---
_id: '7702'
abstract:
- lang: eng
text: Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections
between body segments and are required for coordinated neural signaling along
the anterior-posterior axis. We show here that establishment of select CNS longitudinal
tracts and formation of precise mechanosensory afferent innervation to the same
CNS region are coordinately regulated by the secreted semaphorins Sema-2a and
Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B
(PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes
the initial assembly of a subset of CNS longitudinal projections and subsequent
targeting of chordotonal sensory afferent axons to these same longitudinal connectives,
whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the
absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS
is severely disrupted, resulting in specific larval behavioral deficits. These
results reveal that distinct semaphorin-mediated guidance functions converge at
PlexB and are critical for functional neural circuit assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Zhuhao
full_name: Wu, Zhuhao
last_name: Wu
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Joseph C.
full_name: Ayoob, Joseph C.
last_name: Ayoob
- first_name: Kayam
full_name: Chak, Kayam
last_name: Chak
- first_name: Benjamin J.
full_name: Andreone, Benjamin J.
last_name: Andreone
- first_name: Tomoko
full_name: Ohyama, Tomoko
last_name: Ohyama
- first_name: Rex
full_name: Kerr, Rex
last_name: Kerr
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Marta
full_name: Zlatic, Marta
last_name: Zlatic
- first_name: Alex L.
full_name: Kolodkin, Alex L.
last_name: Kolodkin
citation:
ama: Wu Z, Sweeney LB, Ayoob JC, et al. A combinatorial semaphorin code instructs
the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron.
2011;70(2):281-298. doi:10.1016/j.neuron.2011.02.050
apa: Wu, Z., Sweeney, L. B., Ayoob, J. C., Chak, K., Andreone, B. J., Ohyama, T.,
… Kolodkin, A. L. (2011). A combinatorial semaphorin code instructs the initial
steps of sensory circuit assembly in the Drosophila CNS. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2011.02.050
chicago: Wu, Zhuhao, Lora B. Sweeney, Joseph C. Ayoob, Kayam Chak, Benjamin J. Andreone,
Tomoko Ohyama, Rex Kerr, Liqun Luo, Marta Zlatic, and Alex L. Kolodkin. “A Combinatorial
Semaphorin Code Instructs the Initial Steps of Sensory Circuit Assembly in the
Drosophila CNS.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.02.050.
ieee: Z. Wu et al., “A combinatorial semaphorin code instructs the initial
steps of sensory circuit assembly in the Drosophila CNS,” Neuron, vol.
70, no. 2. Elsevier, pp. 281–298, 2011.
ista: Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L,
Zlatic M, Kolodkin AL. 2011. A combinatorial semaphorin code instructs the initial
steps of sensory circuit assembly in the Drosophila CNS. Neuron. 70(2), 281–298.
mla: Wu, Zhuhao, et al. “A Combinatorial Semaphorin Code Instructs the Initial Steps
of Sensory Circuit Assembly in the Drosophila CNS.” Neuron, vol. 70, no.
2, Elsevier, 2011, pp. 281–98, doi:10.1016/j.neuron.2011.02.050.
short: Z. Wu, L.B. Sweeney, J.C. Ayoob, K. Chak, B.J. Andreone, T. Ohyama, R. Kerr,
L. Luo, M. Zlatic, A.L. Kolodkin, Neuron 70 (2011) 281–298.
date_created: 2020-04-30T10:36:30Z
date_published: 2011-04-28T00:00:00Z
date_updated: 2024-01-31T10:14:29Z
day: '28'
doi: 10.1016/j.neuron.2011.02.050
extern: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 281-298
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A combinatorial semaphorin code instructs the initial steps of sensory circuit
assembly in the Drosophila CNS
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2011'
...
---
_id: '7750'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Robinson MR. Understanding intrasexual competition and sexual selection requires
an evolutionary ecology framework. Behavioral Ecology. 2011;22(6):1143-1144.
doi:10.1093/beheco/arr110
apa: Robinson, M. R. (2011). Understanding intrasexual competition and sexual selection
requires an evolutionary ecology framework. Behavioral Ecology. Oxford
University Press. https://doi.org/10.1093/beheco/arr110
chicago: Robinson, Matthew Richard. “Understanding Intrasexual Competition and Sexual
Selection Requires an Evolutionary Ecology Framework.” Behavioral Ecology.
Oxford University Press, 2011. https://doi.org/10.1093/beheco/arr110.
ieee: M. R. Robinson, “Understanding intrasexual competition and sexual selection
requires an evolutionary ecology framework,” Behavioral Ecology, vol. 22,
no. 6. Oxford University Press, pp. 1143–1144, 2011.
ista: Robinson MR. 2011. Understanding intrasexual competition and sexual selection
requires an evolutionary ecology framework. Behavioral Ecology. 22(6), 1143–1144.
mla: Robinson, Matthew Richard. “Understanding Intrasexual Competition and Sexual
Selection Requires an Evolutionary Ecology Framework.” Behavioral Ecology,
vol. 22, no. 6, Oxford University Press, 2011, pp. 1143–44, doi:10.1093/beheco/arr110.
short: M.R. Robinson, Behavioral Ecology 22 (2011) 1143–1144.
date_created: 2020-04-30T11:01:43Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2021-01-12T08:15:16Z
day: '01'
doi: 10.1093/beheco/arr110
extern: '1'
intvolume: ' 22'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1143-1144
publication: Behavioral Ecology
publication_identifier:
issn:
- 1465-7279
- 1045-2249
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Understanding intrasexual competition and sexual selection requires an evolutionary
ecology framework
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2011'
...
---
_id: '469'
abstract:
- lang: eng
text: 'Spontaneous release of glutamate is important for maintaining synaptic strength
and controlling spike timing in the brain. Mechanisms regulating spontaneous exocytosis
remain poorly understood. Extracellular calcium concentration ([Ca2+]o) regulates
Ca2+ entry through voltage-activated calcium channels (VACCs) and consequently
is a pivotal determinant of action potential-evoked vesicle fusion. Extracellular
Ca 2+ also enhances spontaneous release, but via unknown mechanisms. Here we report
that external Ca2+ triggers spontaneous glutamate release more weakly than evoked
release in mouse neocortical neurons. Blockade of VACCs has no effect on the spontaneous
release rate or its dependence on [Ca2+]o. Intracellular [Ca2+] slowly increases
in a minority of neurons following increases in [Ca2+]o. Furthermore, the enhancement
of spontaneous release by extracellular calcium is insensitive to chelation of
intracellular calcium by BAPTA. Activation of the calcium-sensing receptor (CaSR),
a G-protein-coupled receptor present in nerve terminals, by several specific agonists
increased spontaneous glutamate release. The frequency of spontaneous synaptic
transmission was decreased in CaSR mutant neurons. The concentration-effect relationship
for extracellular calcium regulation of spontaneous release was well described
by a combination of CaSR-dependent and CaSR-independent mechanisms. Overall these
results indicate that extracellular Ca2+ does not trigger spontaneous glutamate
release by simply increasing calcium influx but stimulates CaSR and thereby promotes
resting spontaneous glutamate release. '
author:
- first_name: Nicholas
full_name: Vyleta, Nicholas
id: 36C4978E-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Stephen
full_name: Smith, Stephen
last_name: Smith
citation:
ama: Vyleta N, Smith S. Spontaneous glutamate release is independent of calcium
influx and tonically activated by the calcium-sensing receptor. European Journal
of Neuroscience. 2011;31(12):4593-4606. doi:10.1523/JNEUROSCI.6398-10.2011
apa: Vyleta, N., & Smith, S. (2011). Spontaneous glutamate release is independent
of calcium influx and tonically activated by the calcium-sensing receptor. European
Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.6398-10.2011
chicago: Vyleta, Nicholas, and Stephen Smith. “Spontaneous Glutamate Release Is
Independent of Calcium Influx and Tonically Activated by the Calcium-Sensing Receptor.”
European Journal of Neuroscience. Wiley-Blackwell, 2011. https://doi.org/10.1523/JNEUROSCI.6398-10.2011.
ieee: N. Vyleta and S. Smith, “Spontaneous glutamate release is independent of calcium
influx and tonically activated by the calcium-sensing receptor,” European Journal
of Neuroscience, vol. 31, no. 12. Wiley-Blackwell, pp. 4593–4606, 2011.
ista: Vyleta N, Smith S. 2011. Spontaneous glutamate release is independent of calcium
influx and tonically activated by the calcium-sensing receptor. European Journal
of Neuroscience. 31(12), 4593–4606.
mla: Vyleta, Nicholas, and Stephen Smith. “Spontaneous Glutamate Release Is Independent
of Calcium Influx and Tonically Activated by the Calcium-Sensing Receptor.” European
Journal of Neuroscience, vol. 31, no. 12, Wiley-Blackwell, 2011, pp. 4593–606,
doi:10.1523/JNEUROSCI.6398-10.2011.
short: N. Vyleta, S. Smith, European Journal of Neuroscience 31 (2011) 4593–4606.
date_created: 2018-12-11T11:46:39Z
date_published: 2011-03-23T00:00:00Z
date_updated: 2021-01-12T08:00:49Z
day: '23'
department:
- _id: PeJo
doi: 10.1523/JNEUROSCI.6398-10.2011
intvolume: ' 31'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097128/
month: '03'
oa: 1
oa_version: Submitted Version
page: 4593 - 4606
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7353'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spontaneous glutamate release is independent of calcium influx and tonically
activated by the calcium-sensing receptor
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2011'
...
---
_id: '490'
abstract:
- lang: eng
text: 'BioSig is an open source software library for biomedical signal processing.
The aim of the BioSig project is to foster research in biomedical signal processing
by providing free and open source software tools for many different application
areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer
interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research.
Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram
(ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG),
or respiration signals is a very relevant element of the BioSig project. Specifically,
BioSig provides solutions for data acquisition, artifact processing, quality control,
feature extraction, classification, modeling, and data visualization, to name
a few. In this paper, we highlight several methods to help students and researchers
to work more efficiently with biomedical signals. '
article_number: '935364'
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: Tilmann
full_name: Sander, Tilmann
last_name: Sander
citation:
ama: 'Schlögl A, Vidaurre C, Sander T. BioSig: The free and open source software
library for biomedical signal processing. Computational Intelligence and Neuroscience.
2011;2011. doi:10.1155/2011/935364'
apa: 'Schlögl, A., Vidaurre, C., & Sander, T. (2011). BioSig: The free and open
source software library for biomedical signal processing. Computational Intelligence
and Neuroscience. Hindawi Publishing Corporation. https://doi.org/10.1155/2011/935364'
chicago: 'Schlögl, Alois, Carmen Vidaurre, and Tilmann Sander. “BioSig: The Free
and Open Source Software Library for Biomedical Signal Processing.” Computational
Intelligence and Neuroscience. Hindawi Publishing Corporation, 2011. https://doi.org/10.1155/2011/935364.'
ieee: 'A. Schlögl, C. Vidaurre, and T. Sander, “BioSig: The free and open source
software library for biomedical signal processing,” Computational Intelligence
and Neuroscience, vol. 2011. Hindawi Publishing Corporation, 2011.'
ista: 'Schlögl A, Vidaurre C, Sander T. 2011. BioSig: The free and open source software
library for biomedical signal processing. Computational Intelligence and Neuroscience.
2011, 935364.'
mla: 'Schlögl, Alois, et al. “BioSig: The Free and Open Source Software Library
for Biomedical Signal Processing.” Computational Intelligence and Neuroscience,
vol. 2011, 935364, Hindawi Publishing Corporation, 2011, doi:10.1155/2011/935364.'
short: A. Schlögl, C. Vidaurre, T. Sander, Computational Intelligence and Neuroscience
2011 (2011).
date_created: 2018-12-11T11:46:45Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:02Z
day: '01'
ddc:
- '005'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.1155/2011/935364
file:
- access_level: open_access
checksum: 8263bbf255171f2054f43f3db5f53b6e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:44Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4642'
file_name: IST-2018-947-v1+1_2011_Schloegl_BioSig.pdf
file_size: 2863551
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 2011'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Computational Intelligence and Neuroscience
publication_status: published
publisher: Hindawi Publishing Corporation
publist_id: '7330'
pubrep_id: '947'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'BioSig: The free and open source software library for biomedical signal processing'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 2011
year: '2011'
...
---
_id: '491'
abstract:
- lang: eng
text: In their search for antigens, lymphocytes continuously shuttle among blood
vessels, lymph vessels, and lymphatic tissues. Chemokines mediate entry of lymphocytes
into lymphatic tissues, and sphingosine 1-phosphate (S1P) promotes localization
of lymphocytes to the vasculature. Both signals are sensed through G protein-coupled
receptors (GPCRs). Most GPCRs undergo ligand-dependent homologous receptor desensitization,
a process that decreases their signaling output after previous exposure to high
ligand concentration. Such desensitization can explain why lymphocytes do not
take an intermediate position between two signals but rather oscillate between
them. The desensitization of S1P receptor 1 (S1PR1) is mediated by GPCR kinase
2 (GRK2). Deletion of GRK2 in lymphocytes compromises desensitization by high
vascular S1P concentrations, thereby reducing responsiveness to the chemokine
signal and trapping the cells in the vascular compartment. The desensitization
kinetics of S1PR1 allows lymphocytes to dynamically shuttle between vasculature
and lymphatic tissue, although the positional information in both compartments
is static.
article_number: pe43
author:
- first_name: Alexander
full_name: Eichner, Alexander
id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87
last_name: Eichner
- 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: Eichner A, Sixt MK. Setting the clock for recirculating lymphocytes. Science
Signaling. 2011;4(198). doi:10.1126/scisignal.2002617
apa: Eichner, A., & Sixt, M. K. (2011). Setting the clock for recirculating
lymphocytes. Science Signaling. American Association for the Advancement
of Science. https://doi.org/10.1126/scisignal.2002617
chicago: Eichner, Alexander, and Michael K Sixt. “Setting the Clock for Recirculating
Lymphocytes.” Science Signaling. American Association for the Advancement
of Science, 2011. https://doi.org/10.1126/scisignal.2002617.
ieee: A. Eichner and M. K. Sixt, “Setting the clock for recirculating lymphocytes,”
Science Signaling, vol. 4, no. 198. American Association for the Advancement
of Science, 2011.
ista: Eichner A, Sixt MK. 2011. Setting the clock for recirculating lymphocytes.
Science Signaling. 4(198), pe43.
mla: Eichner, Alexander, and Michael K. Sixt. “Setting the Clock for Recirculating
Lymphocytes.” Science Signaling, vol. 4, no. 198, pe43, American Association
for the Advancement of Science, 2011, doi:10.1126/scisignal.2002617.
short: A. Eichner, M.K. Sixt, Science Signaling 4 (2011).
date_created: 2018-12-11T11:46:46Z
date_published: 2011-11-08T00:00:00Z
date_updated: 2021-01-12T08:01:02Z
day: '08'
department:
- _id: MiSi
doi: 10.1126/scisignal.2002617
intvolume: ' 4'
issue: '198'
language:
- iso: eng
month: '11'
oa_version: None
publication: Science Signaling
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7329'
quality_controlled: '1'
scopus_import: 1
status: public
title: Setting the clock for recirculating lymphocytes
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2011'
...
---
_id: '518'
abstract:
- lang: eng
text: Cancer stem cells or cancer initiating cells are believed to contribute to
cancer recurrence after therapy. MicroRNAs (miRNAs) are short RNA molecules with
fundamental roles in gene regulation. The role of miRNAs in cancer stem cells
is only poorly understood. Here, we report miRNA expression profiles of glioblastoma
stem cell-containing CD133 + cell populations. We find that miR-9, miR-9 * (referred
to as miR-9/9 *), miR-17 and miR-106b are highly abundant in CD133 + cells. Furthermore,
inhibition of miR-9/9 * or miR-17 leads to reduced neurosphere formation and stimulates
cell differentiation. Calmodulin-binding transcription activator 1 (CAMTA1) is
a putative transcription factor, which induces the expression of the anti-proliferative
cardiac hormone natriuretic peptide A (NPPA). We identify CAMTA1 as an miR-9/9
* and miR-17 target. CAMTA1 expression leads to reduced neurosphere formation
and tumour growth in nude mice, suggesting that CAMTA1 can function as tumour
suppressor. Consistently, CAMTA1 and NPPA expression correlate with patient survival.
Our findings could provide a basis for novel strategies of glioblastoma therapy.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Schraivogel, Daniel
last_name: Schraivogel
- first_name: Lasse
full_name: Weinmann, Lasse
last_name: Weinmann
- first_name: Dagmar
full_name: Beier, Dagmar
last_name: Beier
- first_name: Ghazaleh
full_name: Tabatabai, Ghazaleh
last_name: Tabatabai
- first_name: Alexander
full_name: Eichner, Alexander
id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87
last_name: Eichner
- first_name: Jia
full_name: Zhu, Jia
last_name: Zhu
- first_name: Martina
full_name: Anton, Martina
last_name: Anton
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Michael
full_name: Weller, Michael
last_name: Weller
- first_name: Christoph
full_name: Beier, Christoph
last_name: Beier
- first_name: Gunter
full_name: Meister, Gunter
last_name: Meister
citation:
ama: Schraivogel D, Weinmann L, Beier D, et al. CAMTA1 is a novel tumour suppressor
regulated by miR-9/9 * in glioblastoma stem cells. EMBO Journal. 2011;30(20):4309-4322.
doi:10.1038/emboj.2011.301
apa: Schraivogel, D., Weinmann, L., Beier, D., Tabatabai, G., Eichner, A., Zhu,
J., … Meister, G. (2011). CAMTA1 is a novel tumour suppressor regulated by miR-9/9
* in glioblastoma stem cells. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2011.301
chicago: Schraivogel, Daniel, Lasse Weinmann, Dagmar Beier, Ghazaleh Tabatabai,
Alexander Eichner, Jia Zhu, Martina Anton, et al. “CAMTA1 Is a Novel Tumour Suppressor
Regulated by MiR-9/9 * in Glioblastoma Stem Cells.” EMBO Journal. Wiley-Blackwell,
2011. https://doi.org/10.1038/emboj.2011.301.
ieee: D. Schraivogel et al., “CAMTA1 is a novel tumour suppressor regulated
by miR-9/9 * in glioblastoma stem cells,” EMBO Journal, vol. 30, no. 20.
Wiley-Blackwell, pp. 4309–4322, 2011.
ista: Schraivogel D, Weinmann L, Beier D, Tabatabai G, Eichner A, Zhu J, Anton M,
Sixt MK, Weller M, Beier C, Meister G. 2011. CAMTA1 is a novel tumour suppressor
regulated by miR-9/9 * in glioblastoma stem cells. EMBO Journal. 30(20), 4309–4322.
mla: Schraivogel, Daniel, et al. “CAMTA1 Is a Novel Tumour Suppressor Regulated
by MiR-9/9 * in Glioblastoma Stem Cells.” EMBO Journal, vol. 30, no. 20,
Wiley-Blackwell, 2011, pp. 4309–22, doi:10.1038/emboj.2011.301.
short: D. Schraivogel, L. Weinmann, D. Beier, G. Tabatabai, A. Eichner, J. Zhu,
M. Anton, M.K. Sixt, M. Weller, C. Beier, G. Meister, EMBO Journal 30 (2011) 4309–4322.
date_created: 2018-12-11T11:46:55Z
date_published: 2011-10-19T00:00:00Z
date_updated: 2021-01-12T08:01:19Z
day: '19'
department:
- _id: MiSi
doi: 10.1038/emboj.2011.301
external_id:
pmid:
- '21857646'
intvolume: ' 30'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199389/
month: '10'
oa: 1
oa_version: Submitted Version
page: 4309 - 4322
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7301'
quality_controlled: '1'
scopus_import: 1
status: public
title: CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma
stem cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2011'
...
---
_id: '531'
abstract:
- lang: eng
text: Software transactional memories (STM) are described in the literature with
assumptions of sequentially consistent program execution and atomicity of high
level operations like read, write, and abort. However, in a realistic setting,
processors use relaxed memory models to optimize hardware performance. Moreover,
the atomicity of operations depends on the underlying hardware. This paper presents
the first approach to verify STMs under relaxed memory models with atomicity of
32 bit loads and stores, and read-modify-write operations. We describe RML, a
simple language for expressing concurrent programs. We develop a semantics of
RML parametrized by a relaxed memory model. We then present our tool, FOIL, which
takes as input the RML description of an STM algorithm restricted to two threads
and two variables, and the description of a memory model, and automatically determines
the locations of fences, which if inserted, ensure the correctness of the restricted
STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and
McRT STM under the memory models of sequential consistency, total store order,
partial store order, and relaxed memory order for two threads and two variables.
Finally, we extend the verification results for DSTM and TL2 to an arbitrary number
of threads and variables by manually proving that the structural properties of
STMs are satisfied at the hardware level of atomicity under the considered relaxed
memory models.
article_processing_charge: No
article_type: original
author:
- first_name: Rachid
full_name: Guerraoui, Rachid
last_name: Guerraoui
- 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: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
citation:
ama: Guerraoui R, Henzinger TA, Singh V. Verification of STM on relaxed memory models.
Formal Methods in System Design. 2011;39(3):297-331. doi:10.1007/s10703-011-0131-3
apa: Guerraoui, R., Henzinger, T. A., & Singh, V. (2011). Verification of STM
on relaxed memory models. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-011-0131-3
chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Verification of
STM on Relaxed Memory Models.” Formal Methods in System Design. Springer,
2011. https://doi.org/10.1007/s10703-011-0131-3.
ieee: R. Guerraoui, T. A. Henzinger, and V. Singh, “Verification of STM on relaxed
memory models,” Formal Methods in System Design, vol. 39, no. 3. Springer,
pp. 297–331, 2011.
ista: Guerraoui R, Henzinger TA, Singh V. 2011. Verification of STM on relaxed memory
models. Formal Methods in System Design. 39(3), 297–331.
mla: Guerraoui, Rachid, et al. “Verification of STM on Relaxed Memory Models.” Formal
Methods in System Design, vol. 39, no. 3, Springer, 2011, pp. 297–331, doi:10.1007/s10703-011-0131-3.
short: R. Guerraoui, T.A. Henzinger, V. Singh, Formal Methods in System Design 39
(2011) 297–331.
date_created: 2018-12-11T11:47:00Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10703-011-0131-3
intvolume: ' 39'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://infoscience.epfl.ch/record/178042/files/art3A10.10072Fs10703-011-0131-3.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 297 - 331
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '7288'
quality_controlled: '1'
scopus_import: 1
status: public
title: Verification of STM on relaxed memory models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2011'
...
---
_id: '5379'
abstract:
- lang: eng
text: Computing the winning set for Büchi objectives in alternating games on graphs
is a central problem in computer aided verification with a large number of applications.
The long standing best known upper bound for solving the problem is ̃O(n·m), where
n is the number of vertices and m is the number of edges in the graph. We are
the first to break the ̃O(n·m) boundary by presenting a new technique that reduces
the running time to O(n2). This bound also leads to O(n2) time algorithms for
computing the set of almost-sure winning vertices for Büchi objectives (1) in
alternating games with probabilistic transitions (improving an earlier bound of
O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier
bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3
an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique
can be used to compute the maximal end-component decomposition of a graph in time
O(n2), which is an improvement over earlier bounds for m > n4/3. Finally, we show
how to maintain the winning set for Büchi objectives in alternating games under
a sequence of edge insertions or a sequence of edge deletions in O(n) amortized
time per operation. This is the first dynamic algorithm for this problem.
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: Chatterjee K, Henzinger MH. An O(N2) Time Algorithm for Alternating Büchi
Games. IST Austria; 2011. doi:10.15479/AT:IST-2011-0009
apa: Chatterjee, K., & Henzinger, M. H. (2011). An O(n2) time algorithm for
alternating Büchi games. IST Austria. https://doi.org/10.15479/AT:IST-2011-0009
chicago: Chatterjee, Krishnendu, and Monika H Henzinger. An O(N2) Time Algorithm
for Alternating Büchi Games. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0009.
ieee: K. Chatterjee and M. H. Henzinger, An O(n2) time algorithm for alternating
Büchi games. IST Austria, 2011.
ista: Chatterjee K, Henzinger MH. 2011. An O(n2) time algorithm for alternating
Büchi games, IST Austria, 20p.
mla: Chatterjee, Krishnendu, and Monika H. Henzinger. An O(N2) Time Algorithm
for Alternating Büchi Games. IST Austria, 2011, doi:10.15479/AT:IST-2011-0009.
short: K. Chatterjee, M.H. Henzinger, An O(N2) Time Algorithm for Alternating Büchi
Games, IST Austria, 2011.
date_created: 2018-12-12T11:38:59Z
date_published: 2011-07-11T00:00:00Z
date_updated: 2023-02-23T11:15:12Z
day: '11'
ddc:
- '000'
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0009
file:
- access_level: open_access
checksum: 0b354264229045d982332fd2cb5b9a26
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:43Z
date_updated: 2020-07-14T12:46:39Z
file_id: '5504'
file_name: IST-2011-0009_IST-2011-0009.pdf
file_size: 388665
relation: main_file
file_date_updated: 2020-07-14T12:46:39Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '15'
related_material:
record:
- id: '3165'
relation: later_version
status: public
status: public
title: An O(n2) time algorithm for alternating Büchi games
type: technical_report
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2011'
...
---
_id: '5380'
abstract:
- lang: eng
text: 'We consider 2-player games played on a finite state space for an infinite
number of rounds. The games are concurrent: in each round, the two players (player
1 and player 2) choose their moves independently and simultaneously; the current
state and the two moves determine the successor state. We study concurrent games
with ω-regular winning conditions specified as parity objectives. We consider
the qualitative analysis problems: the computation of the almost-sure and limit-sure
winning set of states, where player 1 can ensure to win with probability 1 and
with probability arbitrarily close to 1, respectively. In general the almost-sure
and limit-sure winning strategies require both infinite-memory as well as infinite-precision
(to describe probabilities). We study the bounded-rationality problem for qualitative
analysis of concurrent parity games, where the strategy set for player 1 is restricted
to bounded-resource strategies. In terms of precision, strategies can be deterministic,
uniform, finite-precision or infinite-precision; and in terms of memory, strategies
can be memoryless, finite-memory or infinite-memory. We present a precise and
complete characterization of the qualitative winning sets for all combinations
of classes of strategies. In particular, we show that uniform memoryless strategies
are as powerful as finite-precision infinite-memory strategies, and infinite-precision
memoryless strategies are as powerful as infinite-precision finite-memory strategies. We
show that the winning sets can be computed in O(n2d+3) time, where n is the size
of the game structure and 2d is the number of priorities (or colors), and our
algorithms are symbolic. The membership problem of whether a state belongs to
a winning set can be decided in NP ∩ coNP. While this complexity is the same as
for the simpler class of turn-based parity games, where in each state only one
of the two players has a choice of moves, our algorithms,that are obtained by
characterization of the winning sets as μ-calculus formulas, are considerably
more involved than those for turn-based games.'
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
citation:
ama: Chatterjee K. Bounded Rationality in Concurrent Parity Games. IST Austria;
2011. doi:10.15479/AT:IST-2011-0008
apa: Chatterjee, K. (2011). Bounded rationality in concurrent parity games.
IST Austria. https://doi.org/10.15479/AT:IST-2011-0008
chicago: Chatterjee, Krishnendu. Bounded Rationality in Concurrent Parity Games.
IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0008.
ieee: K. Chatterjee, Bounded rationality in concurrent parity games. IST
Austria, 2011.
ista: Chatterjee K. 2011. Bounded rationality in concurrent parity games, IST Austria,
53p.
mla: Chatterjee, Krishnendu. Bounded Rationality in Concurrent Parity Games.
IST Austria, 2011, doi:10.15479/AT:IST-2011-0008.
short: K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria,
2011.
date_created: 2018-12-12T11:39:00Z
date_published: 2011-07-11T00:00:00Z
date_updated: 2023-02-23T11:22:53Z
day: '11'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0008
file:
- access_level: open_access
checksum: 0fd38186409be819a911c4990fa79d1f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:22Z
date_updated: 2020-07-14T12:46:39Z
file_id: '5544'
file_name: IST-2011-0008_IST-2011-0008.pdf
file_size: 500399
relation: main_file
file_date_updated: 2020-07-14T12:46:39Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '53'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '16'
related_material:
record:
- id: '3338'
relation: later_version
status: public
status: public
title: Bounded rationality in concurrent parity games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5381'
abstract:
- lang: eng
text: "In two-player finite-state stochastic games of partial obser- vation on graphs,
in every state of the graph, the players simultaneously choose an action, and
their joint actions determine a probability distri- bution over the successor
states. The game is played for infinitely many rounds and thus the players construct
an infinite path in the graph. We consider reachability objectives where the first
player tries to ensure a target state to be visited almost-surely (i.e., with
probability 1) or pos- itively (i.e., with positive probability), no matter the
strategy of the second player.\r\n\r\nWe classify such games according to the
information and to the power of randomization available to the players. On the
basis of information, the game can be one-sided with either (a) player 1, or (b)
player 2 having partial observation (and the other player has perfect observation),
or two- sided with (c) both players having partial observation. On the basis of
randomization, (a) the players may not be allowed to use randomization (pure strategies),
or (b) they may choose a probability distribution over actions but the actual
random choice is external and not visible to the player (actions invisible), or
(c) they may use full randomization.\r\n\r\nOur main results for pure strategies
are as follows: (1) For one-sided games with player 2 perfect observation we show
that (in contrast to full randomized strategies) belief-based (subset-construction
based) strate- gies are not sufficient, and present an exponential upper bound
on mem- ory both for almost-sure and positive winning strategies; we show that
the problem of deciding the existence of almost-sure and positive winning strategies
for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid
the explicit exponential construction. (2) For one-sided games with player 1 perfect
observation we show that non-elementary memory is both necessary and sufficient
for both almost-sure and posi- tive winning strategies. (3) We show that for the
general (two-sided) case finite-memory strategies are sufficient for both positive
and almost-sure winning, and at least non-elementary memory is required. We establish
the equivalence of the almost-sure winning problems for pure strategies and for
randomized strategies with actions invisible. Our equivalence re- sult exhibit
serious flaws in previous results in the literature: we show a non-elementary
memory lower bound for almost-sure winning whereas an exponential upper bound
was previously claimed."
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Partial-Observation Stochastic Games: How to Win
When Belief Fails. IST Austria; 2011. doi:10.15479/AT:IST-2011-0007'
apa: 'Chatterjee, K., & Doyen, L. (2011). Partial-observation stochastic
games: How to win when belief fails. IST Austria. https://doi.org/10.15479/AT:IST-2011-0007'
chicago: 'Chatterjee, Krishnendu, and Laurent Doyen. Partial-Observation Stochastic
Games: How to Win When Belief Fails. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0007.'
ieee: 'K. Chatterjee and L. Doyen, Partial-observation stochastic games: How
to win when belief fails. IST Austria, 2011.'
ista: 'Chatterjee K, Doyen L. 2011. Partial-observation stochastic games: How to
win when belief fails, IST Austria, 43p.'
mla: 'Chatterjee, Krishnendu, and Laurent Doyen. Partial-Observation Stochastic
Games: How to Win When Belief Fails. IST Austria, 2011, doi:10.15479/AT:IST-2011-0007.'
short: 'K. Chatterjee, L. Doyen, Partial-Observation Stochastic Games: How to Win
When Belief Fails, IST Austria, 2011.'
date_created: 2018-12-12T11:39:00Z
date_published: 2011-07-05T00:00:00Z
date_updated: 2023-02-23T11:05:48Z
day: '05'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0007
file:
- access_level: open_access
checksum: 06bf6dfc97f6006e3fd0e9a3f31bc961
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:27Z
date_updated: 2020-07-14T12:46:39Z
file_id: '5488'
file_name: IST-2011-0007_IST-2011-0007.pdf
file_size: 574055
relation: main_file
file_date_updated: 2020-07-14T12:46:39Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '43'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '17'
related_material:
record:
- id: '1903'
relation: later_version
status: public
- id: '2211'
relation: later_version
status: public
- id: '2955'
relation: later_version
status: public
status: public
title: 'Partial-observation stochastic games: How to win when belief fails'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5382'
abstract:
- lang: eng
text: 'We consider two-player stochastic games played on a finite state space for
an infinite num- ber of rounds. The games are concurrent: in each round, the two
players (player 1 and player 2) choose their moves independently and simultaneously;
the current state and the two moves determine a probability distribution over
the successor states. We also consider the important special case of turn-based
stochastic games where players make moves in turns, rather than concurrently.
We study concurrent games with ω-regular winning conditions specified as parity
objectives. The value for player 1 for a parity objective is the maximal probability
with which the player can guarantee the satisfaction of the objective against
all strategies of the opponent. We study the problem of continuity and robustness
of the value function in concurrent and turn-based stochastic parity games with
respect to imprecision in the transition probabilities. We present quantitative
bounds on the difference of the value function (in terms of the imprecision of
the transition probabilities) and show the value continuity for structurally equivalent
concurrent games (two games are structurally equivalent if the support of the
transition func- tion is same and the probabilities differ). We also show robustness
of optimal strategies for structurally equivalent turn-based stochastic parity
games. Finally we show that the value continuity property breaks without the structurally
equivalent assumption (even for Markov chains) and show that our quantitative
bound is asymptotically optimal. Hence our results are tight (the assumption is
both necessary and sufficient) and optimal (our quantitative bound is asymptotically
optimal).'
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
citation:
ama: Chatterjee K. Robustness of Structurally Equivalent Concurrent Parity Games.
IST Austria; 2011. doi:10.15479/AT:IST-2011-0006
apa: Chatterjee, K. (2011). Robustness of structurally equivalent concurrent
parity games. IST Austria. https://doi.org/10.15479/AT:IST-2011-0006
chicago: Chatterjee, Krishnendu. Robustness of Structurally Equivalent Concurrent
Parity Games. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0006.
ieee: K. Chatterjee, Robustness of structurally equivalent concurrent parity
games. IST Austria, 2011.
ista: Chatterjee K. 2011. Robustness of structurally equivalent concurrent parity
games, IST Austria, 18p.
mla: Chatterjee, Krishnendu. Robustness of Structurally Equivalent Concurrent
Parity Games. IST Austria, 2011, doi:10.15479/AT:IST-2011-0006.
short: K. Chatterjee, Robustness of Structurally Equivalent Concurrent Parity Games,
IST Austria, 2011.
date_created: 2018-12-12T11:39:00Z
date_published: 2011-06-27T00:00:00Z
date_updated: 2023-02-23T11:23:01Z
day: '27'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0006
file:
- access_level: open_access
checksum: 1322b652d6ab07eb5248298a3f91c1cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:24Z
date_updated: 2020-07-14T12:46:40Z
file_id: '5546'
file_name: IST-2011-0006_IST-2011-0006.pdf
file_size: 335997
relation: main_file
file_date_updated: 2020-07-14T12:46:40Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '18'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '18'
related_material:
record:
- id: '3341'
relation: later_version
status: public
status: public
title: Robustness of structurally equivalent concurrent parity games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5383'
abstract:
- lang: eng
text: We present a new decidable logic called TREX for expressing constraints about
imperative tree data structures. In particular, TREX supports a transitive closure
operator that can express reachability constraints, which often appear in data
structure invariants. We show that our logic is closed under weakest precondition
computation, which enables its use for automated software verification. We further
show that satisfiability of formulas in TREX is decidable in NP. The low complexity
makes it an attractive alternative to more expensive logics such as monadic second-order
logic (MSOL) over trees, which have been traditionally used for reasoning about
tree data structures.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Marco
full_name: Muñiz, Marco
last_name: Muñiz
- first_name: Viktor
full_name: Kuncak, Viktor
last_name: Kuncak
citation:
ama: Wies T, Muñiz M, Kuncak V. On an Efficient Decision Procedure for Imperative
Tree Data Structures. IST Austria; 2011. doi:10.15479/AT:IST-2011-0005
apa: Wies, T., Muñiz, M., & Kuncak, V. (2011). On an efficient decision procedure
for imperative tree data structures. IST Austria. https://doi.org/10.15479/AT:IST-2011-0005
chicago: Wies, Thomas, Marco Muñiz, and Viktor Kuncak. On an Efficient Decision
Procedure for Imperative Tree Data Structures. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0005.
ieee: T. Wies, M. Muñiz, and V. Kuncak, On an efficient decision procedure for
imperative tree data structures. IST Austria, 2011.
ista: Wies T, Muñiz M, Kuncak V. 2011. On an efficient decision procedure for imperative
tree data structures, IST Austria, 25p.
mla: Wies, Thomas, et al. On an Efficient Decision Procedure for Imperative Tree
Data Structures. IST Austria, 2011, doi:10.15479/AT:IST-2011-0005.
short: T. Wies, M. Muñiz, V. Kuncak, On an Efficient Decision Procedure for Imperative
Tree Data Structures, IST Austria, 2011.
date_created: 2018-12-12T11:39:01Z
date_published: 2011-04-26T00:00:00Z
date_updated: 2023-02-23T11:22:16Z
day: '26'
ddc:
- '000'
- '006'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2011-0005
file:
- access_level: open_access
checksum: b20029184c4a819c5f4466a4a3d238b5
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:01Z
date_updated: 2020-07-14T12:46:40Z
file_id: '5462'
file_name: IST-2011-0005_IST-2011-0005.pdf
file_size: 619053
relation: main_file
file_date_updated: 2020-07-14T12:46:40Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '25'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '19'
related_material:
record:
- id: '3323'
relation: later_version
status: public
status: public
title: On an efficient decision procedure for imperative tree data structures
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5384'
abstract:
- lang: eng
text: 'We consider probabilistic automata on infinite words with acceptance defined
by parity conditions. We consider three qualitative decision problems: (i) the
positive decision problem asks whether there is a word that is accepted with positive
probability; (ii) the almost decision problem asks whether there is a word that
is accepted with probability 1; and (iii) the limit decision problem asks whether
for every ε > 0 there is a word that is accepted with probability at least 1 −
ε. We unify and generalize several decidability results for probabilistic automata
over infinite words, and identify a robust (closed under union and intersection)
subclass of probabilistic automata for which all the qualitative decision problems
are decidable for parity conditions. We also show that if the input words are
restricted to lasso shape words, then the positive and almost problems are decidable
for all probabilistic automata with parity conditions.'
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: Mathieu
full_name: Tracol, Mathieu
id: 3F54FA38-F248-11E8-B48F-1D18A9856A87
last_name: Tracol
citation:
ama: Chatterjee K, Tracol M. Decidable Problems for Probabilistic Automata on
Infinite Words. IST Austria; 2011. doi:10.15479/AT:IST-2011-0004
apa: Chatterjee, K., & Tracol, M. (2011). Decidable problems for probabilistic
automata on infinite words. IST Austria. https://doi.org/10.15479/AT:IST-2011-0004
chicago: Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic
Automata on Infinite Words. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0004.
ieee: K. Chatterjee and M. Tracol, Decidable problems for probabilistic automata
on infinite words. IST Austria, 2011.
ista: Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata
on infinite words, IST Austria, 30p.
mla: Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic
Automata on Infinite Words. IST Austria, 2011, doi:10.15479/AT:IST-2011-0004.
short: K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on
Infinite Words, IST Austria, 2011.
date_created: 2018-12-12T11:39:01Z
date_published: 2011-04-11T00:00:00Z
date_updated: 2023-02-23T11:05:53Z
day: '11'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0004
file:
- access_level: open_access
checksum: f5a0f664fadc335990f5fcf138df19f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:23Z
date_updated: 2020-07-14T12:46:40Z
file_id: '5545'
file_name: IST-2011-004_IST-2011-0004.pdf
file_size: 570827
relation: main_file
file_date_updated: 2020-07-14T12:46:40Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '30'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '20'
related_material:
record:
- id: '2957'
relation: later_version
status: public
status: public
title: Decidable problems for probabilistic automata on infinite words
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5385'
abstract:
- lang: eng
text: There is recently a significant effort to add quantitative objectives to formal
verification and synthesis. We introduce and investigate the extension of temporal
logics with quantitative atomic assertions, aiming for a general and flexible
framework for quantitative-oriented specifications. In the heart of quantitative
objectives lies the accumulation of values along a computation. It is either the
accumulated summation, as with the energy objectives, or the accumulated average,
as with the mean-payoff objectives. We investigate the extension of temporal logics
with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is
a numeric variable of the system, c is a constant rational number, and Sum(v)
and Avg(v) denote the accumulated sum and average of the values of v from the
beginning of the computation up to the current point of time. We also allow the
path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring
to the average value along an entire computation. We study the border of decidability
for extensions of various temporal logics. In particular, we show that extending
the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by
prefix-accumulation assertions and extending LTL with path-accumulation assertions,
result in temporal logics whose model-checking problem is decidable. The extended
logics allow to significantly extend the currently known energy and mean-payoff
objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”,
allowing, for example, to specify constraints on the average waiting time between
a request and a grant. On the negative side, we show that the fragment we point
to is, in a sense, the maximal logic whose extension with prefix-accumulation
assertions permits a decidable model-checking procedure. Extending a temporal
logic that has the EG or EU modalities, and in particular CTL and LTL, makes the
problem undecidable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- 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: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal Specifications
with Accumulative Values. IST Austria; 2011. doi:10.15479/AT:IST-2011-0003
apa: Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2011). Temporal
specifications with accumulative values. IST Austria. https://doi.org/10.15479/AT:IST-2011-0003
chicago: Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman.
Temporal Specifications with Accumulative Values. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0003.
ieee: U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, Temporal specifications
with accumulative values. IST Austria, 2011.
ista: Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications
with accumulative values, IST Austria, 14p.
mla: Boker, Udi, et al. Temporal Specifications with Accumulative Values.
IST Austria, 2011, doi:10.15479/AT:IST-2011-0003.
short: U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications
with Accumulative Values, IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-04-04T00:00:00Z
date_updated: 2023-02-23T11:23:41Z
day: '04'
ddc:
- '000'
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.15479/AT:IST-2011-0003
ec_funded: 1
file:
- access_level: open_access
checksum: 8491d0d48c4911620ecd5350b413c11e
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:00Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5461'
file_name: IST-2011-0003_IST-2011-0003.pdf
file_size: 366281
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '14'
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '21'
related_material:
record:
- id: '2038'
relation: later_version
status: public
- id: '3356'
relation: later_version
status: public
status: public
title: Temporal specifications with accumulative values
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5386'
abstract:
- lang: eng
text: 'We introduce TopoCut: a new way to integrate knowledge about topological
properties (TPs) into random field image segmentation model. Instead of including
TPs as additional constraints during minimization of the energy function, we devise
an efficient algorithm for modifying the unary potentials such that the resulting
segmentation is guaranteed with the desired properties. Our method is more flexible
in the sense that it handles more topology constraints than previous methods,
which were only able to enforce pairwise or global connectivity. In particular,
our method is very fast, making it for the first time possible to enforce global
topological properties in practical image segmentation tasks.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Chen C, Freedman D, Lampert C. Enforcing Topological Constraints in Random
Field Image Segmentation. IST Austria; 2011. doi:10.15479/AT:IST-2011-0002
apa: Chen, C., Freedman, D., & Lampert, C. (2011). Enforcing topological
constraints in random field image segmentation. IST Austria. https://doi.org/10.15479/AT:IST-2011-0002
chicago: Chen, Chao, Daniel Freedman, and Christoph Lampert. Enforcing Topological
Constraints in Random Field Image Segmentation. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0002.
ieee: C. Chen, D. Freedman, and C. Lampert, Enforcing topological constraints
in random field image segmentation. IST Austria, 2011.
ista: Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in
random field image segmentation, IST Austria, 69p.
mla: Chen, Chao, et al. Enforcing Topological Constraints in Random Field Image
Segmentation. IST Austria, 2011, doi:10.15479/AT:IST-2011-0002.
short: C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random
Field Image Segmentation, IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-03-28T00:00:00Z
date_updated: 2023-02-23T11:22:48Z
day: '28'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.15479/AT:IST-2011-0002
file:
- access_level: open_access
checksum: ad64c2add5fe2ad10e9d5c669f3f9526
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:34Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5495'
file_name: IST-2011-0002_IST-2011-0002.pdf
file_size: 26390601
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '69'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '22'
related_material:
record:
- id: '3336'
relation: later_version
status: public
status: public
title: Enforcing topological constraints in random field image segmentation
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '5387'
abstract:
- lang: eng
text: We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy
parity objectives. In system design, the parity objective is used to encode ω-regular
specifications, and the mean-payoff and energy objectives can be used to model
quantitative resource constraints. The energy condition re- quires that the resource
level never drops below 0, and the mean-payoff condi- tion requires that the limit-average
value of the resource consumption is within a threshold. While these two (energy
and mean-payoff) classical conditions are equivalent for two-player games, we
show that they differ for MDPs. We show that the problem of deciding whether a
state is almost-sure winning (i.e., winning with probability 1) in energy parity
MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable
in polynomial time, improving a recent PSPACE bound.
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Energy and Mean-Payoff Parity Markov Decision Processes.
IST Austria; 2011. doi:10.15479/AT:IST-2011-0001
apa: Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov
decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2011-0001
chicago: Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity
Markov Decision Processes. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0001.
ieee: K. Chatterjee and L. Doyen, Energy and mean-payoff parity Markov decision
processes. IST Austria, 2011.
ista: Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision
processes, IST Austria, 20p.
mla: Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity
Markov Decision Processes. IST Austria, 2011, doi:10.15479/AT:IST-2011-0001.
short: K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes,
IST Austria, 2011.
date_created: 2018-12-12T11:39:02Z
date_published: 2011-02-16T00:00:00Z
date_updated: 2023-02-23T11:23:11Z
day: '16'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2011-0001
file:
- access_level: open_access
checksum: 824d6c70e6d3feb3e836b009e0b3cf73
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:52:57Z
date_updated: 2020-07-14T12:46:41Z
file_id: '5458'
file_name: IST-2011-0001_IST-2011-0001.pdf
file_size: 329976
relation: main_file
file_date_updated: 2020-07-14T12:46:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '23'
related_material:
record:
- id: '3345'
relation: later_version
status: public
status: public
title: Energy and mean-payoff parity Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '580'
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: 'Hosten O. Quantum physics: How to catch a wave. Nature. 2011;474(7350):170-171.
doi:10.1038/474170a'
apa: 'Hosten, O. (2011). Quantum physics: How to catch a wave. Nature. Nature
Publishing Group. https://doi.org/10.1038/474170a'
chicago: 'Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature. Nature
Publishing Group, 2011. https://doi.org/10.1038/474170a.'
ieee: 'O. Hosten, “Quantum physics: How to catch a wave,” Nature, vol. 474,
no. 7350. Nature Publishing Group, pp. 170–171, 2011.'
ista: 'Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350),
170–171.'
mla: 'Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature, vol.
474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:10.1038/474170a.'
short: O. Hosten, Nature 474 (2011) 170–171.
date_created: 2018-12-11T11:47:18Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T08:03:34Z
day: '08'
doi: 10.1038/474170a
extern: 1
intvolume: ' 474'
issue: '7350'
month: '06'
page: 170 - 171
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7224'
quality_controlled: 0
status: public
title: 'Quantum physics: How to catch a wave'
type: journal_article
volume: 474
year: '2011'
...
---
_id: '585'
abstract:
- lang: eng
text: |+
We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.
alternative_title:
- Optics InfoBase Conference Papers
author:
- first_name: David
full_name: Schmid, David
last_name: Schmid
- first_name: Shiraz
full_name: Hazrat, Shiraz
last_name: Hazrat
- first_name: Radhika
full_name: Rangarajan, Radhika
last_name: Rangarajan
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Stephan
full_name: Quint, Stephan
last_name: Quint
- first_name: Paul
full_name: Kwiat, Paul G
last_name: Kwiat
citation:
ama: 'Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards
achieving precise birefringent focusing. In: OSA; 2011. doi:10.1364/CLEO_AT.2011.JThB130'
apa: 'Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., & Kwiat,
P. (2011). Methods towards achieving precise birefringent focusing. Presented
at the QELS: Quantum Electronics and Laser Science, OSA. https://doi.org/10.1364/CLEO_AT.2011.JThB130'
chicago: Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan
Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.”
OSA, 2011. https://doi.org/10.1364/CLEO_AT.2011.JThB130.
ieee: 'D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods
towards achieving precise birefringent focusing,” presented at the QELS: Quantum
Electronics and Laser Science, 2011.'
ista: 'Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods
towards achieving precise birefringent focusing. QELS: Quantum Electronics and
Laser Science, Optics InfoBase Conference Papers, .'
mla: Schmid, David, et al. Methods towards Achieving Precise Birefringent Focusing.
OSA, 2011, doi:10.1364/CLEO_AT.2011.JThB130.
short: D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:,
OSA, 2011.
conference:
name: 'QELS: Quantum Electronics and Laser Science'
date_created: 2018-12-11T11:47:20Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:44Z
day: '01'
doi: 10.1364/CLEO_AT.2011.JThB130
extern: 1
month: '01'
publication_status: published
publisher: OSA
publist_id: '7220'
quality_controlled: 0
status: public
title: Methods towards achieving precise birefringent focusing
type: conference
year: '2011'
...
...
---
_id: '586'
abstract:
- lang: eng
text: We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a
high-finesse optical cavity. We observe robust continuous wave lasing in the atypical
regime where single atoms can considerably affect the cavity field. Consequently,
we discover unusual lasing threshold behavior in the system causing jumps in lasing
power, and propose a model to explain the effect. We also measure the intermode
laser linewidth, and observe values as low as 80Hz. The tunable gain properties
of this laser suggest multiple directions for future research.
author:
- first_name: Geert
full_name: Vrijsen, Geert
last_name: Vrijsen
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Jongmin
full_name: Lee, Jongmin
last_name: Lee
- first_name: Simon
full_name: Bernon, Simon
last_name: Bernon
- first_name: Mark
full_name: Kasevich, Mark A
last_name: Kasevich
citation:
ama: Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold
atom gain medium in a high-finesse optical cavity. Physical Review Letters.
2011;107(6). doi:10.1103/PhysRevLett.107.063904
apa: Vrijsen, G., Hosten, O., Lee, J., Bernon, S., & Kasevich, M. (2011). Raman
lasing with a cold atom gain medium in a high-finesse optical cavity. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.063904
chicago: Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich.
“Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.”
Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.063904.
ieee: G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with
a cold atom gain medium in a high-finesse optical cavity,” Physical Review
Letters, vol. 107, no. 6. American Physical Society, 2011.
ista: Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with
a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters.
107(6).
mla: Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse
Optical Cavity.” Physical Review Letters, vol. 107, no. 6, American Physical
Society, 2011, doi:10.1103/PhysRevLett.107.063904.
short: G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters
107 (2011).
date_created: 2018-12-11T11:47:20Z
date_published: 2011-08-04T00:00:00Z
date_updated: 2021-01-12T08:05:05Z
day: '04'
doi: 10.1103/PhysRevLett.107.063904
extern: 1
intvolume: ' 107'
issue: '6'
month: '08'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7223'
quality_controlled: 0
status: public
title: Raman lasing with a cold atom gain medium in a high-finesse optical cavity
type: journal_article
volume: 107
year: '2011'
...
---
_id: '597'
abstract:
- lang: eng
text: The macromolecular assembly required to initiate transcription of protein-coding
genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein
complexes and is approximately 3.5 MDa in size. At the heart of this assembly
is the Mediator complex, which helps regulate PIC activity and interacts with
the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol
II interface is not well-characterized, whereas attempts to structurally define
the Mediator-pol II interaction in yeast have relied on incomplete assemblies
of Mediator and/or pol II and have yielded inconsistent interpretations. We have
assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified
components and have characterized its structural organization using cryo-electron
microscopy and single-particle reconstruction techniques. The orientation of pol
II within this assembly was determined by crystal structure docking and further
validated with projection matching experiments, allowing the structural organization
of the entire human PIC to be envisioned. Significantly, pol II orientation within
the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined
the location of other PIC components relative to pol II itself. Pol II surfaces
required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II
cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered
along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding
additional factors; and no major structural re-organization is necessary to accommodate
the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol
II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural
basis for Mediator-dependent control of PIC assembly and function. Finally, parallel
structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF
plays a key role in stabilizing pol II orientation within the assembly.
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patricia
full_name: Grob, Patricia
last_name: Grob
- first_name: Christopher
full_name: Ebmeier, Christopher
last_name: Ebmeier
- first_name: Eva
full_name: Nogales, Eva
last_name: Nogales
- first_name: Dylan
full_name: Taatjes, Dylan
last_name: Taatjes
citation:
ama: Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 2011;9(3).
doi:10.1371/journal.pbio.1000603
apa: Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., & Taatjes, D. (2011).
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000603
chicago: Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and
Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF
Assembly.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000603.
ieee: C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly,” PLoS Biology,
vol. 9, no. 3. Public Library of Science, 2011.
ista: Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture
of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).
mla: Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA
Polymerase II-TFIIF Assembly.” PLoS Biology, vol. 9, no. 3, Public Library
of Science, 2011, doi:10.1371/journal.pbio.1000603.
short: C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9
(2011).
date_created: 2018-12-11T11:47:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T08:05:25Z
day: '01'
doi: 10.1371/journal.pbio.1000603
extern: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7209'
status: public
title: Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2011'
...