Distributions.” Computational Statistics & Data Analysis, vol. 87,
no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.
short: A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis
87 (2015) 57–72.
corr_author: '1'
date_created: 2018-12-11T11:55:13Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2025-09-23T08:45:54Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.csda.2015.01.017
external_id:
arxiv:
- '1404.6617'
isi:
- '000352661000005'
fulldoi: https://doi.org/10.1016/j.csda.2015.01.017
intvolume: ' 87'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.6617
month: '07'
oa: 1
oa_version: Preprint
page: 57 - 72
publication: Computational Statistics & Data Analysis
publication_status: published
publisher: Elsevier
publist_id: '5062'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faithfulness and learning hypergraphs from discrete distributions
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 87
year: '2015'
...
---
_id: '2025'
abstract:
- lang: eng
text: Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular
trafficking. Among them, the Rab, Arf, and Rho families function in successive
steps of vesicle transport, in forming vesicles from donor membranes, directing
vesicle trafficking toward target membranes and docking vesicles onto target membranes.
These proteins act as molecular switches that are controlled by a cycle of GTP
binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs)
and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs
in the regulation of the endocytic pathway using fluorescently labeled yeast mating
pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion
of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of
fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells
show defective α-factor binding to the cell surface. Interestingly, Ste2p, the
α-factor receptor, was mis-localized from the plasma membrane to the vacuole in
glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent
function, as well as the GAP activity, of Glo3p is important for both α-factor
binding and Ste2p localization at the cell surface. Additionally, we found that
deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi
compartments and causes a defect in transport from the TGN to the plasma membrane.
Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN
transport pathway, but not in the early endosome-to-TGN transport pathway. These
findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell
surface proteins.
article_processing_charge: No
author:
- first_name: Daiki
full_name: Kawada, Daiki
last_name: Kawada
- first_name: Hiromu
full_name: Kobayashi, Hiromu
last_name: Kobayashi
- first_name: Tsuyoshi
full_name: Tomita, Tsuyoshi
last_name: Tomita
- first_name: Eisuke
full_name: Nakata, Eisuke
last_name: Nakata
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshimaa, Jiro
last_name: Toshimaa
citation:
ama: Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required
for the endocytic recycling of cell surface proteins. Biochimica et Biophysica
Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009
apa: Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D.
E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular
Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009
chicago: Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto
Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP
Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica
et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.
ieee: D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.
ista: Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima
J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling
of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research.
1853(1), 144–156.
mla: Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic
Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.
short: D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus,
J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research
1853 (2015) 144–156.
date_created: 2018-12-11T11:55:17Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2025-09-23T14:51:55Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1016/j.bbamcr.2014.10.009
external_id:
isi:
- '000347598100014'
file:
- access_level: open_access
checksum: 5bb328edebb6a91337cadd7d63f961b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:18Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4936'
file_name: IST-2016-615-v1+1_BBAMCR.pdf
file_size: 926685
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
fulldoi: https://doi.org/10.1016/j.bbamcr.2014.10.009
has_accepted_license: '1'
intvolume: ' 1853'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Submitted Version
page: 144 - 156
publication: Biochimica et Biophysica Acta - Molecular Cell Research
publication_status: published
publisher: Elsevier
publist_id: '5047'
pubrep_id: '615'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface
proteins
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1853
year: '2015'
...