---
_id: '5745'
article_processing_charge: No
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
last_name: Gupta
citation:
ama: 'Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In:
Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin,
Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:10.1007/978-3-642-33386-6_10'
apa: 'Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction.
In Automated Technology for Verification and Analysis (Vol. 7561, pp. 107–121).
Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33386-6_10'
chicago: 'Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof
Reduction.” In Automated Technology for Verification and Analysis, 7561:107–21.
LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. https://doi.org/10.1007/978-3-642-33386-6_10.'
ieee: 'A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,”
in Automated Technology for Verification and Analysis, vol. 7561, Berlin,
Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.'
ista: 'Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction.
In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.'
mla: Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.”
Automated Technology for Verification and Analysis, vol. 7561, Springer
Berlin Heidelberg, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10.
short: A. Gupta, in:, Automated Technology for Verification and Analysis, Springer
Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121.
conference:
end_date: 2012-10-06
location: Thiruvananthapuram, Kerala, India
name: ATVA 2012
start_date: 2012-10-03
date_created: 2018-12-18T13:01:46Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-09-05T14:15:29Z
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-33386-6_10
ec_funded: 1
file:
- access_level: open_access
checksum: 68415837a315de3cc4d120f6019d752c
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:07:35Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5746'
file_name: 2012_ATVA_Gupta.pdf
file_size: 465502
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 7561'
language:
- iso: eng
oa: 1
oa_version: None
page: 107-121
place: Berlin, Heidelberg
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Automated Technology for Verification and Analysis
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783642333859'
- '9783642333866'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
pubrep_id: '180'
quality_controlled: '1'
series_title: LNCS
status: public
title: Improved Single Pass Algorithms for Resolution Proof Reduction
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7561
year: '2012'
...
---
_id: '3251'
abstract:
- lang: eng
text: Many infinite state systems can be seen as well-structured transition systems
(WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also
a simulation relation. WSTS are an attractive target for formal analysis because
there exist generic algorithms that decide interesting verification problems for
this class. Among the most popular algorithms are acceleration-based forward analyses
for computing the covering set. Termination of these algorithms can only be guaranteed
for flattable WSTS. Yet, many WSTS of practical interest are not flattable and
the question whether any given WSTS is flattable is itself undecidable. We therefore
propose an analysis that computes the covering set and captures the essence of
acceleration-based algorithms, but sacrifices precision for guaranteed termination.
Our analysis is an abstract interpretation whose abstract domain builds on the
ideal completion of the well-quasi-ordered state space, and a widening operator
that mimics acceleration and controls the loss of precision of the analysis. We
present instances of our framework for various classes of WSTS. Our experience
with a prototype implementation indicates that, despite the inherent precision
loss, our analysis often computes the precise covering set of the analyzed system.
acknowledgement: This research was supported in part by the European Research Council
(ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF)
project S11402-N23.
alternative_title:
- LNCS
author:
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition
systems. In: Vol 7148. Springer; 2012:445-460. doi:10.1007/978-3-642-27940-9_29'
apa: 'Zufferey, D., Wies, T., & Henzinger, T. A. (2012). Ideal abstractions
for well structured transition systems (Vol. 7148, pp. 445–460). Presented at
the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia,
PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_29'
chicago: Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions
for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_29.
ieee: 'D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured
transition systems,” presented at the VMCAI: Verification, Model Checking and
Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460.'
ista: 'Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured
transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 7148, 445–460.'
mla: Zufferey, Damien, et al. Ideal Abstractions for Well Structured Transition
Systems. Vol. 7148, Springer, 2012, pp. 445–60, doi:10.1007/978-3-642-27940-9_29.
short: D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460.
conference:
end_date: 2012-01-24
location: Philadelphia, PA, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2012-01-22
date_created: 2018-12-11T12:02:16Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2023-09-07T11:36:36Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-27940-9_29
ec_funded: 1
file:
- access_level: open_access
checksum: f2f0d55efa32309ad1fe65a5fcaad90c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:35Z
date_updated: 2020-07-14T12:46:05Z
file_id: '4759'
file_name: IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf
file_size: 217104
relation: main_file
file_date_updated: 2020-07-14T12:46:05Z
has_accepted_license: '1'
intvolume: ' 7148'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 445 - 460
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '3406'
pubrep_id: '100'
quality_controlled: '1'
related_material:
record:
- id: '1405'
relation: dissertation_contains
status: public
status: public
title: Ideal abstractions for well structured transition systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7148
year: '2012'
...
---
_id: '3157'
abstract:
- lang: eng
text: Colorectal tumours that are wild type for KRAS are often sensitive to EGFR
blockade, but almost always develop resistance within several months of initiating
therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies
are largely unknown. This situation is in marked contrast to that of small-molecule
targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations
in the genes encoding the protein targets render the tumours resistant to the
effects of the drugs. The simplest hypothesis to account for the development of
resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at
low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis
would seem readily testable, there is no evidence in pre-clinical models to support
it, nor is there data from patients. To test this hypothesis, we determined whether
mutant KRAS DNA could be detected in the circulation of 28 patients receiving
monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that
9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed
detectable mutations in KRAS in their sera, three of which developed multiple
different KRAS mutations. The appearance of these mutations was very consistent,
generally occurring between 5 and 6months following treatment. Mathematical modelling
indicated that the mutations were present in expanded subclones before the initiation
of panitumumab treatment. These results suggest that the emergence of KRAS mutations
is a mediator of acquired resistance to EGFR blockade and that these mutations
can be detected in a non-invasive manner. They explain why solid tumours develop
resistance to targeted therapies in a highly reproducible fashion.
author:
- first_name: Luis
full_name: Diaz Jr, Luis
last_name: Diaz Jr
- first_name: Richard
full_name: Williams, Richard
last_name: Williams
- first_name: Jian
full_name: Wu, Jian
last_name: Wu
- first_name: Isaac
full_name: Kinde, Isaac
last_name: Kinde
- first_name: Joel
full_name: Hecht, Joel
last_name: Hecht
- first_name: Jordan
full_name: Berlin, Jordan
last_name: Berlin
- first_name: Benjamin
full_name: Allen, Benjamin
last_name: Allen
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
- first_name: Kenneth
full_name: Kinzler, Kenneth
last_name: Kinzler
- first_name: Kelly
full_name: Oliner, Kelly
last_name: Oliner
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
citation:
ama: Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance
to targeted EGFR blockade in colorectal cancers. Nature. 2012;486(7404):537-540.
doi:10.1038/nature11219
apa: Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein,
B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade
in colorectal cancers. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11219
chicago: Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan
Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance
to Targeted EGFR Blockade in Colorectal Cancers.” Nature. Nature Publishing
Group, 2012. https://doi.org/10.1038/nature11219.
ieee: L. Diaz Jr et al., “The molecular evolution of acquired resistance
to targeted EGFR blockade in colorectal cancers,” Nature, vol. 486, no.
7404. Nature Publishing Group, pp. 537–540, 2012.
ista: Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I,
Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution
of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature.
486(7404), 537–540.
mla: Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted
EGFR Blockade in Colorectal Cancers.” Nature, vol. 486, no. 7404, Nature
Publishing Group, 2012, pp. 537–40, doi:10.1038/nature11219.
short: L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen,
I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486
(2012) 537–540.
date_created: 2018-12-11T12:01:43Z
date_published: 2012-06-28T00:00:00Z
date_updated: 2023-09-07T11:40:43Z
day: '28'
department:
- _id: KrCh
doi: 10.1038/nature11219
ec_funded: 1
external_id:
pmid:
- '22722843'
intvolume: ' 486'
issue: '7404'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/
month: '06'
oa: 1
oa_version: Submitted Version
page: 537 - 540
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3537'
quality_controlled: '1'
related_material:
record:
- id: '1400'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The molecular evolution of acquired resistance to targeted EGFR blockade in
colorectal cancers
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 486
year: '2012'
...
---
_id: '3260'
abstract:
- lang: eng
text: "Many scenarios in the living world, where individual organisms compete for
winning positions (or resources), have properties of auctions. Here we study the
evolution of bids in biological auctions. For each auction, n individuals are
drawn at random from a population of size N. Each individual makes a bid which
entails a cost. The winner obtains a benefit of a certain value. Costs and benefits
are translated into reproductive success (fitness). Therefore, successful bidding
strategies spread in the population. We compare two types of auctions. In “biological
all-pay auctions”, the costs are the bid for every participating individual. In
“biological second price all-pay auctions”, the cost for everyone other than the
winner is the bid, but the cost for the winner is the second highest bid. Second
price all-pay auctions are generalizations of the “war of attrition” introduced
by Maynard Smith. We study evolutionary dynamics in both types of auctions. We
calculate pairwise invasion plots and evolutionarily stable distributions over
the continuous strategy space. We find that the average bid in second price all-pay
auctions is higher than in all-pay auctions, but the average cost for the winner
is similar in both auctions. In both cases, the average bid is a declining function
of the number of participants, n. The more individuals participate in an auction
the smaller is the chance of winning, and thus expensive bids must be avoided.\r\n"
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Reiter J, Nowak M. Evolutionary dynamics of biological auctions.
Theoretical Population Biology. 2012;81(1):69-80. doi:10.1016/j.tpb.2011.11.003
apa: Chatterjee, K., Reiter, J., & Nowak, M. (2012). Evolutionary dynamics of
biological auctions. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2011.11.003
chicago: Chatterjee, Krishnendu, Johannes Reiter, and Martin Nowak. “Evolutionary
Dynamics of Biological Auctions.” Theoretical Population Biology. Academic
Press, 2012. https://doi.org/10.1016/j.tpb.2011.11.003.
ieee: K. Chatterjee, J. Reiter, and M. Nowak, “Evolutionary dynamics of biological
auctions,” Theoretical Population Biology, vol. 81, no. 1. Academic Press,
pp. 69–80, 2012.
ista: Chatterjee K, Reiter J, Nowak M. 2012. Evolutionary dynamics of biological
auctions. Theoretical Population Biology. 81(1), 69–80.
mla: Chatterjee, Krishnendu, et al. “Evolutionary Dynamics of Biological Auctions.”
Theoretical Population Biology, vol. 81, no. 1, Academic Press, 2012, pp.
69–80, doi:10.1016/j.tpb.2011.11.003.
short: K. Chatterjee, J. Reiter, M. Nowak, Theoretical Population Biology 81 (2012)
69–80.
date_created: 2018-12-11T12:02:19Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-09-07T11:40:43Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.tpb.2011.11.003
ec_funded: 1
external_id:
pmid:
- '22120126'
intvolume: ' 81'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279759/ '
month: '02'
oa: 1
oa_version: Submitted Version
page: 69 - 80
pmid: 1
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
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '3388'
quality_controlled: '1'
related_material:
record:
- id: '1400'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Evolutionary dynamics of biological auctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2012'
...
---
_id: '3258'
abstract:
- lang: eng
text: CA3 pyramidal neurons are important for memory formation and pattern completion
in the hippocampal network. It is generally thought that proximal synapses from
the mossy fibers activate these neurons most efficiently, whereas distal inputs
from the perforant path have a weaker modulatory influence. We used confocally
targeted patch-clamp recording from dendrites and axons to map the activation
of rat CA3 pyramidal neurons at the subcellular level. Our results reveal two
distinct dendritic domains. In the proximal domain, action potentials initiated
in the axon backpropagate actively with large amplitude and fast time course.
In the distal domain, Na+ channel–mediated dendritic spikes are efficiently initiated
by waveforms mimicking synaptic events. CA3 pyramidal neuron dendrites showed
a high Na+-to-K+ conductance density ratio, providing ideal conditions for active
backpropagation and dendritic spike initiation. Dendritic spikes may enhance the
computational power of CA3 pyramidal neurons in the hippocampal network.
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (TR
3/B10) and the European Union (European Research Council Advanced grant to P.J.).
article_processing_charge: No
article_type: original
author:
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Hua
full_name: Hu, Hua
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Kim S, Guzmán J, Hu H, Jonas PM. Active dendrites support efficient initiation
of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience.
2012;15(4):600-606. doi:10.1038/nn.3060
apa: Kim, S., Guzmán, J., Hu, H., & Jonas, P. M. (2012). Active dendrites support
efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3060
chicago: Kim, Sooyun, José Guzmán, Hua Hu, and Peter M Jonas. “Active Dendrites
Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal
Neurons.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3060.
ieee: S. Kim, J. Guzmán, H. Hu, and P. M. Jonas, “Active dendrites support efficient
initiation of dendritic spikes in hippocampal CA3 pyramidal neurons,” Nature
Neuroscience, vol. 15, no. 4. Nature Publishing Group, pp. 600–606, 2012.
ista: Kim S, Guzmán J, Hu H, Jonas PM. 2012. Active dendrites support efficient
initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience.
15(4), 600–606.
mla: Kim, Sooyun, et al. “Active Dendrites Support Efficient Initiation of Dendritic
Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience, vol.
15, no. 4, Nature Publishing Group, 2012, pp. 600–06, doi:10.1038/nn.3060.
short: S. Kim, J. Guzmán, H. Hu, P.M. Jonas, Nature Neuroscience 15 (2012) 600–606.
date_created: 2018-12-11T12:02:18Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2023-09-07T11:43:52Z
day: '01'
department:
- _id: PeJo
doi: 10.1038/nn.3060
external_id:
pmid:
- '22388958'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617474/
month: '04'
oa: 1
oa_version: Published Version
page: 600 - 606
pmid: 1
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Nature Neuroscience
publication_identifier:
issn:
- 1546-1726
publication_status: published
publisher: Nature Publishing Group
publist_id: '3390'
quality_controlled: '1'
related_material:
record:
- id: '2964'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Active dendrites support efficient initiation of dendritic spikes in hippocampal
CA3 pyramidal neurons
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2012'
...