---
_id: '5388'
abstract:
- lang: eng
text: "We present an algorithmic method for the synthesis of concurrent programs
that are optimal with respect to quantitative performance measures. The input
consists of a sequential sketch, that is, a program that does not contain synchronization
constructs, and of a parametric performance model that assigns costs to actions
such as locking, context switching, and idling. The quantitative synthesis problem
is to automatically introduce synchronization constructs into the sequential sketch
so that both correctness is guaranteed and worst-case (or average-case) performance
is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe
show that for worst-case performance, the problem can be modeled\r\nas a 2-player
graph game with quantitative (limit-average) objectives, and\r\nfor average-case
performance, as a 2 1/2 -player graph game (with probabilistic transitions). In
both cases, the optimal correct program is derived from an optimal strategy in
the corresponding quantitative game. We prove that the respective game problems
are computationally expensive (NP-complete), and present several techniques that
overcome the theoretical difficulty in cases of concurrent programs of practical
interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic
syn- thesis of programs that access a concurrent list. For certain parameter val-
ues, our method automatically synthesizes various classical synchronization schemes
for implementing a concurrent list, such as fine-grained locking or a lazy algorithm.
For other parameter values, a new, hybrid synchronization style is synthesized,
which uses both the lazy approach and coarse-grained locks (instead of standard
fine-grained locks). The trade-off occurs because while fine-grained locking tends
to decrease the cost that is due to waiting for locks, it increases cache size
requirements."
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: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. Quantitative
Synthesis for Concurrent Programs. IST Austria; 2010. doi:10.15479/AT:IST-2010-0004
apa: Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., & Singh,
R. (2010). Quantitative synthesis for concurrent programs. IST Austria.
https://doi.org/10.15479/AT:IST-2010-0004
chicago: Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna,
and Rohit Singh. Quantitative Synthesis for Concurrent Programs. IST Austria,
2010. https://doi.org/10.15479/AT:IST-2010-0004.
ieee: K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative
synthesis for concurrent programs. IST Austria, 2010.
ista: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative
synthesis for concurrent programs, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. Quantitative Synthesis for Concurrent Programs.
IST Austria, 2010, doi:10.15479/AT:IST-2010-0004.
short: K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative
Synthesis for Concurrent Programs, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-10-07T00:00:00Z
date_updated: 2023-02-23T11:24:08Z
day: '07'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2010-0004
file:
- access_level: open_access
checksum: da38782d2388a6fa32109d10bb9bad67
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5515'
file_name: IST-2010-0004_IST-2010-0004.pdf
file_size: 429101
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '24'
related_material:
record:
- id: '3366'
relation: later_version
status: public
status: public
title: Quantitative synthesis for concurrent programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5389'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the im- plementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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
citation:
ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation Distances. IST Austria;
2010. doi:10.15479/AT:IST-2010-0003
apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances.
IST Austria. https://doi.org/10.15479/AT:IST-2010-0003
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. Simulation
Distances. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0003.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances.
IST Austria, 2010.
ista: Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria,
24p.
mla: Cerny, Pavol, et al. Simulation Distances. IST Austria, 2010, doi:10.15479/AT:IST-2010-0003.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria,
2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2023-02-23T12:09:16Z
day: '04'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0003
file:
- access_level: open_access
checksum: 284ded99764e32a583a8ea83fcea254b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5547'
file_name: IST-2010-0003_IST-2010-0003.pdf
file_size: 367246
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '25'
related_material:
record:
- id: '3249'
relation: later_version
status: public
- id: '4393'
relation: later_version
status: public
status: public
title: Simulation distances
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5390'
abstract:
- lang: eng
text: The class of ω regular languages provide a robust specification language in
verification. Every ω-regular condition can be decomposed into a safety part and
a liveness part. The liveness part ensures that something good happens “eventually.”
Two main strengths of the classical, infinite-limit formulation of liveness are
robustness (independence from the granularity of transitions) and simplicity (abstraction
of complicated time bounds). However, the classical liveness formulation suffers
from the drawback that the time until something good happens may be unbounded.
A stronger formulation of liveness, so-called finitary liveness, overcomes this
drawback, while still retaining robustness and simplicity. Finitary liveness requires
that there exists an unknown, fixed bound b such that something good happens within
b transitions. In this work we consider the finitary parity and Streett (fairness)
conditions. We present the topological, automata-theoretic and logical characterization
of finitary languages defined by finitary parity and Streett conditions. We (a)
show that the finitary parity and Streett languages are Σ2-complete; (b) present
a complete characterization of the expressive power of various classes of automata
with finitary and infinitary conditions (in particular we show that non-deterministic
finitary parity and Streett automata cannot be determinized to deterministic finitary
parity or Streett automata); and (c) show that the languages defined by non-deterministic
finitary parity automata exactly characterize the star-free fragment of ωB-regular
languages.
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: Nathanaël
full_name: Fijalkow, Nathanaël
last_name: Fijalkow
citation:
ama: Chatterjee K, Fijalkow N. Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages. IST Austria; 2010. doi:10.15479/AT:IST-2010-0002
apa: Chatterjee, K., & Fijalkow, N. (2010). Topological, automata-theoretic
and logical characterization of finitary languages. IST Austria. https://doi.org/10.15479/AT:IST-2010-0002
chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0002.
ieee: K. Chatterjee and N. Fijalkow, Topological, automata-theoretic and logical
characterization of finitary languages. IST Austria, 2010.
ista: Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical
characterization of finitary languages, IST Austria, 21p.
mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010, doi:10.15479/AT:IST-2010-0002.
short: K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2020-07-14T23:04:41Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2010-0002
file:
- access_level: open_access
checksum: 283d3604d76dd4d5161585d4c8625fbe
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:10Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5532'
file_name: IST-2010-0002_IST-2010-0002.pdf
file_size: 395662
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '26'
status: public
title: Topological, automata-theoretic and logical characterization of finitary languages
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5391'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each node consists an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
imple- mentation and proved that the corrected version is linearizable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model Checking
of Linearizability of Concurrent List Implementations. IST Austria; 2010.
doi:10.15479/AT:IST-2010-0001
apa: Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations. IST
Austria. https://doi.org/10.15479/AT:IST-2010-0001
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. Model Checking of Linearizability of Concurrent List Implementations.
IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0001.
ieee: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model
checking of linearizability of concurrent list implementations. IST Austria,
2010.
ista: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations, IST Austria, 27p.
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. IST Austria, 2010, doi:10.15479/AT:IST-2010-0001.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking
of Linearizability of Concurrent List Implementations, IST Austria, 2010.
date_created: 2018-12-12T11:39:04Z
date_published: 2010-04-19T00:00:00Z
date_updated: 2023-02-23T12:09:09Z
day: '19'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0001
file:
- access_level: open_access
checksum: 986645caad7dd85a6a091488f6c646dc
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:44Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5505'
file_name: IST-2010-0001_IST-2010-0001.pdf
file_size: 372286
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '27'
related_material:
record:
- id: '4390'
relation: later_version
status: public
status: public
title: Model checking of linearizability of concurrent list implementations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5940'
article_processing_charge: No
author:
- first_name: Gabriel
full_name: Juhás, Gabriel
last_name: Juhás
- first_name: Igor
full_name: Kazlov, Igor
id: 4A997E50-F248-11E8-B48F-1D18A9856A87
last_name: Kazlov
- first_name: Ana
full_name: Juhásová, Ana
last_name: Juhásová
citation:
ama: 'Juhás G, Kazlov I, Juhásová A. Instance Deadlock: A Mystery behind Frozen
Programs. In: Applications and Theory of Petri Nets. Berlin, Heidelberg:
Springer Berlin Heidelberg; 2010:1-17. doi:10.1007/978-3-642-13675-7_1'
apa: 'Juhás, G., Kazlov, I., & Juhásová, A. (2010). Instance Deadlock: A Mystery
behind Frozen Programs. In Applications and Theory of Petri Nets (pp. 1–17).
Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-13675-7_1'
chicago: 'Juhás, Gabriel, Igor Kazlov, and Ana Juhásová. “Instance Deadlock: A Mystery
behind Frozen Programs.” In Applications and Theory of Petri Nets, 1–17.
Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. https://doi.org/10.1007/978-3-642-13675-7_1.'
ieee: 'G. Juhás, I. Kazlov, and A. Juhásová, “Instance Deadlock: A Mystery behind
Frozen Programs,” in Applications and Theory of Petri Nets, Berlin, Heidelberg:
Springer Berlin Heidelberg, 2010, pp. 1–17.'
ista: 'Juhás G, Kazlov I, Juhásová A. 2010.Instance Deadlock: A Mystery behind Frozen
Programs. In: Applications and Theory of Petri Nets. , 1–17.'
mla: 'Juhás, Gabriel, et al. “Instance Deadlock: A Mystery behind Frozen Programs.”
Applications and Theory of Petri Nets, Springer Berlin Heidelberg, 2010,
pp. 1–17, doi:10.1007/978-3-642-13675-7_1.'
short: G. Juhás, I. Kazlov, A. Juhásová, in:, Applications and Theory of Petri Nets,
Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, pp. 1–17.
date_created: 2019-02-08T09:33:41Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2022-04-01T13:45:24Z
doi: 10.1007/978-3-642-13675-7_1
extern: '1'
language:
- iso: eng
oa_version: None
page: 1-17
place: Berlin, Heidelberg
publication: Applications and Theory of Petri Nets
publication_identifier:
isbn:
- '9783642136740'
- '9783642136757'
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Berlin Heidelberg
status: public
title: 'Instance Deadlock: A Mystery behind Frozen Programs'
type: book_chapter
user_id: 4A997E50-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '598'
abstract:
- lang: eng
text: It is not well understood how the human Mediator complex, transcription factor
IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription.
Activator binding alters Mediator structure, yet the functional consequences of
such structural shifts remain unknown. The p53 C terminus and its activation domain
interact with different Mediator subunits, and we find that each interaction differentially
affects Mediator structure; strikingly, distinct p53-Mediator structures differentially
affect Pol II activity. Only the p53 activation domain induces the formation of
a large pocket domain at the Mediator-Pol II interaction site, and this correlates
with activation of stalled Pol II to a productively elongating state. Moreover,
we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain
phosphorylation and identify substantial differences in Pol II C-terminal domain
processing that correspond to distinct p53-Mediator structural states. Our results
define a fundamental mechanism by which p53 activates transcription and suggest
that Mediator structural shifts trigger activation of stalled Pol II complexes.
article_processing_charge: No
author:
- first_name: Krista
full_name: Meyer, Krista
last_name: Meyer
- first_name: Shih
full_name: Lin, Shih
last_name: Lin
- 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: Yuefeng
full_name: Gao, Yuefeng
last_name: Gao
- first_name: Dylan
full_name: Taatjes, Dylan
last_name: Taatjes
citation:
ama: Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. P53 activates transcription by
directing structural shifts in Mediator. Nature Structural and Molecular Biology.
2010;17(6):753-760. doi:10.1038/nsmb.1816
apa: Meyer, K., Lin, S., Bernecky, C., Gao, Y., & Taatjes, D. (2010). P53 activates
transcription by directing structural shifts in Mediator. Nature Structural
and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.1816
chicago: Meyer, Krista, Shih Lin, Carrie Bernecky, Yuefeng Gao, and Dylan Taatjes.
“P53 Activates Transcription by Directing Structural Shifts in Mediator.” Nature
Structural and Molecular Biology. Nature Publishing Group, 2010. https://doi.org/10.1038/nsmb.1816.
ieee: K. Meyer, S. Lin, C. Bernecky, Y. Gao, and D. Taatjes, “P53 activates transcription
by directing structural shifts in Mediator,” Nature Structural and Molecular
Biology, vol. 17, no. 6. Nature Publishing Group, pp. 753–760, 2010.
ista: Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. 2010. P53 activates transcription
by directing structural shifts in Mediator. Nature Structural and Molecular Biology.
17(6), 753–760.
mla: Meyer, Krista, et al. “P53 Activates Transcription by Directing Structural
Shifts in Mediator.” Nature Structural and Molecular Biology, vol. 17,
no. 6, Nature Publishing Group, 2010, pp. 753–60, doi:10.1038/nsmb.1816.
short: K. Meyer, S. Lin, C. Bernecky, Y. Gao, D. Taatjes, Nature Structural and
Molecular Biology 17 (2010) 753–760.
date_created: 2018-12-11T11:47:24Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2021-01-12T08:05:28Z
day: '01'
doi: 10.1038/nsmb.1816
extern: '1'
intvolume: ' 17'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932482/
month: '06'
oa: 1
oa_version: None
page: 753 - 760
publication: Nature Structural and Molecular Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7210'
status: public
title: P53 activates transcription by directing structural shifts in Mediator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2010'
...
---
_id: '6142'
abstract:
- lang: eng
text: Defining the mutational landscape when individuals of a species grow separately
and diverge over many generations can provide insights into trait evolution. A
specific example of this involves studying changes associated with domestication
where different lines of the same wild stock have been cultivated independently
in different standard environments. Whole genome sequence comparison of such lines
permits estimation of mutation rates, inference of genes' ancestral states and
ancestry of existing strains, and correction of sequencing errors in genome databases.
Here we study domestication of the C. elegans Bristol strain as a model, and report
the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference
wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from
shortly after the Bristol strain was isolated until methods to freeze C. elegans
were developed. We find that during this time the two strains have accumulated
1208 genetic differences. We describe phenotypic variation between N2 and LSJ1
in the rate at which embryos develop, the rate of production of eggs, the maturity
of eggs at laying, and feeding behavior, all the result of post-isolation changes.
We infer the ancestral alleles in the original Bristol isolate and highlight 2038
likely sequencing errors in the original N2 reference genome sequence. Many of
these changes modify genome annotation. Our study provides a starting point to
further investigate genotype-phenotype association and offers insights into the
process of selection as a result of laboratory domestication.
article_number: e13922
author:
- first_name: Katherine P.
full_name: Weber, Katherine P.
last_name: Weber
- first_name: Subhajyoti
full_name: De, Subhajyoti
last_name: De
- first_name: Iwanka
full_name: Kozarewa, Iwanka
last_name: Kozarewa
- first_name: Daniel J.
full_name: Turner, Daniel J.
last_name: Turner
- first_name: M. Madan
full_name: Babu, M. Madan
last_name: Babu
- 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: Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing
highlights genetic changes associated with laboratory domestication of C. elegans.
PLoS ONE. 2010;5(11). doi:10.1371/journal.pone.0013922
apa: Weber, K. P., De, S., Kozarewa, I., Turner, D. J., Babu, M. M., & de Bono,
M. (2010). Whole genome sequencing highlights genetic changes associated with
laboratory domestication of C. elegans. PLoS ONE. Public Library of Science.
https://doi.org/10.1371/journal.pone.0013922
chicago: Weber, Katherine P., Subhajyoti De, Iwanka Kozarewa, Daniel J. Turner,
M. Madan Babu, and Mario de Bono. “Whole Genome Sequencing Highlights Genetic
Changes Associated with Laboratory Domestication of C. Elegans.” PLoS ONE.
Public Library of Science, 2010. https://doi.org/10.1371/journal.pone.0013922.
ieee: K. P. Weber, S. De, I. Kozarewa, D. J. Turner, M. M. Babu, and M. de Bono,
“Whole genome sequencing highlights genetic changes associated with laboratory
domestication of C. elegans,” PLoS ONE, vol. 5, no. 11. Public Library
of Science, 2010.
ista: Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. 2010. Whole genome
sequencing highlights genetic changes associated with laboratory domestication
of C. elegans. PLoS ONE. 5(11), e13922.
mla: Weber, Katherine P., et al. “Whole Genome Sequencing Highlights Genetic Changes
Associated with Laboratory Domestication of C. Elegans.” PLoS ONE, vol.
5, no. 11, e13922, Public Library of Science, 2010, doi:10.1371/journal.pone.0013922.
short: K.P. Weber, S. De, I. Kozarewa, D.J. Turner, M.M. Babu, M. de Bono, PLoS
ONE 5 (2010).
date_created: 2019-03-20T15:20:30Z
date_published: 2010-11-11T00:00:00Z
date_updated: 2021-01-12T08:06:20Z
day: '11'
ddc:
- '570'
doi: 10.1371/journal.pone.0013922
extern: '1'
external_id:
pmid:
- '21085631'
file:
- access_level: open_access
checksum: a01e6bbe15f044c0c79a26d7d881953e
content_type: application/pdf
creator: kschuh
date_created: 2019-03-20T15:22:48Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6143'
file_name: 2010_PLOS_Weber.PDF
file_size: 578059
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
issn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Whole genome sequencing highlights genetic changes associated with laboratory
domestication of 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: 5
year: '2010'
...
---
_id: '619'
abstract:
- lang: eng
text: Sinclair Ross’s novel As for Me and My House has long since been canonized
as Canadian prairie fiction. Accordingly, it has been the subject of many critical
studies and academic papers. Most commentators have concentrated on such literary
issues as the representation of the western landscape or the reliability of the
female narrator. But so far little consideration has been given to the social
and cultural implications of the novel. Few attempts have been made to analyze
the text from a cultural perspective including such social markers as class, gender
and ethnicity. That is all the more surprising because Sinclair Ross has often
been credited for being a realistic author and As for Me and My House has often
been interpreted as a regional novel characteristic of a particular time and place.
author:
- first_name: Waldemar
full_name: Zacharasiewicz, Waldemar
last_name: Zacharasiewicz
- first_name: Fritz
full_name: Kirsch, Fritz Peter
last_name: Kirsch
citation:
ama: 'Zacharasiewicz W, Kirsch F. “This is a fundamentalist town”: The Prairie Town
as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My
House. In: Social and Cultural Interaction and Literary Landscapes in the Canadian
West : Impressions of an Exploratory Field Trip and Academic Interaction in the
Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien.
Facultas.WUV; 2010:173-179.'
apa: 'Zacharasiewicz, W., & Kirsch, F. (2010). “This is a fundamentalist town”:
The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s
As for Me and My House. In Social and cultural interaction and literary landscapes
in the Canadian West : impressions of an exploratory field trip and academic interaction
in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest
canadien (pp. 173–179). Facultas.WUV.'
chicago: 'Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist
Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair
Ross’s As for Me and My House.” In Social and Cultural Interaction and Literary
Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and
Academic Interaction in the Canadian West : Rapports Interculturels et Paysages
Littéraires Dans l’Ouest Canadien, 173–79. Facultas.WUV, 2010.'
ieee: 'W. Zacharasiewicz and F. Kirsch, “‘This is a fundamentalist town’: The Prairie
Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and
My House,” in Social and cultural interaction and literary landscapes in the
Canadian West : impressions of an exploratory field trip and academic interaction
in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest
canadien, Facultas.WUV, 2010, pp. 173–179.'
ista: 'Zacharasiewicz W, Kirsch F. 2010.“This is a fundamentalist town”: The Prairie
Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and
My House. In: Social and cultural interaction and literary landscapes in the Canadian
West : impressions of an exploratory field trip and academic interaction in the
Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien.
, 173–179.'
mla: 'Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’:
The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s
As for Me and My House.” Social and Cultural Interaction and Literary Landscapes
in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction
in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest
Canadien, Facultas.WUV, 2010, pp. 173–79.'
short: 'W. Zacharasiewicz, F. Kirsch, in:, Social and Cultural Interaction and Literary
Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and
Academic Interaction in the Canadian West : Rapports Interculturels et Paysages
Littéraires Dans l’Ouest Canadien, Facultas.WUV, 2010, pp. 173–179.'
date_created: 2018-12-11T11:47:32Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:06:40Z
day: '01'
extern: 1
month: '01'
page: 173 - 179
publication: 'Social and cultural interaction and literary landscapes in the Canadian
West : impressions of an exploratory field trip and academic interaction in the
Canadian West : Rapports interculturels et paysages littéraires dans l''Ouest canadien'
publication_status: published
publisher: Facultas.WUV
publist_id: '7185'
quality_controlled: 0
status: public
title: '“This is a fundamentalist town”: The Prairie Town as a Site of Social and
Cultural Conflict in Sinclair Ross’s As for Me and My House'
type: book_chapter
year: '2010'
...
---
_id: '6198'
abstract:
- lang: eng
text: 'Stroke is a major public health problem leading to high rates of death and
disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors
(NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are
crucial for neuronal injury after stroke insult. However, directly inhibiting
NMDARs or nNOS can cause severe side effects because they have key physiological
functions in the CNS. Here we show that cerebral ischemia induces the interaction
of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95
interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS
(nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic
damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series
of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction,
ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively,
had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic
damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and
reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit
NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect
on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke,
perhaps without major side effects. '
author:
- first_name: L
full_name: Zhou, L
last_name: Zhou
- first_name: F
full_name: Li, F
last_name: Li
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
- first_name: CX
full_name: Luo, CX
last_name: Luo
- first_name: HY
full_name: Wu, HY
last_name: Wu
- first_name: MM
full_name: Zhu, MM
last_name: Zhu
- first_name: W
full_name: Lu, W
last_name: Lu
- first_name: X
full_name: Ji, X
last_name: Ji
- first_name: QG
full_name: Zhou, QG
last_name: Zhou
- first_name: DY
full_name: Zhu, DY
last_name: Zhu
citation:
ama: Zhou L, Li F, Xu H, et al. Treatment of cerebral ischemia by disrupting ischemia-induced
interaction of nNOS with PSD-95. Nature Medicine. 2010;16(12):1439-1443.
doi:10.1038/nm.2245
apa: Zhou, L., Li, F., Xu, H., Luo, C., Wu, H., Zhu, M., … Zhu, D. (2010). Treatment
of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95.
Nature Medicine. Nature Publishing Group. https://doi.org/10.1038/nm.2245
chicago: Zhou, L, F Li, Haibing Xu, CX Luo, HY Wu, MM Zhu, W Lu, X Ji, QG Zhou,
and DY Zhu. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction
of NNOS with PSD-95.” Nature Medicine. Nature Publishing Group, 2010. https://doi.org/10.1038/nm.2245.
ieee: L. Zhou et al., “Treatment of cerebral ischemia by disrupting ischemia-induced
interaction of nNOS with PSD-95,” Nature Medicine, vol. 16, no. 12. Nature
Publishing Group, pp. 1439–1443, 2010.
ista: Zhou L, Li F, Xu H, Luo C, Wu H, Zhu M, Lu W, Ji X, Zhou Q, Zhu D. 2010. Treatment
of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95.
Nature Medicine. 16(12), 1439–1443.
mla: Zhou, L., et al. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced
Interaction of NNOS with PSD-95.” Nature Medicine, vol. 16, no. 12, Nature
Publishing Group, 2010, pp. 1439–43, doi:10.1038/nm.2245.
short: L. Zhou, F. Li, H. Xu, C. Luo, H. Wu, M. Zhu, W. Lu, X. Ji, Q. Zhou, D. Zhu,
Nature Medicine 16 (2010) 1439–1443.
date_created: 2019-04-04T14:55:32Z
date_published: 2010-11-21T00:00:00Z
date_updated: 2021-01-12T08:06:43Z
day: '21'
doi: 10.1038/nm.2245
extern: '1'
external_id:
pmid:
- '21102461'
intvolume: ' 16'
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1439-1443
pmid: 1
publication: Nature Medicine
publication_identifier:
issn:
- 1078-8956
- 1546-170x
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
status: public
title: Treatment of cerebral ischemia by disrupting ischemia-induced interaction of
nNOS with PSD-95
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2010'
...
---
_id: '6320'
abstract:
- lang: eng
text: We study the average order of the divisor function, as it ranges over the
values of binary quartic forms that are reducible over ℚ.
arxiv: 1
author:
- first_name: Régis de la
full_name: Bretèche, Régis de la
last_name: Bretèche
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bretèche R de la, Browning TD. Le problème des diviseurs pour des formes binaires
de degré 4. Crelles Journal. 2010;2010(646):1-44. doi:10.1515/crelle.2010.064
apa: Bretèche, R. de la, & Browning, T. D. (2010). Le problème des diviseurs
pour des formes binaires de degré 4. Crelles Journal. Walter de Gruyter
GmbH. https://doi.org/10.1515/crelle.2010.064
chicago: Bretèche, Régis de la, and Timothy D Browning. “Le Problème Des Diviseurs
Pour Des Formes Binaires de Degré 4.” Crelles Journal. Walter de Gruyter
GmbH, 2010. https://doi.org/10.1515/crelle.2010.064.
ieee: R. de la Bretèche and T. D. Browning, “Le problème des diviseurs pour des
formes binaires de degré 4,” Crelles Journal, vol. 2010, no. 646. Walter
de Gruyter GmbH, pp. 1–44, 2010.
ista: Bretèche R de la, Browning TD. 2010. Le problème des diviseurs pour des formes
binaires de degré 4. Crelles Journal. 2010(646), 1–44.
mla: Bretèche, Régis de la, and Timothy D. Browning. “Le Problème Des Diviseurs
Pour Des Formes Binaires de Degré 4.” Crelles Journal, vol. 2010, no. 646,
Walter de Gruyter GmbH, 2010, pp. 1–44, doi:10.1515/crelle.2010.064.
short: R. de la Bretèche, T.D. Browning, Crelles Journal 2010 (2010) 1–44.
date_created: 2019-04-16T13:51:40Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T08:07:04Z
day: '01'
doi: 10.1515/crelle.2010.064
extern: '1'
external_id:
arxiv:
- 0808.2340v2
intvolume: ' 2010'
issue: '646'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0808.2340v2
month: '09'
oa: 1
oa_version: Preprint
page: 1-44
publication: Crelles Journal
publication_status: published
publisher: Walter de Gruyter GmbH
quality_controlled: '1'
status: public
title: Le problème des diviseurs pour des formes binaires de degré 4
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 2010
year: '2010'
...
---
_id: '1465'
abstract:
- lang: eng
text: We prove a generating function formula for the Betti numbers of Nakajima quiver
varieties. We prove that it is a q-deformation of the Weyl-Kac character formula.
In particular this implies that the constant term of the polynomial counting the
number of absolutely indecomposable representations of a quiver equals the multiplicity
of a certain weight in the corresponding Kac-Moody algebra, which was conjectured
by Kac in 1982.
acknowledgement: This work has been supported by a Royal Society University Research
Fellowship, NSF grants DMS-0305505 and DMS-0604775 and an Alfred Sloan Fellowship
2005-2007.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: Hausel T. Kac’s conjecture from Nakajima quiver varieties. Inventiones Mathematicae.
2010;181(1):21-37. doi:10.1007/s00222-010-0241-3
apa: Hausel, T. (2010). Kac’s conjecture from Nakajima quiver varieties. Inventiones
Mathematicae. Springer. https://doi.org/10.1007/s00222-010-0241-3
chicago: Hausel, Tamás. “Kac’s Conjecture from Nakajima Quiver Varieties.” Inventiones
Mathematicae. Springer, 2010. https://doi.org/10.1007/s00222-010-0241-3.
ieee: T. Hausel, “Kac’s conjecture from Nakajima quiver varieties,” Inventiones
Mathematicae, vol. 181, no. 1. Springer, pp. 21–37, 2010.
ista: Hausel T. 2010. Kac’s conjecture from Nakajima quiver varieties. Inventiones
Mathematicae. 181(1), 21–37.
mla: Hausel, Tamás. “Kac’s Conjecture from Nakajima Quiver Varieties.” Inventiones
Mathematicae, vol. 181, no. 1, Springer, 2010, pp. 21–37, doi:10.1007/s00222-010-0241-3.
short: T. Hausel, Inventiones Mathematicae 181 (2010) 21–37.
date_created: 2018-12-11T11:52:11Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:56Z
day: '01'
doi: 10.1007/s00222-010-0241-3
extern: 1
intvolume: ' 181'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0811.1569
month: '07'
oa: 1
page: 21 - 37
publication: Inventiones Mathematicae
publication_status: published
publisher: Springer
publist_id: '5730'
quality_controlled: 0
status: public
title: Kac's conjecture from Nakajima quiver varieties
type: journal_article
volume: 181
year: '2010'
...
---
_id: '1466'
abstract:
- lang: eng
text: In Hausel et al. (2008) [10] we presented a conjecture generalizing the Cauchy
formula for Macdonald polynomial. This conjecture encodes the mixed Hodge polynomials
of the character varieties of representations of the fundamental group of a punctured
Riemann surface of genus g. We proved several results which support this conjecture.
Here we announce new results which are consequences of those in Hausel et al.
(2008) [10].
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Emmanuel
full_name: Letellier, Emmanuel
last_name: Letellier
- first_name: Fernando
full_name: Rodríguez Villegas, Fernando
last_name: Rodríguez Villegas
citation:
ama: Hausel T, Letellier E, Rodríguez Villegas F. Topology of character varieties
and representations of quivers. Comptes Rendus Mathematique. 2010;348(3-4):131-135.
doi:10.1016/j.crma.2010.01.025
apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2010). Topology of
character varieties and representations of quivers. Comptes Rendus Mathematique.
Elsevier. https://doi.org/10.1016/j.crma.2010.01.025
chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Topology
of Character Varieties and Representations of Quivers.” Comptes Rendus Mathematique.
Elsevier, 2010. https://doi.org/10.1016/j.crma.2010.01.025.
ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Topology of character
varieties and representations of quivers,” Comptes Rendus Mathematique,
vol. 348, no. 3–4. Elsevier, pp. 131–135, 2010.
ista: Hausel T, Letellier E, Rodríguez Villegas F. 2010. Topology of character varieties
and representations of quivers. Comptes Rendus Mathematique. 348(3–4), 131–135.
mla: Hausel, Tamás, et al. “Topology of Character Varieties and Representations
of Quivers.” Comptes Rendus Mathematique, vol. 348, no. 3–4, Elsevier,
2010, pp. 131–35, doi:10.1016/j.crma.2010.01.025.
short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Comptes Rendus Mathematique
348 (2010) 131–135.
date_created: 2018-12-11T11:52:11Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2021-01-12T06:50:56Z
day: '01'
doi: 10.1016/j.crma.2010.01.025
extern: 1
intvolume: ' 348'
issue: 3-4
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0905.3491
month: '02'
oa: 1
page: 131 - 135
publication: Comptes Rendus Mathematique
publication_status: published
publisher: Elsevier
publist_id: '5731'
quality_controlled: 0
status: public
title: Topology of character varieties and representations of quivers
type: journal_article
volume: 348
year: '2010'
...
---
_id: '1468'
abstract:
- lang: eng
text: 'This chapter surveys the motivations, related results, and progress made
towards the following problem, raised by Hitchin in 1995: What is the space of
L2 harmonic forms on the moduli space of Higgs bundles on a Riemann surface?'
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: 'Hausel T. S-Duality in HyperkäHler Hodge Theory. In: The Many Facets of
Geometry: A Tribute to Nigel Hitchin. Oxford University Press; 2010. doi:10.1093/acprof:oso/9780199534920.003.0016'
apa: 'Hausel, T. (2010). S-Duality in HyperkäHler Hodge Theory. In The Many Facets
of Geometry: A Tribute to Nigel Hitchin. Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199534920.003.0016'
chicago: 'Hausel, Tamás. “S-Duality in HyperkäHler Hodge Theory.” In The Many
Facets of Geometry: A Tribute to Nigel Hitchin. Oxford University Press, 2010.
https://doi.org/10.1093/acprof:oso/9780199534920.003.0016.'
ieee: 'T. Hausel, “S-Duality in HyperkäHler Hodge Theory,” in The Many Facets
of Geometry: A Tribute to Nigel Hitchin, Oxford University Press, 2010.'
ista: 'Hausel T. 2010.S-Duality in HyperkäHler Hodge Theory. In: The Many Facets
of Geometry: A Tribute to Nigel Hitchin. .'
mla: 'Hausel, Tamás. “S-Duality in HyperkäHler Hodge Theory.” The Many Facets
of Geometry: A Tribute to Nigel Hitchin, Oxford University Press, 2010, doi:10.1093/acprof:oso/9780199534920.003.0016.'
short: 'T. Hausel, in:, The Many Facets of Geometry: A Tribute to Nigel Hitchin,
Oxford University Press, 2010.'
date_created: 2018-12-11T11:52:12Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T06:50:57Z
day: '01'
doi: 10.1093/acprof:oso/9780199534920.003.0016
extern: 1
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0709.0504
month: '09'
oa: 1
publication: 'The Many Facets of Geometry: A Tribute to Nigel Hitchin'
publication_status: published
publisher: Oxford University Press
publist_id: '5729'
quality_controlled: 0
status: public
title: S-Duality in HyperkäHler Hodge Theory
type: book_chapter
year: '2010'
...
---
_id: '14983'
abstract:
- lang: eng
text: 'This chapter tackles a difficult challenge: presenting signal processing
material to non-experts. This chapter is meant to be comprehensible to people
who have some math background, including a course in linear algebra and basic
statistics, but do not specialize in mathematics, engineering, or related fields.
Some formulas assume the reader is familiar with matrices and basic matrix operations,
but not more advanced material. Furthermore, we tried to make the chapter readable
even if you skip the formulas. Nevertheless, we include some simple methods to
demonstrate the basics of adaptive data processing, then we proceed with some
advanced methods that are fundamental in adaptive signal processing, and are likely
to be useful in a variety of applications. The advanced algorithms are also online
available [30]. In the second part, these techniques are applied to some real-world
BCI data.'
acknowledgement: This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5
Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore,
we thank Matthias Krauledat for fruitful discussions and tools for generating Fig.
5.
alternative_title:
- The Frontiers Collection
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Carmen
full_name: Vidaurre, Carmen
last_name: Vidaurre
- first_name: Klaus-Robert
full_name: Müller, Klaus-Robert
last_name: Müller
citation:
ama: 'Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory
Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. Brain-Computer Interfaces.
1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:10.1007/978-3-642-02091-9_18'
apa: 'Schlögl, A., Vidaurre, C., & Müller, K.-R. (2010). Adaptive Methods in
BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &
B. Allison (Eds.), Brain-Computer Interfaces (1st ed., pp. 331–355). Berlin,
Heidelberg: Springer. https://doi.org/10.1007/978-3-642-02091-9_18'
chicago: 'Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods
in BCI Research - An Introductory Tutorial.” In Brain-Computer Interfaces,
edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed.,
331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. https://doi.org/10.1007/978-3-642-02091-9_18.'
ieee: 'A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research
- An Introductory Tutorial,” in Brain-Computer Interfaces, 1st ed., B.
Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer,
2010, pp. 331–355.'
ista: 'Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research
- An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection,
, 331–355.'
mla: Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory
Tutorial.” Brain-Computer Interfaces, edited by Bernhard Graimann et al.,
1st ed., Springer, 2010, pp. 331–55, doi:10.1007/978-3-642-02091-9_18.
short: A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller,
B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg,
2010, pp. 331–355.
date_created: 2024-02-14T09:56:00Z
date_published: 2010-09-06T00:00:00Z
date_updated: 2024-02-19T09:47:25Z
day: '06'
department:
- _id: ScienComp
doi: 10.1007/978-3-642-02091-9_18
edition: '1'
editor:
- first_name: Bernhard
full_name: Graimann, Bernhard
last_name: Graimann
- first_name: Gert
full_name: Pfurtscheller, Gert
last_name: Pfurtscheller
- first_name: Brendan
full_name: Allison, Brendan
last_name: Allison
language:
- iso: eng
month: '09'
oa_version: None
page: 331-355
place: Berlin, Heidelberg
publication: Brain-Computer Interfaces
publication_identifier:
eisbn:
- '9783642020919'
isbn:
- '9783642020902'
issn:
- 1612-3018
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: FRONTCOLL
status: public
title: Adaptive Methods in BCI Research - An Introductory Tutorial
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '13409'
abstract:
- lang: eng
text: The immobilization of molecular switches onto inorganic supports has recently
become a hot topic as it can give rise to novel hybrid materials in which the
properties of the two components are mutually enhanced. Even more attractive is
the concept of “transferring” the switchable characteristics of single layers
of organic molecules onto the underlying inorganic components, rendering them
responsive to external stimuli as well. Of the various molecular switches studied,
azobenzene (AB) has arguably attracted most attention due to its simple molecular
structure, and because its “trigger” (light) is a noninvasive one, it can be delivered
instantaneously, and into a precise location. In order to fully realize its potential,
however, it is necessary to immobilize AB onto solid supports. It is the goal
of this manuscript to comprehensively yet concisely review such hybrid systems
which comprise AB forming well-defined self-assembled monolayers (SAMs) on planar
and curved (colloidal and nanoporous) inorganic surfaces. I discuss methods to
immobilize AB derivatives onto surfaces, strategies to ensure efficient AB isomerization,
ways to monitor the switching process, properties of these switchable hybrid materials,
and, last but not least, their emerging applications.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Klajn R. Immobilized azobenzenes for the construction of photoresponsive materials.
Pure and Applied Chemistry. 2010;82(12):2247-2279. doi:10.1351/pac-con-10-09-04
apa: Klajn, R. (2010). Immobilized azobenzenes for the construction of photoresponsive
materials. Pure and Applied Chemistry. De Gruyter. https://doi.org/10.1351/pac-con-10-09-04
chicago: Klajn, Rafal. “Immobilized Azobenzenes for the Construction of Photoresponsive
Materials.” Pure and Applied Chemistry. De Gruyter, 2010. https://doi.org/10.1351/pac-con-10-09-04.
ieee: R. Klajn, “Immobilized azobenzenes for the construction of photoresponsive
materials,” Pure and Applied Chemistry, vol. 82, no. 12. De Gruyter, pp.
2247–2279, 2010.
ista: Klajn R. 2010. Immobilized azobenzenes for the construction of photoresponsive
materials. Pure and Applied Chemistry. 82(12), 2247–2279.
mla: Klajn, Rafal. “Immobilized Azobenzenes for the Construction of Photoresponsive
Materials.” Pure and Applied Chemistry, vol. 82, no. 12, De Gruyter, 2010,
pp. 2247–79, doi:10.1351/pac-con-10-09-04.
short: R. Klajn, Pure and Applied Chemistry 82 (2010) 2247–2279.
date_created: 2023-08-01T09:48:11Z
date_published: 2010-10-15T00:00:00Z
date_updated: 2023-08-08T07:58:13Z
day: '15'
doi: 10.1351/pac-con-10-09-04
extern: '1'
intvolume: ' 82'
issue: '12'
keyword:
- General Chemical Engineering
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1351/pac-con-10-09-04
month: '10'
oa: 1
oa_version: Published Version
page: 2247-2279
publication: Pure and Applied Chemistry
publication_identifier:
eissn:
- 1365-3075
issn:
- 0033-4545
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
scopus_import: '1'
status: public
title: Immobilized azobenzenes for the construction of photoresponsive materials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2010'
...
---
_id: '13410'
abstract:
- lang: eng
text: A range (Au, Pt, Pd) of metal nanoparticles (MNPs) has been prepared and functionalized
with (a) redox-active stalks containing tetrathiafulvalene (TTF) units, (b) [2]pseudorotaxanes
formed between these stalks and cyclobis(paraquat-p-phenylene) (CBPQT4+) rings,
and (c) bistable [2]rotaxane molecules where the dumbbell component contains a
1,5-dioxynaphthalene (DNP) unit, as well as a TTF unit, encircled by a CBPQT4+
ring. It transpires that the molecules present in (a) and (c) and the supermolecules
described in (b) retain their switching characteristics, previously observed in
solution, when they are immobilized onto MNPs. Moreover, their oxidation potentials
depend on the fraction, χ, of the molecules or supermolecules on the surface of
the nanoparticles. A variation in χ affects the oxidation potentials of the TTF
units to the extent that switching can be subjected to fine tuning as a result.
Specifically, increasing χ results in positive shifts (i) in the oxidation potentials
of the TTF unit in (a)−(c) and (ii) the reduction potentials of the CBPQT4+ rings
in (c). These shifts can be attributed to an increase in the electrostatic potential
surrounding the MNPs. Both the magnitude and the direction of these shifts are
reproduced by a model, based on the Poisson−Boltzmann equation coupled with charge-regulating
boundary conditions. Furthermore, the kinetics of relaxation from the metastable
state coconformation (MSCC) to the ground-state coconformation (GSCC) of the bistable
[2]rotaxane molecules also depends on χ, as well as on the nanoparticle diameter.
Increasing either of these parameters accelerates the rate of relaxation from
the MSCC to the GSCC. This rate is a function of (i) the activation energy for
the relaxation process associated with the bistable [2]rotaxane molecules in solution
and (ii) the electrostatic potential surrounding the MNPs. The electrostatic potential
depends on (i) the diameter of the MNPs, (ii) the amount of the bistable [2]rotaxane
molecules on the surface of the MNPs, and (iii) the equilibrium distribution of
the CBPQT4+ rings between the DNP and TTF recognition sites in the GSCC. This
electrostatic potential has also been quantified using the Poisson−Boltzmann equation,
leading to faithful estimates of the rate constants.
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Coskun, Ali
last_name: Coskun
- first_name: Paul J.
full_name: Wesson, Paul J.
last_name: Wesson
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Ali
full_name: Trabolsi, Ali
last_name: Trabolsi
- first_name: Lei
full_name: Fang, Lei
last_name: Fang
- first_name: Mark A.
full_name: Olson, Mark A.
last_name: Olson
- first_name: Sanjeev K.
full_name: Dey, Sanjeev K.
last_name: Dey
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
- first_name: J. Fraser
full_name: Stoddart, J. Fraser
last_name: Stoddart
citation:
ama: 'Coskun A, Wesson PJ, Klajn R, et al. Molecular-mechanical switching at the
nanoparticle−solvent interface: Practice and theory. Journal of the American
Chemical Society. 2010;132(12):4310-4320. doi:10.1021/ja9102327'
apa: 'Coskun, A., Wesson, P. J., Klajn, R., Trabolsi, A., Fang, L., Olson, M. A.,
… Stoddart, J. F. (2010). Molecular-mechanical switching at the nanoparticle−solvent
interface: Practice and theory. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/ja9102327'
chicago: 'Coskun, Ali, Paul J. Wesson, Rafal Klajn, Ali Trabolsi, Lei Fang, Mark
A. Olson, Sanjeev K. Dey, Bartosz A. Grzybowski, and J. Fraser Stoddart. “Molecular-Mechanical
Switching at the Nanoparticle−solvent Interface: Practice and Theory.” Journal
of the American Chemical Society. American Chemical Society, 2010. https://doi.org/10.1021/ja9102327.'
ieee: 'A. Coskun et al., “Molecular-mechanical switching at the nanoparticle−solvent
interface: Practice and theory,” Journal of the American Chemical Society,
vol. 132, no. 12. American Chemical Society, pp. 4310–4320, 2010.'
ista: 'Coskun A, Wesson PJ, Klajn R, Trabolsi A, Fang L, Olson MA, Dey SK, Grzybowski
BA, Stoddart JF. 2010. Molecular-mechanical switching at the nanoparticle−solvent
interface: Practice and theory. Journal of the American Chemical Society. 132(12),
4310–4320.'
mla: 'Coskun, Ali, et al. “Molecular-Mechanical Switching at the Nanoparticle−solvent
Interface: Practice and Theory.” Journal of the American Chemical Society,
vol. 132, no. 12, American Chemical Society, 2010, pp. 4310–20, doi:10.1021/ja9102327.'
short: A. Coskun, P.J. Wesson, R. Klajn, A. Trabolsi, L. Fang, M.A. Olson, S.K.
Dey, B.A. Grzybowski, J.F. Stoddart, Journal of the American Chemical Society
132 (2010) 4310–4320.
date_created: 2023-08-01T09:48:27Z
date_published: 2010-03-31T00:00:00Z
date_updated: 2023-08-08T08:00:31Z
day: '31'
doi: 10.1021/ja9102327
extern: '1'
external_id:
pmid:
- '20218598'
intvolume: ' 132'
issue: '12'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '03'
oa_version: None
page: 4310-4320
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Molecular-mechanical switching at the nanoparticle−solvent interface: Practice
and theory'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2010'
...
---
_id: '13411'
abstract:
- lang: eng
text: Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide
a basis for sensors that “remember” whether the sample has ever exceeded the melting
temperature of the matrix. The operation of these sensors rests on the ability
to photoinduce metastable electric dipoles on NP surfaces – upon melting, these
dipoles drive NP aggregation, precipitation, and crosslinking. These events are
manifested by a pronounced color change.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Kevin P.
full_name: Browne, Kevin P.
last_name: Browne
- first_name: Siowling
full_name: Soh, Siowling
last_name: Soh
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Klajn R, Browne KP, Soh S, Grzybowski BA. Nanoparticles that “remember” temperature.
Small. 2010;6(13):1385-1387. doi:10.1002/smll.200902272
apa: Klajn, R., Browne, K. P., Soh, S., & Grzybowski, B. A. (2010). Nanoparticles
that “remember” temperature. Small. Wiley. https://doi.org/10.1002/smll.200902272
chicago: Klajn, Rafal, Kevin P. Browne, Siowling Soh, and Bartosz A. Grzybowski.
“Nanoparticles That ‘Remember’ Temperature.” Small. Wiley, 2010. https://doi.org/10.1002/smll.200902272.
ieee: R. Klajn, K. P. Browne, S. Soh, and B. A. Grzybowski, “Nanoparticles that
‘remember’ temperature,” Small, vol. 6, no. 13. Wiley, pp. 1385–1387, 2010.
ista: Klajn R, Browne KP, Soh S, Grzybowski BA. 2010. Nanoparticles that “remember”
temperature. Small. 6(13), 1385–1387.
mla: Klajn, Rafal, et al. “Nanoparticles That ‘Remember’ Temperature.” Small,
vol. 6, no. 13, Wiley, 2010, pp. 1385–87, doi:10.1002/smll.200902272.
short: R. Klajn, K.P. Browne, S. Soh, B.A. Grzybowski, Small 6 (2010) 1385–1387.
date_created: 2023-08-01T09:48:38Z
date_published: 2010-07-05T00:00:00Z
date_updated: 2023-08-08T08:15:25Z
day: '05'
doi: 10.1002/smll.200902272
extern: '1'
external_id:
pmid:
- '20521264'
intvolume: ' 6'
issue: '13'
keyword:
- Biomaterials
- Biotechnology
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 1385-1387
pmid: 1
publication: Small
publication_identifier:
eissn:
- 1613-6829
issn:
- 1613-6810
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoparticles that “remember” temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '13412'
abstract:
- lang: eng
text: Nanoparticles (NPs) and molecular/supramolecular switches have attracted considerable
interest during the past decade on account of their unique properties and prominent
roles in the fields of organic chemistry and materials science. Materials derived
from the combination of these two components are now emerging in the literature.
This critical review evaluates materials which comprise NPs functionalised with
well-defined self-assembled monolayers of molecular and supramolecular switches.
We draw attention to the fact that immobilisation of switches on NPs does not,
in general, hamper their switching ability, although it can impart new properties
on the supporting particles. This premise leads us to the discussion of systems
in which switching on the surfaces of NPs can be used to modulate reversibly a
range of NP properties—optical, fluorescent, electrical, magnetic—as well as the
controlled release of small molecules. Finally, we discuss examples in which molecular
switches direct reversible self-assembly of NPs (308 references).
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: J. Fraser
full_name: Stoddart, J. Fraser
last_name: Stoddart
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Klajn R, Stoddart JF, Grzybowski BA. Nanoparticles functionalised with reversible
molecular and supramolecular switches. Chemical Society Reviews. 2010;39(6):2203-2237.
doi:10.1039/b920377j
apa: Klajn, R., Stoddart, J. F., & Grzybowski, B. A. (2010). Nanoparticles functionalised
with reversible molecular and supramolecular switches. Chemical Society Reviews.
Royal Society of Chemistry. https://doi.org/10.1039/b920377j
chicago: Klajn, Rafal, J. Fraser Stoddart, and Bartosz A. Grzybowski. “Nanoparticles
Functionalised with Reversible Molecular and Supramolecular Switches.” Chemical
Society Reviews. Royal Society of Chemistry, 2010. https://doi.org/10.1039/b920377j.
ieee: R. Klajn, J. F. Stoddart, and B. A. Grzybowski, “Nanoparticles functionalised
with reversible molecular and supramolecular switches,” Chemical Society Reviews,
vol. 39, no. 6. Royal Society of Chemistry, pp. 2203–2237, 2010.
ista: Klajn R, Stoddart JF, Grzybowski BA. 2010. Nanoparticles functionalised with
reversible molecular and supramolecular switches. Chemical Society Reviews. 39(6),
2203–2237.
mla: Klajn, Rafal, et al. “Nanoparticles Functionalised with Reversible Molecular
and Supramolecular Switches.” Chemical Society Reviews, vol. 39, no. 6,
Royal Society of Chemistry, 2010, pp. 2203–37, doi:10.1039/b920377j.
short: R. Klajn, J.F. Stoddart, B.A. Grzybowski, Chemical Society Reviews 39 (2010)
2203–2237.
date_created: 2023-08-01T09:49:07Z
date_published: 2010-04-21T00:00:00Z
date_updated: 2023-08-08T08:19:00Z
day: '21'
doi: 10.1039/b920377j
extern: '1'
external_id:
pmid:
- '20407689'
intvolume: ' 39'
issue: '6'
keyword:
- General Chemistry
language:
- iso: eng
month: '04'
oa_version: None
page: 2203-2237
pmid: 1
publication: Chemical Society Reviews
publication_identifier:
eissn:
- 1460-4744
issn:
- 0306-0012
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoparticles functionalised with reversible molecular and supramolecular switches
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2010'
...
---
_id: '901'
abstract:
- lang: eng
text: 'Background: Surveying deleterious variation in human populations is crucial
for our understanding, diagnosis and potential treatment of human genetic pathologies.
A number of recent genome-wide analyses focused on the prevalence of segregating
deleterious alleles in the nuclear genome. However, such studies have not been
conducted for the mitochondrial genome.Results: We present a systematic survey
of polymorphisms in the human mitochondrial genome, including those predicted
to be deleterious and those that correspond to known pathogenic mutations. Analyzing
4458 completely sequenced mitochondrial genomes we characterize the genetic diversity
of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes)
and non-African (M and N haplotypes) populations. We find that the overall level
of polymorphism is higher in the mitochondrial compared to the nuclear genome,
although the mitochondrial genome appears to be under stronger selection as indicated
by proportionally fewer nonsynonymous than synonymous substitutions. The African
mitochondrial genomes show higher heterozygosity, a greater number of polymorphic
sites and higher frequencies of polymorphisms for synonymous, benign and damaging
polymorphism than non-African genomes. However, African genomes carry significantly
fewer SNPs that have been previously characterized as pathogenic compared to non-African
genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category
of polymorphisms that are more abundant in non-African genomes is best explained
by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms
segregating in non-African populations. This further suggests that, contrary to
the common disease-common variant hypothesis, pathogenic mutations are largely
population-specific and different SNPs may be associated with the same disease
in different populations. Therefore, to obtain a comprehensive picture of the
deleterious variability in the human population, as well as to improve the diagnostics
of individuals carrying African mitochondrial haplotypes, it is necessary to survey
different populations independently.Reviewers: This article was reviewed by Dr
Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David
Rand (nominated by Dr Laurence Hurst).'
acknowledgement: We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance
with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science
and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 2010;5. doi:10.1186/1745-6150-5-68
apa: Breen, M., & Kondrashov, F. (2010). Mitochondrial pathogenic mutations
are population-specific. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-5-68
chicago: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct. BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-68.
ieee: M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,”
Biology Direct, vol. 5. BioMed Central, 2010.
ista: Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 5.
mla: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010,
doi:10.1186/1745-6150-5-68.
short: M. Breen, F. Kondrashov, Biology Direct 5 (2010).
date_created: 2018-12-11T11:49:06Z
date_published: 2010-12-31T00:00:00Z
date_updated: 2021-01-12T08:21:46Z
day: '31'
doi: 10.1186/1745-6150-5-68
extern: 1
intvolume: ' 5'
month: '12'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6749'
quality_controlled: 0
status: public
title: Mitochondrial pathogenic mutations are population-specific
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: 5
year: '2010'
...
---
_id: '9012'
abstract:
- lang: eng
text: In this Letter, we characterize experimentally the diffusiophoretic motion
of colloids and λ-DNA toward higher concentration of solutes, using microfluidic
technology to build spatially and temporally controlled concentration gradients.
We then demonstrate that segregation and spatial patterning of the particles can
be achieved from temporal variations of the solute concentration profile. This
segregation takes the form of a strong trapping potential, stemming from an osmotically
induced rectification mechanism of the solute time-dependent variations. Depending
on the spatial and temporal symmetry of the solute signal, localization patterns
with various shapes can be achieved. These results highlight the role of solute
contrasts in out-of-equilibrium processes occurring in soft matter.
article_number: '138302'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Benjamin
full_name: Abécassis, Benjamin
last_name: Abécassis
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility
and pattern formation under rectified diffusiophoresis. Physical Review Letters.
2010;104(13). doi:10.1103/physrevlett.104.138302
apa: Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., & Bocquet,
L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.138302
chicago: Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe
Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified
Diffusiophoresis.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/physrevlett.104.138302.
ieee: J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet,
“Colloidal motility and pattern formation under rectified diffusiophoresis,” Physical
Review Letters, vol. 104, no. 13. American Physical Society, 2010.
ista: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal
motility and pattern formation under rectified diffusiophoresis. Physical Review
Letters. 104(13), 138302.
mla: Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under
Rectified Diffusiophoresis.” Physical Review Letters, vol. 104, no. 13,
138302, American Physical Society, 2010, doi:10.1103/physrevlett.104.138302.
short: J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical
Review Letters 104 (2010).
date_created: 2021-01-19T10:25:04Z
date_published: 2010-04-02T00:00:00Z
date_updated: 2023-02-23T13:46:40Z
day: '02'
doi: 10.1103/physrevlett.104.138302
extern: '1'
external_id:
arxiv:
- '1004.1256 '
pmid:
- '20481918'
intvolume: ' 104'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.1256
month: '04'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colloidal motility and pattern formation under rectified diffusiophoresis
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 104
year: '2010'
...