---
OA_type: free access
_id: '10906'
abstract:
- lang: eng
text: HSF(C) is a tool that automates verification of safety and liveness properties
for C programs. This paper describes the verification approach taken by HSF(C)
and provides instructions on how to install and use the tool.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergey
full_name: Grebenshchikov, Sergey
last_name: Grebenshchikov
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Nuno P.
full_name: Lopes, Nuno P.
last_name: Lopes
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software
verifier based on Horn clauses. In: Flanagan C, König B, eds. Tools and Algorithms
for the Construction and Analysis of Systems. Vol 7214. LNCS. Berlin, Heidelberg:
Springer; 2012:549-551. doi:10.1007/978-3-642-28756-5_46'
apa: 'Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., & Rybalchenko,
A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan &
B. König (Eds.), Tools and Algorithms for the Construction and Analysis of
Systems (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-28756-5_46'
chicago: 'Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea,
and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In
Tools and Algorithms for the Construction and Analysis of Systems, edited
by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer,
2012. https://doi.org/10.1007/978-3-642-28756-5_46.'
ieee: 'S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko,
“HSF(C): A software verifier based on Horn clauses,” in Tools and Algorithms
for the Construction and Analysis of Systems, Tallinn, Estonia, 2012, vol.
7214, pp. 549–551.'
ista: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C):
A software verifier based on Horn clauses. Tools and Algorithms for the Construction
and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and
Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.'
mla: 'Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn
Clauses.” Tools and Algorithms for the Construction and Analysis of Systems,
edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51,
doi:10.1007/978-3-642-28756-5_46.'
short: S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:,
C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis
of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.
conference:
end_date: 2012-04-01
location: Tallinn, Estonia
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2012-03-24
corr_author: '1'
das_tickbox: '1'
date_created: 2022-03-21T08:03:30Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2026-07-28T09:23:52Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-28756-5_46
editor:
- first_name: Cormac
full_name: Flanagan, Cormac
last_name: Flanagan
- first_name: Barbara
full_name: König, Barbara
last_name: König
intvolume: ' 7214'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-642-28756-5_46
month: '04'
oa: 1
oa_version: Published Version
page: 549-551
place: Berlin, Heidelberg
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783642287565'
eissn:
- 1611-3349
isbn:
- '9783642287558'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: 'HSF(C): A software verifier based on Horn clauses'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7214
year: '2012'
...
---
_id: '506'
article_processing_charge: No
article_type: original
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. Journal
of Cell Biology. 2012;197(3):347-349. doi:10.1083/jcb.201204039'
apa: 'Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead.
Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201204039'
chicago: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.”
Journal of Cell Biology. Rockefeller University Press, 2012. https://doi.org/10.1083/jcb.201204039.'
ieee: 'M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” Journal
of Cell Biology, vol. 197, no. 3. Rockefeller University Press, pp. 347–349,
2012.'
ista: 'Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal
of Cell Biology. 197(3), 347–349.'
mla: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.”
Journal of Cell Biology, vol. 197, no. 3, Rockefeller University Press,
2012, pp. 347–49, doi:10.1083/jcb.201204039.'
short: M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T11:46:51Z
date_published: 2012-04-30T00:00:00Z
date_updated: 2026-07-28T09:22:21Z
day: '30'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1083/jcb.201204039
external_id:
isi:
- '000303467800004'
file:
- access_level: open_access
checksum: 45c02be33ebd99fc3077d60b9c90bdfa
content_type: application/pdf
creator: kschuh
date_created: 2019-02-12T09:03:09Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5957'
file_name: 2012_CellBiology_Sixt.pdf
file_size: 986566
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 197'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/3.0/
month: '04'
oa: 1
oa_version: Published Version
page: 347 - 349
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '7314'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell migration: Fibroblasts find a new way to get ahead'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA
3.0)
short: CC BY-NC-SA (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2012'
...
---
OA_place: repository
OA_type: green
_id: '10904'
abstract:
- lang: eng
text: Multi-dimensional mean-payoff and energy games provide the mathematical foundation
for the quantitative study of reactive systems, and play a central role in the
emerging quantitative theory of verification and synthesis. In this work, we study
the strategy synthesis problem for games with such multi-dimensional objectives
along with a parity condition, a canonical way to express ω-regular conditions.
While in general, the winning strategies in such games may require infinite memory,
for synthesis the most relevant problem is the construction of a finite-memory
winning strategy (if one exists). Our main contributions are as follows. First,
we show a tight exponential bound (matching upper and lower bounds) on the memory
required for finite-memory winning strategies in both multi-dimensional mean-payoff
and energy games along with parity objectives. This significantly improves the
triple exponential upper bound for multi energy games (without parity) that could
be derived from results in literature for games on VASS (vector addition systems
with states). Second, we present an optimal symbolic and incremental algorithm
to compute a finite-memory winning strategy (if one exists) in such games. Finally,
we give a complete characterization of when finite memory of strategies can be
traded off for randomness. In particular, we show that for one-dimension mean-payoff
parity games, randomized memoryless strategies are as powerful as their pure finite-memory
counterparts.
acknowledgement: 'Author supported by Austrian Science Fund (FWF) Grant No P 23499-N23,
FWF NFN Grant No S11407 (RiSE), ERC Start Grant (279307: Graph Games), Microsoft
faculty fellowship.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Mickael
full_name: Randour, Mickael
last_name: Randour
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Chatterjee K, Randour M, Raskin J-F. Strategy synthesis for multi-dimensional
quantitative objectives. In: Koutny M, Ulidowski I, eds. CONCUR 2012 - Concurrency
Theory. Vol 7454. Berlin, Heidelberg: Springer; 2012:115-131. doi:10.1007/978-3-642-32940-1_10'
apa: 'Chatterjee, K., Randour, M., & Raskin, J.-F. (2012). Strategy synthesis
for multi-dimensional quantitative objectives. In M. Koutny & I. Ulidowski
(Eds.), CONCUR 2012 - Concurrency Theory (Vol. 7454, pp. 115–131). Berlin,
Heidelberg: Springer. https://doi.org/10.1007/978-3-642-32940-1_10'
chicago: 'Chatterjee, Krishnendu, Mickael Randour, and Jean-François Raskin. “Strategy
Synthesis for Multi-Dimensional Quantitative Objectives.” In CONCUR 2012 -
Concurrency Theory, edited by Maciej Koutny and Irek Ulidowski, 7454:115–31.
Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-32940-1_10.'
ieee: K. Chatterjee, M. Randour, and J.-F. Raskin, “Strategy synthesis for multi-dimensional
quantitative objectives,” in CONCUR 2012 - Concurrency Theory, Newcastle
upon Tyne, United Kingdom, 2012, vol. 7454, pp. 115–131.
ista: 'Chatterjee K, Randour M, Raskin J-F. 2012. Strategy synthesis for multi-dimensional
quantitative objectives. CONCUR 2012 - Concurrency Theory. CONCUR: Conference
on Concurrency Theory, LNCS, vol. 7454, 115–131.'
mla: Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative
Objectives.” CONCUR 2012 - Concurrency Theory, edited by Maciej Koutny
and Irek Ulidowski, vol. 7454, Springer, 2012, pp. 115–31, doi:10.1007/978-3-642-32940-1_10.
short: K. Chatterjee, M. Randour, J.-F. Raskin, in:, M. Koutny, I. Ulidowski (Eds.),
CONCUR 2012 - Concurrency Theory, Springer, Berlin, Heidelberg, 2012, pp. 115–131.
conference:
end_date: 2012-09-07
location: Newcastle upon Tyne, United Kingdom
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2012-09-04
corr_author: '1'
date_created: 2022-03-21T08:00:21Z
date_published: 2012-09-15T00:00:00Z
date_updated: 2026-07-28T11:24:51Z
day: '15'
department:
- _id: KrCh
doi: 10.1007/978-3-642-32940-1_10
ec_funded: 1
editor:
- first_name: Maciej
full_name: Koutny, Maciej
last_name: Koutny
- first_name: Irek
full_name: Ulidowski, Irek
last_name: Ulidowski
external_id:
arxiv:
- '1201.5073'
intvolume: ' 7454'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1201.5073
month: '09'
oa: 1
oa_version: Preprint
page: 115-131
place: Berlin, Heidelberg
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: CONCUR 2012 - Concurrency Theory
publication_identifier:
eisbn:
- '9783642329401'
eissn:
- 1611-3349
isbn:
- '9783642329395'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
record:
- id: '2716'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Strategy synthesis for multi-dimensional quantitative objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7454
year: '2012'
...
---
OA_type: free access
_id: '3243'
abstract:
- lang: eng
text: 'Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick
Danowski gibt seine Einschätzung ab. '
article_processing_charge: No
article_type: comment
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. Zwischen Technologie und Kommunikation. Büchereiperspektiven.
2012;2012(1):11.
apa: Danowski, P. (2012). Zwischen Technologie und Kommunikation. Büchereiperspektiven.
Büchereiverband Österreichs.
chicago: Danowski, Patrick. “Zwischen Technologie und Kommunikation.” Büchereiperspektiven.
Büchereiverband Österreichs, 2012.
ieee: P. Danowski, “Zwischen Technologie und Kommunikation,” Büchereiperspektiven,
vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012.
ista: Danowski P. 2012. Zwischen Technologie und Kommunikation. Büchereiperspektiven.
2012(1), 11.
mla: Danowski, Patrick. “Zwischen Technologie und Kommunikation.” Büchereiperspektiven,
vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11.
short: P. Danowski, Büchereiperspektiven 2012 (2012) 11.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:02:13Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2026-07-28T09:15:13Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
intvolume: ' 2012'
issue: '1'
language:
- iso: ger
main_file_link:
- open_access: '1'
url: https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf
month: '03'
oa: 1
oa_version: Published Version
page: '11'
popular_science: '1'
publication: Büchereiperspektiven
publication_identifier:
issn:
- 1607-7172
publication_status: published
publisher: Büchereiverband Österreichs
publist_id: '3433'
status: public
title: Zwischen Technologie und Kommunikation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2012
year: '2012'
...
---
OA_type: closed access
_id: '2950'
abstract:
- lang: eng
text: Contractile actomyosin rings drive various fundamental morphogenetic processes
ranging from cytokinesis to wound healing. Actomyosin rings are generally thought
to function by circumferential contraction. Here, we show that the spreading of
the enveloping cell layer (EVL) over the yolk cell during zebrafish gastrulation
is driven by a contractile actomyosin ring. In contrast to previous suggestions,
we find that this ring functions not only by circumferential contraction but also
by a flow-friction mechanism. This generates a pulling force through resistance
against retrograde actomyosin flow. EVL spreading proceeds normally in situations
where circumferential contraction is unproductive, indicating that the flow-friction
mechanism is sufficient. Thus, actomyosin rings can function in epithelial morphogenesis
through a combination of cable-constriction and flow-friction mechanisms.
acknowledged_ssus:
- _id: SSU
acknowledgement: We are grateful to M. Sixt, T. Bollenbach, and E. Martin-Blanco for
advice and the service facilities of the IST Austria and MPI-CBG for continuous
help. M.B., G.S., S.W.G., and C.-P.H. synergistically and equally developed the
presented ideas and the experimental and theoretical approaches. M.B. and P.C. performed
the experiments; G.S. developed the theory; and R.H., F.O., and J.R. contributed
to the experimental work. This work was supported by a grant from the Fonds zur
Förderung der wissenschaftlichen Forschung (FWF) and the Deutsche Forschungsgemeinschaft
(DFG) (I930-B20) to C.-P.H., S.W.G., and G.S.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Felix
full_name: Oswald, Felix
last_name: Oswald
- first_name: Julia
full_name: Roensch, Julia
id: 4220E59C-F248-11E8-B48F-1D18A9856A87
last_name: Roensch
- first_name: Stephan
full_name: Grill, Stephan
last_name: Grill
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Behrndt M, Salbreux G, Campinho P, et al. Forces driving epithelial spreading
in zebrafish gastrulation. Science. 2012;338(6104):257-260. doi:10.1126/science.1224143
apa: Behrndt, M., Salbreux, G., Campinho, P., Hauschild, R., Oswald, F., Roensch,
J., … Heisenberg, C.-P. J. (2012). Forces driving epithelial spreading in zebrafish
gastrulation. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.1224143
chicago: Behrndt, Martin, Guillaume Salbreux, Pedro Campinho, Robert Hauschild,
Felix Oswald, Julia Roensch, Stephan Grill, and Carl-Philipp J Heisenberg. “Forces
Driving Epithelial Spreading in Zebrafish Gastrulation.” Science. American
Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224143.
ieee: M. Behrndt et al., “Forces driving epithelial spreading in zebrafish
gastrulation,” Science, vol. 338, no. 6104. American Association for the
Advancement of Science, pp. 257–260, 2012.
ista: Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill
S, Heisenberg C-PJ. 2012. Forces driving epithelial spreading in zebrafish gastrulation.
Science. 338(6104), 257–260.
mla: Behrndt, Martin, et al. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.”
Science, vol. 338, no. 6104, American Association for the Advancement of
Science, 2012, pp. 257–60, doi:10.1126/science.1224143.
short: M. Behrndt, G. Salbreux, P. Campinho, R. Hauschild, F. Oswald, J. Roensch,
S. Grill, C.-P.J. Heisenberg, Science 338 (2012) 257–260.
corr_author: '1'
date_created: 2018-12-11T12:00:30Z
date_published: 2012-10-12T00:00:00Z
date_updated: 2026-07-29T10:07:18Z
day: '12'
department:
- _id: CaHe
- _id: Bio
doi: 10.1126/science.1224143
external_id:
isi:
- '000309712300046'
pmid:
- '23066079'
intvolume: ' 338'
isi: 1
issue: '6104'
language:
- iso: eng
month: '10'
oa_version: None
page: 257 - 260
pmid: 1
project:
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I930-B20
name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '3778'
quality_controlled: '1'
related_material:
record:
- id: '1403'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Forces driving epithelial spreading in zebrafish gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 338
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.
article_processing_charge: No
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: 2026-07-29T10:15:25Z
day: '28'
department:
- _id: KrCh
doi: 10.1038/nature11219
ec_funded: 1
external_id:
isi:
- '000305760600044'
pmid:
- '22722843'
intvolume: ' 486'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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"
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: 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.
corr_author: '1'
date_created: 2018-12-11T12:02:19Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2026-07-29T10:15:25Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.tpb.2011.11.003
ec_funded: 1
external_id:
isi:
- '000298938200006'
pmid:
- '22120126'
intvolume: ' 81'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 81
year: '2012'
...
---
DOAJ_listed: '1'
OA_type: closed access
_id: '22482'
abstract:
- lang: eng
text: An ecohydrological model Tethys‐Chloris (T&C) described in the companion
paper is applied to two semiarid systems characterized by different climate and
vegetation cover conditions. The Lucky Hills watershed in Arizona represents a
typical small, “unit‐source” catchment of a desert shrub system of the U.S. southwest.
Two nested basins of the Reynolds Creek Experimental watershed (Idaho, U.S.A.),
the Reynolds Creek Mountain East and Tollgate catchments, are representative of
a semiarid cold climate with seasonal snow cover. Both exhibit a highly non‐uniform
vegetation cover. A range of ecohydrological metrics of the long‐term model performance
is presented to highlight the model capabilities in reproducing hydrological and
vegetation dynamics both at the plot and the watershed scales. A diverse set of
observations is used to confirm the simulated dynamics. Highly satisfactory results
are obtained without significant (or any) calibration efforts despite the large
phase‐space dimensionality of the model, the uncertainty of imposed boundary conditions,
and limited data availability. It is argued that a significant investment into
the model design based on the description of physical, biophysical, and ecological
processes leads to such a consistent simulation skill. The simulated patterns
mimic the outcome of hydrological and vegetation dynamics with high realism, as
confirmed from spatially distributed remote sensing data. Further community efforts
are warranted to address the issue of thorough quantitative assessment. The current
lack of appropriate data hampers the development and testing of process‐based
ecohydrological models. It is further argued that the mechanistic nature of the
T&C model can be valuable for designing virtual experiments and developing
questions of scientific inquiry at a range of spatiotemporal scales.
article_number: 2011MS000087
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: V. Y.
full_name: Ivanov, V. Y.
last_name: Ivanov
- first_name: E.
full_name: Caporali, E.
last_name: Caporali
citation:
ama: 'Fatichi S, Ivanov VY, Caporali E. A mechanistic ecohydrological model to investigate
complex interactions in cold and warm water‐controlled environments: 2. Spatiotemporal
analyses. Journal of Advances in Modeling Earth Systems. 2012;4(2). doi:10.1029/2011ms000087'
apa: 'Fatichi, S., Ivanov, V. Y., & Caporali, E. (2012). A mechanistic ecohydrological
model to investigate complex interactions in cold and warm water‐controlled environments:
2. Spatiotemporal analyses. Journal of Advances in Modeling Earth Systems.
American Geophysical Union. https://doi.org/10.1029/2011ms000087'
chicago: 'Fatichi, Simone, V. Y. Ivanov, and E. Caporali. “A Mechanistic Ecohydrological
Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments:
2. Spatiotemporal Analyses.” Journal of Advances in Modeling Earth Systems.
American Geophysical Union, 2012. https://doi.org/10.1029/2011ms000087.'
ieee: 'S. Fatichi, V. Y. Ivanov, and E. Caporali, “A mechanistic ecohydrological
model to investigate complex interactions in cold and warm water‐controlled environments:
2. Spatiotemporal analyses,” Journal of Advances in Modeling Earth Systems,
vol. 4, no. 2. American Geophysical Union, 2012.'
ista: 'Fatichi S, Ivanov VY, Caporali E. 2012. A mechanistic ecohydrological model
to investigate complex interactions in cold and warm water‐controlled environments:
2. Spatiotemporal analyses. Journal of Advances in Modeling Earth Systems. 4(2),
2011MS000087.'
mla: 'Fatichi, Simone, et al. “A Mechanistic Ecohydrological Model to Investigate
Complex Interactions in Cold and Warm Water‐controlled Environments: 2. Spatiotemporal
Analyses.” Journal of Advances in Modeling Earth Systems, vol. 4, no. 2,
2011MS000087, American Geophysical Union, 2012, doi:10.1029/2011ms000087.'
short: S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Advances in Modeling Earth
Systems 4 (2012).
das_tickbox: '1'
date_created: 2026-07-27T12:30:23Z
date_published: 2012-05-30T00:00:00Z
date_updated: 2026-08-03T14:04:42Z
day: '30'
doi: 10.1029/2011ms000087
extern: '1'
intvolume: ' 4'
issue: '2'
language:
- iso: eng
month: '05'
oa_version: None
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A mechanistic ecohydrological model to investigate complex interactions in
cold and warm water‐controlled environments: 2. Spatiotemporal analyses'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 4
year: '2012'
...
---
OA_type: closed access
_id: '22518'
abstract:
- lang: eng
text: "Interannual variability of precipitation can directly or indirectly affect
many hydrological, ecological, and biogeochemical processes that, in turn, influence
climate. Despite the significant importance of the phenomenon, few studies have
attempted to elucidate spatial patterns of this variability at the global scale.
This study uses land gauge precipitation records of the Global Historical Climatology
Network, version 2, as well as reanalysis data to provide an assessment of the
spatial organization of characteristics of precipitation interannual variability.
The coefficient of variation, skewness, and short- and long-range dependence of
the precipitation variability are analyzed. Among the major inferences is that
the coefficient of variation of annual precipitation shows a significant correlation
with intra-annual seasonality. Specifically, subyearly precipitation anomalies
occurring in locations with pronounced seasonality affect the total yearly amount,
imposing a higher variability in the annual precipitation fluctuations. Furthermore,
the study illustrates that a positive skewness of the distribution of annual precipitation
is a robust property worldwide and its magnitude is related to the coefficient
of variation. Additionally, annual precipitation exhibits very weak small-lag
autocorrelation. Conversely, the intensity of long-memory–long-range dependence
is significantly larger than zero, hinting that organized long-term variations
are an important feature of the interannual variability of precipitation.\r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: V. Yu.
full_name: Ivanov, V. Yu.
last_name: Ivanov
- first_name: E.
full_name: Caporali, E.
last_name: Caporali
citation:
ama: 'Fatichi S, Ivanov VY, Caporali E. Investigating interannual variability of
precipitation at the global scale: Is there a connection with seasonality? Journal
of Climate. 2012;25(16):5512-5523. doi:10.1175/jcli-d-11-00356.1'
apa: 'Fatichi, S., Ivanov, V. Y., & Caporali, E. (2012). Investigating interannual
variability of precipitation at the global scale: Is there a connection with seasonality?
Journal of Climate. American Meteorological Society. https://doi.org/10.1175/jcli-d-11-00356.1'
chicago: 'Fatichi, Simone, V. Yu. Ivanov, and E. Caporali. “Investigating Interannual
Variability of Precipitation at the Global Scale: Is There a Connection with Seasonality?”
Journal of Climate. American Meteorological Society, 2012. https://doi.org/10.1175/jcli-d-11-00356.1.'
ieee: 'S. Fatichi, V. Y. Ivanov, and E. Caporali, “Investigating interannual variability
of precipitation at the global scale: Is there a connection with seasonality?,”
Journal of Climate, vol. 25, no. 16. American Meteorological Society, pp.
5512–5523, 2012.'
ista: 'Fatichi S, Ivanov VY, Caporali E. 2012. Investigating interannual variability
of precipitation at the global scale: Is there a connection with seasonality?
Journal of Climate. 25(16), 5512–5523.'
mla: 'Fatichi, Simone, et al. “Investigating Interannual Variability of Precipitation
at the Global Scale: Is There a Connection with Seasonality?” Journal of Climate,
vol. 25, no. 16, American Meteorological Society, 2012, pp. 5512–23, doi:10.1175/jcli-d-11-00356.1.'
short: S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Climate 25 (2012) 5512–5523.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2012-08-15T00:00:00Z
date_updated: 2026-08-06T09:54:05Z
day: '15'
doi: 10.1175/jcli-d-11-00356.1
extern: '1'
intvolume: ' 25'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 5512-5523
publication: Journal of Climate
publication_identifier:
eissn:
- 1520-0442
issn:
- 0894-8755
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Investigating interannual variability of precipitation at the global scale:
Is there a connection with seasonality?'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 25
year: '2012'
...
---
_id: '2263'
abstract:
- lang: eng
text: Nestin-cre transgenic mice have been widely used to direct recombination to
neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here
we report that a readily utilized, and the only commercially available, Nestin-cre
line is insufficient for directing recombination in early embryonic NSCs and NPCs.
Analysis of recombination efficiency in multiple cre-dependent reporters and a
genetic mosaic line revealed consistent temporal and spatial patterns of recombination
in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found
robust recombination in NSCs and NPCs in ventricular and subventricular zones
of the cerebral cortices as early as embryonic day 12.5. In addition we found
that the rate of Nestin-cre driven recombination only reaches sufficiently high
levels in NSCs and NPCs during late embryonic and early postnatal periods. These
findings are important when commercially available cre lines are considered for
directing recombination to embryonic NSCs and NPCs.
article_processing_charge: No
author:
- first_name: Huixuan
full_name: Liang, Huixuan
last_name: Liang
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: H.
full_name: Ghashghaei, H.
last_name: Ghashghaei
citation:
ama: Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient
for recombination in early embryonic neural progenitors. Biology Open.
2012;1(12):1200-1203. doi:10.1242/bio.20122287
apa: Liang, H., Hippenmeyer, S., & Ghashghaei, H. (2012). A Nestin-cre transgenic
mouse is insufficient for recombination in early embryonic neural progenitors.
Biology Open. Company of Biologists. https://doi.org/10.1242/bio.20122287
chicago: Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic
Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.”
Biology Open. Company of Biologists, 2012. https://doi.org/10.1242/bio.20122287.
ieee: H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse
is insufficient for recombination in early embryonic neural progenitors,” Biology
Open, vol. 1, no. 12. Company of Biologists, pp. 1200–1203, 2012.
ista: Liang H, Hippenmeyer S, Ghashghaei H. 2012. A Nestin-cre transgenic mouse
is insufficient for recombination in early embryonic neural progenitors. Biology
Open. 1(12), 1200–1203.
mla: Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination
in Early Embryonic Neural Progenitors.” Biology Open, vol. 1, no. 12, Company
of Biologists, 2012, pp. 1200–03, doi:10.1242/bio.20122287.
short: H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203.
date_created: 2018-12-11T11:56:38Z
date_published: 2012-12-15T00:00:00Z
date_updated: 2026-08-12T09:32:12Z
day: '15'
ddc:
- '576'
department:
- _id: SiHi
doi: 10.1242/bio.20122287
external_id:
isi:
- '000209205700005'
file:
- access_level: open_access
checksum: 605a1800b81227848c361fd6ba7d22ba
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:09Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4990'
file_name: IST-2015-387-v1+1_1200.full.pdf
file_size: 726695
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 1'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 1200 - 1203
publication: Biology Open
publication_status: published
publisher: Company of Biologists
publist_id: '4682'
pubrep_id: '387'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic
neural progenitors
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2012'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22538'
abstract:
- lang: eng
text: 'Numerous studies have explored the role of vegetation in controlling and
mediating hydrological states and fluxes at the level of individual processes,
which has led to improvements in our understanding of plot-scale dynamics. Relatively
less effort has been directed toward spatially-explicit studies of vegetation-hydrology
interactions at larger scales of a landscape. Only few continuous, process-oriented
ecohydrological models had been proposed with structures of varying complexity.
This study contributes to their further evolution and presents a novel ecohydrological
model, Tethys-Chloris. The model synthesizes the state-of-the-art knowledge on
individual processes and coupling mechanisms drawn from the disciplines of hydrology,
plant physiology, and ecology. Specifically, the model reproduces all essential
components of the hydrological cycle: it resolves the mass and energy budgets
in the atmospheric surface layer at the hourly scale, while representing up to
two layers of vegetation; it includes a module of snowpack evolution; it describes
the saturated and unsaturated soil water dynamics, processes of runoff generation
and flow routing. The component of vegetation dynamics parameterizes life cycle
processes of different plant functional types, including photosynthesis, phenology,
carbon allocation, and tissue turnover. This study presents a confirmation of
the long-term, plot-scale model performance by simulating two types of ecosystems
corresponding to different climate conditions. A consistent and highly satisfactory
model skill in reproducing the energy and water budgets as well as physiological
cycles of plants with minimum calibration overhead is demonstrated. Furthermore,
these applications demonstrate that the model permits the identification of data
types and observation frequencies crucial for appropriate evaluation of modeled
dynamics. More importantly, through a synthesis of a wide array of process representations,
the model ensures that climate, soil, vegetation, and topography collectively
identify essential modes controlling ecohydrological systems, i.e., that satisfactory
performance is a result of appropriate mimicking of internal processes.'
article_number: 2011MS000086
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: V. Y.
full_name: Ivanov, V. Y.
last_name: Ivanov
- first_name: E.
full_name: Caporali, E.
last_name: Caporali
citation:
ama: 'Fatichi S, Ivanov VY, Caporali E. A mechanistic ecohydrological model to investigate
complex interactions in cold and warm water‐controlled environments: 1. Theoretical
framework and plot‐scale analysis. Journal of Advances in Modeling Earth Systems.
2012;4(2). doi:10.1029/2011ms000086'
apa: 'Fatichi, S., Ivanov, V. Y., & Caporali, E. (2012). A mechanistic ecohydrological
model to investigate complex interactions in cold and warm water‐controlled environments:
1. Theoretical framework and plot‐scale analysis. Journal of Advances in Modeling
Earth Systems. American Geophysical Union. https://doi.org/10.1029/2011ms000086'
chicago: 'Fatichi, Simone, V. Y. Ivanov, and E. Caporali. “A Mechanistic Ecohydrological
Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments:
1. Theoretical Framework and Plot‐scale Analysis.” Journal of Advances in Modeling
Earth Systems. American Geophysical Union, 2012. https://doi.org/10.1029/2011ms000086.'
ieee: 'S. Fatichi, V. Y. Ivanov, and E. Caporali, “A mechanistic ecohydrological
model to investigate complex interactions in cold and warm water‐controlled environments:
1. Theoretical framework and plot‐scale analysis,” Journal of Advances in Modeling
Earth Systems, vol. 4, no. 2. American Geophysical Union, 2012.'
ista: 'Fatichi S, Ivanov VY, Caporali E. 2012. A mechanistic ecohydrological model
to investigate complex interactions in cold and warm water‐controlled environments:
1. Theoretical framework and plot‐scale analysis. Journal of Advances in Modeling
Earth Systems. 4(2), 2011MS000086.'
mla: 'Fatichi, Simone, et al. “A Mechanistic Ecohydrological Model to Investigate
Complex Interactions in Cold and Warm Water‐controlled Environments: 1. Theoretical
Framework and Plot‐scale Analysis.” Journal of Advances in Modeling Earth Systems,
vol. 4, no. 2, 2011MS000086, American Geophysical Union, 2012, doi:10.1029/2011ms000086.'
short: S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Advances in Modeling Earth
Systems 4 (2012).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2012-05-30T00:00:00Z
date_updated: 2026-08-12T12:02:45Z
day: '30'
doi: 10.1029/2011ms000086
extern: '1'
intvolume: ' 4'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2011MS000086
month: '05'
oa: 1
oa_version: Published Version
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A mechanistic ecohydrological model to investigate complex interactions in
cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale
analysis'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2012'
...
---
_id: '2965'
abstract:
- lang: eng
text: Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern
und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open
Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).
article_processing_charge: No
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: 'Danowski P. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. 2012;65(2):200-212.'
apa: 'Danowski, P. (2012). Kontext Open Access: Creative Commons. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare.'
chicago: 'Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, 2012.'
ieee: 'P. Danowski, “Kontext Open Access: Creative Commons,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 65,
no. 2. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 200–212,
2012.'
ista: 'Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 65(2), 200–212.'
mla: 'Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol.
65, no. 2, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2012,
pp. 200–12.'
short: P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen
und Bibliothekare 65 (2012) 200–212.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:00:35Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2026-08-12T14:15:14Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
checksum: 162eea47d9d840c26b496ba6ae4d1c09
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:42Z
date_updated: 2020-07-14T12:45:57Z
file_id: '4703'
file_name: IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf
file_size: 503345
relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 65'
issue: '2'
language:
- iso: ger
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: ' http://hdl.handle.net/10760/17625'
month: '09'
oa: 1
oa_version: Published Version
page: 200 - 212
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publist_id: '3754'
pubrep_id: '95'
scopus_import: '1'
status: public
title: 'Kontext Open Access: Creative Commons'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 65
year: '2012'
...
---
_id: '3262'
abstract:
- lang: eng
text: Living cells must control the reading out or "expression" of information
encoded in their genomes, and this regulation often is mediated by transcription
factors--proteins that bind to DNA and either enhance or repress the expression
of nearby genes. But the expression of transcription factor proteins is itself
regulated, and many transcription factors regulate their own expression in addition
to responding to other input signals. Here we analyze the simplest of such self-regulatory
circuits, asking how parameters can be chosen to optimize information transmission
from inputs to outputs in the steady state. Some nonzero level of self-regulation
is almost always optimal, with self-activation dominant when transcription factor
concentrations are low and self-repression dominant when concentrations are high.
In steady state the optimal self-activation is never strong enough to induce bistability,
although there is a limit in which the optimal parameters are very close to the
critical point.
acknowledgement: "We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan
for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants
No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W.
M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant
No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania."
article_number: '041903'
article_processing_charge: No
arxiv: 1
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic
networks. III. A self-interacting gene. Physical Review E. 2012;85(4).
doi:10.1103/PhysRevE.85.041903
apa: Tkačik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow
in small genetic networks. III. A self-interacting gene. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.85.041903
chicago: Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information
Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review
E. American Physical Society, 2012. https://doi.org/10.1103/PhysRevE.85.041903.
ieee: G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small
genetic networks. III. A self-interacting gene,” Physical Review E, vol.
85, no. 4. American Physical Society, 2012.
ista: Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small
genetic networks. III. A self-interacting gene. Physical Review E. 85(4), 041903.
mla: Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks.
III. A Self-Interacting Gene.” Physical Review E, vol. 85, no. 4, 041903,
American Physical Society, 2012, doi:10.1103/PhysRevE.85.041903.
short: G. Tkačik, A. Walczak, W. Bialek, Physical Review E 85 (2012).
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:02:20Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2026-08-12T14:29:02Z
day: '01'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.85.041903
external_id:
arxiv:
- '1112.5026'
isi:
- '000302410200006'
intvolume: ' 85'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1112.5026
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '3386'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing information flow in small genetic networks. III. A self-interacting
gene
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2012'
...
---
_id: '2936'
abstract:
- lang: eng
text: The notion of delays arises naturally in many computational models, such as,
in the design of circuits, control systems, and dataflow languages. In this work,
we introduce automata with delay blocks (ADBs), extending finite state automata
with variable time delay blocks, for deferring individual transition output symbols,
in a discrete-time setting. We show that the ADB languages strictly subsume the
regular languages, and are incomparable in expressive power to the context-free
languages. We show that ADBs are closed under union, concatenation and Kleene
star, and under intersection with regular languages, but not closed under complementation
and intersection with other ADB languages. We show that the emptiness and the
membership problems are decidable in polynomial time for ADBs, whereas the universality
problem is undecidable. Finally we consider the linear-time model checking problem,
i.e., whether the language of an ADB is contained in a regular language, and show
that the model checking problem is PSPACE-complete. Copyright 2012 ACM.
acknowledgement: 'This work has been financially supported in part by the European
Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract
# 270180 (NOPTILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008
(Modeling and control of Networked vehicle systems in persistent autonomous operations);
by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic
Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start
grant (279307: Graph Games); Microsoft faculty fellows award; ERC Advanced grant
QUAREM; and FWF Grant No S11403-N23 (RiSE).'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: 'Chatterjee K, Henzinger TA, Prabhu V. Finite automata with time delay blocks.
In: Proceedings of the 10th ACM International Conference on Embedded Software.
ACM; 2012:43-52. doi:10.1145/2380356.2380370'
apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2012). Finite automata
with time delay blocks. In Proceedings of the 10th ACM international conference
on Embedded software (pp. 43–52). Tampere, Finland: ACM. https://doi.org/10.1145/2380356.2380370'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Finite
Automata with Time Delay Blocks.” In Proceedings of the 10th ACM International
Conference on Embedded Software, 43–52. ACM, 2012. https://doi.org/10.1145/2380356.2380370.
ieee: K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Finite automata with time
delay blocks,” in Proceedings of the 10th ACM international conference on Embedded
software, Tampere, Finland, 2012, pp. 43–52.
ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2012. Finite automata with time delay
blocks. Proceedings of the 10th ACM international conference on Embedded software.
EMSOFT: Embedded Software , 43–52.'
mla: Chatterjee, Krishnendu, et al. “Finite Automata with Time Delay Blocks.” Proceedings
of the 10th ACM International Conference on Embedded Software, ACM, 2012,
pp. 43–52, doi:10.1145/2380356.2380370.
short: K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Proceedings of the 10th ACM
International Conference on Embedded Software, ACM, 2012, pp. 43–52.
conference:
end_date: 2012-10-12
location: Tampere, Finland
name: 'EMSOFT: Embedded Software '
start_date: 2012-10-07
date_created: 2018-12-11T12:00:26Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2026-08-12T14:34:15Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/2380356.2380370
ec_funded: 1
external_id:
arxiv:
- '1207.7019'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.7019
month: '10'
oa: 1
oa_version: Preprint
page: 43 - 52
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the 10th ACM international conference on Embedded software
publication_status: published
publisher: ACM
publist_id: '3799'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finite automata with time delay blocks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...