---
_id: '1944'
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology
(IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions)
of the European Union
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants. Current Opinion in Plant Biology.
2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002
apa: Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking
and PIN-mediated cell polarity during tropic responses in plants. Current Opinion
in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002
chicago: Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking
and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current
Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002.
ieee: H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants,” Current Opinion in Plant
Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.
ista: Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated
cell polarity during tropic responses in plants. Current Opinion in Plant Biology.
23(2), 116–123.
mla: Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity
during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol.
23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.
short: H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015)
116–123.
date_created: 2018-12-11T11:54:51Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:54:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2014.12.002
ec_funded: 1
intvolume: ' 23'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 116 - 123
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '5140'
quality_controlled: '1'
scopus_import: 1
status: public
title: Intracellular trafficking and PIN-mediated cell polarity during tropic responses
in plants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2015'
...
---
_id: '1992'
abstract:
- lang: eng
text: "We present a method and a tool for generating succinct representations of
sets of concurrent traces. We focus on trace sets that contain all correct or
all incorrect permutations of events from a given trace. We represent trace sets
as HB-Formulas that are Boolean combinations of happens-before constraints between
events. To generate a representation of incorrect interleavings, our method iteratively
explores interleavings that violate the specification and gathers generalizations
of the discovered interleavings into an HB-Formula; its complement yields a representation
of correct interleavings.\r\n\r\nWe claim that our trace set representations can
drive diverse verification, fault localization, repair, and synthesis techniques
for concurrent programs. We demonstrate this by using our tool in three case studies
involving synchronization synthesis, bug summarization, and abstraction refinement
based verification. In each case study, our initial experimental results have
been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring
missing synchronization from an HB-Formula representing correct interleavings
of a given trace. The algorithm applies rules to rewrite specific patterns in
the HB-Formula into locks, barriers, and wait-notify constructs. In the second
case study, we use an HB-Formula representing incorrect interleavings for bug
summarization. While the HB-Formula itself is a concise counterexample summary,
we present additional inference rules to help identify specific concurrency bugs
such as data races, define-use order violations, and two-stage access bugs. In
the final case study, we present a novel predicate learning procedure that uses
HB-Formulas representing abstract counterexamples to accelerate counterexample-guided
abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure
refines the abstraction to eliminate multiple spurious abstract counterexamples
drawn from the HB-Formula."
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation
of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008'
apa: 'Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach,
T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented
at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta,
and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44.
ACM, 2015. https://doi.org/10.1145/2676726.2677008.
ieee: 'A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct
representation of concurrent trace sets,” presented at the POPL: Principles of
Programming Languages, Mumbai, India, 2015, pp. 433–444.'
ista: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct
representation of concurrent trace sets. POPL: Principles of Programming Languages,
433–444.'
mla: Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets.
ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.
short: A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM,
2015, pp. 433–444.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'POPL: Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:55:05Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/2676726.2677008
file:
- access_level: open_access
checksum: f0d4395b600f410a191256ac0b73af32
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:56Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5314'
file_name: IST-2015-317-v1+1_author_version.pdf
file_size: 399462
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 433 - 444
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5091'
pubrep_id: '317'
quality_controlled: '1'
scopus_import: 1
status: public
title: Succinct representation of concurrent trace sets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1993'
abstract:
- lang: eng
text: 'The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens. '
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2)
and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank
Line V. Ugelvig for help with ant collection and statistical discussion, Xavier
Espadaler for detailed information on the ant collection site, Birgit Lautenschläger
for the electron microscopy images and Eva Sixt for ant drawings. We further thank
Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization
and immune gene primer development, Paul Schmid-Hempel for discussion, and Line
V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript.
S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments;
M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with
intense contributions of A.V.G. and S.T.; all authors approved the manuscript."
article_number: '20141976'
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival
costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal
Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976
apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.1976
chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen
Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.
ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1799. The Royal Society, 2015.
ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus
survival costs mediated by an ectosymbiont in an ant host. Proceedings of the
Royal Society of London Series B Biological Sciences. 282(1799), 20141976.
mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated
by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society,
2015, doi:10.1098/rspb.2014.1976.
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society
of London Series B Biological Sciences 282 (2015).
date_created: 2018-12-11T11:55:06Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2023-02-23T14:06:41Z
day: '22'
department:
- _id: SyCr
doi: 10.1098/rspb.2014.1976
ec_funded: 1
external_id:
pmid:
- '25473011'
intvolume: ' 282'
issue: '1799'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
publist_id: '5090'
quality_controlled: '1'
related_material:
record:
- id: '9740'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '1997'
abstract:
- lang: eng
text: We prove that the three-state toric homogeneous Markov chain model has Markov
degree two. In algebraic terminology this means, that a certain class of toric
ideals is generated by quadratic binomials. This was conjectured by Haws, Martin
del Campo, Takemura and Yoshida, who proved that they are generated by degree
six binomials.
author:
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Noren P. The three-state toric homogeneous Markov chain model has Markov degree
two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296.
doi:10.1016/j.jsc.2014.09.014
apa: Noren, P. (2015). The three-state toric homogeneous Markov chain model has
Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014
chicago: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has
Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.
ieee: P. Noren, “The three-state toric homogeneous Markov chain model has Markov
degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June.
Elsevier, pp. 285–296, 2015.
ista: Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov
degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.
mla: Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov
Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June,
Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.
short: P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.
date_created: 2018-12-11T11:55:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:54:35Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jsc.2014.09.014
issue: May-June
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.0077
month: '05'
oa: 1
oa_version: Preprint
page: 285 - 296
publication: Journal of Symbolic Computation
publication_status: published
publisher: Elsevier
publist_id: '5082'
quality_controlled: '1'
scopus_import: 1
status: public
title: The three-state toric homogeneous Markov chain model has Markov degree two
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68/Part 2
year: '2015'
...
---
_id: '2006'
abstract:
- lang: eng
text: 'The monotone secant conjecture posits a rich class of polynomial systems,
all of whose solutions are real. These systems come from the Schubert calculus
on flag manifolds, and the monotone secant conjecture is a compelling generalization
of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko).
We present some theoretical evidence for this conjecture, as well as computational
evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of
the phenomena we observed in our data. '
article_processing_charge: No
author:
- first_name: Nicolas
full_name: Hein, Nicolas
last_name: Hein
- first_name: Christopher
full_name: Hillar, Christopher
last_name: Hillar
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
- first_name: Zach
full_name: Teitler, Zach
last_name: Teitler
citation:
ama: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone
secant conjecture in the real Schubert calculus. Experimental Mathematics.
2015;24(3):261-269. doi:10.1080/10586458.2014.980044
apa: Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler,
Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental
Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044
chicago: Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank
Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.
ieee: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler,
“The monotone secant conjecture in the real Schubert calculus,” Experimental
Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.
ista: Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015.
The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics.
24(3), 261–269.
mla: Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert
Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis,
2015, pp. 261–69, doi:10.1080/10586458.2014.980044.
short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler,
Experimental Mathematics 24 (2015) 261–269.
date_created: 2018-12-11T11:55:10Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:54:40Z
day: '23'
department:
- _id: CaUh
doi: 10.1080/10586458.2014.980044
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.3436
month: '06'
oa: 1
oa_version: Preprint
page: 261 - 269
publication: Experimental Mathematics
publication_status: published
publisher: Taylor & Francis
publist_id: '5070'
quality_controlled: '1'
scopus_import: 1
status: public
title: The monotone secant conjecture in the real Schubert calculus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '2008'
abstract:
- lang: eng
text: The paper describes a generalized iterative proportional fitting procedure
that can be used for maximum likelihood estimation in a special class of the general
log-linear model. The models in this class, called relational, apply to multivariate
discrete sample spaces that do not necessarily have a Cartesian product structure
and may not contain an overall effect. When applied to the cell probabilities,
the models without the overall effect are curved exponential families and the
values of the sufficient statistics are reproduced by the MLE only up to a constant
of proportionality. The paper shows that Iterative Proportional Fitting, Generalized
Iterative Scaling, and Improved Iterative Scaling fail to work for such models.
The algorithm proposed here is based on iterated Bregman projections. As a by-product,
estimates of the multiplicative parameters are also obtained. An implementation
of the algorithm is available as an R-package.
acknowledgement: Part of the material presented here was contained in the PhD thesis
of the first author to which the second author and Thomas Richardson were advisers.
The authors wish to thank him for several comments and suggestions. We also thank
the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1
uses the idea of Olga Klimova, to whom the authors are also indebted. The second
author was supported in part by Grant K-106154 from the Hungarian National Scientific
Research Fund (OTKA).
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian
Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139
apa: Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential
families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139
chicago: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential
Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.
ieee: A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,”
Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847,
2015.
ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families.
Scandinavian Journal of Statistics. 42(3), 832–847.
mla: Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.”
Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47,
doi:10.1111/sjos.12139.
short: A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.
date_created: 2018-12-11T11:55:11Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:54:41Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/sjos.12139
intvolume: ' 42'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3282
month: '09'
oa: 1
oa_version: Preprint
page: 832 - 847
publication: Scandinavian Journal of Statistics
publication_status: published
publisher: Wiley
publist_id: '5068'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative scaling in curved exponential families
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '2014'
abstract:
- lang: eng
text: The concepts of faithfulness and strong-faithfulness are important for statistical
learning of graphical models. Graphs are not sufficient for describing the association
structure of a discrete distribution. Hypergraphs representing hierarchical log-linear
models are considered instead, and the concept of parametric (strong-) faithfulness
with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence
of uniformly consistent parameter estimators and enables building uniformly consistent
procedures for a hypergraph search. The strength of association in a discrete
distribution can be quantified with various measures, leading to different concepts
of strong-faithfulness. Lower and upper bounds for the proportions of distributions
that do not satisfy strong-faithfulness are computed for different parameterizations
and measures of association.
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete
distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72.
doi:10.1016/j.csda.2015.01.017
apa: Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs
from discrete distributions. Computational Statistics & Data Analysis.
Elsevier. https://doi.org/10.1016/j.csda.2015.01.017
chicago: Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning
Hypergraphs from Discrete Distributions.” Computational Statistics & Data
Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.
ieee: A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs
from discrete distributions,” Computational Statistics & Data Analysis,
vol. 87, no. 7. Elsevier, pp. 57–72, 2015.
ista: Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from
discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.
mla: Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete
Distributions.” Computational Statistics & Data Analysis, vol. 87,
no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.
short: A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis
87 (2015) 57–72.
date_created: 2018-12-11T11:55:13Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:54:43Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.csda.2015.01.017
intvolume: ' 87'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.6617
month: '07'
oa: 1
oa_version: Preprint
page: 57 - 72
publication: Computational Statistics & Data Analysis
publication_status: published
publisher: Elsevier
publist_id: '5062'
quality_controlled: '1'
scopus_import: 1
status: public
title: Faithfulness and learning hypergraphs from discrete distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2015'
...
---
_id: '2025'
abstract:
- lang: eng
text: Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular
trafficking. Among them, the Rab, Arf, and Rho families function in successive
steps of vesicle transport, in forming vesicles from donor membranes, directing
vesicle trafficking toward target membranes and docking vesicles onto target membranes.
These proteins act as molecular switches that are controlled by a cycle of GTP
binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs)
and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs
in the regulation of the endocytic pathway using fluorescently labeled yeast mating
pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion
of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of
fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells
show defective α-factor binding to the cell surface. Interestingly, Ste2p, the
α-factor receptor, was mis-localized from the plasma membrane to the vacuole in
glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent
function, as well as the GAP activity, of Glo3p is important for both α-factor
binding and Ste2p localization at the cell surface. Additionally, we found that
deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi
compartments and causes a defect in transport from the TGN to the plasma membrane.
Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN
transport pathway, but not in the early endosome-to-TGN transport pathway. These
findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell
surface proteins.
author:
- first_name: Daiki
full_name: Kawada, Daiki
last_name: Kawada
- first_name: Hiromu
full_name: Kobayashi, Hiromu
last_name: Kobayashi
- first_name: Tsuyoshi
full_name: Tomita, Tsuyoshi
last_name: Tomita
- first_name: Eisuke
full_name: Nakata, Eisuke
last_name: Nakata
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshimaa, Jiro
last_name: Toshimaa
citation:
ama: Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required
for the endocytic recycling of cell surface proteins. Biochimica et Biophysica
Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009
apa: Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D.
E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular
Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009
chicago: Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto
Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP
Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica
et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.
ieee: D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic
recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.
ista: Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima
J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling
of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research.
1853(1), 144–156.
mla: Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic
Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular
Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.
short: D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus,
J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research
1853 (2015) 144–156.
date_created: 2018-12-11T11:55:17Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:48Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1016/j.bbamcr.2014.10.009
file:
- access_level: open_access
checksum: 5bb328edebb6a91337cadd7d63f961b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:18Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4936'
file_name: IST-2016-615-v1+1_BBAMCR.pdf
file_size: 926685
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 1853'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Submitted Version
page: 144 - 156
publication: Biochimica et Biophysica Acta - Molecular Cell Research
publication_status: published
publisher: Elsevier
publist_id: '5047'
pubrep_id: '615'
quality_controlled: '1'
scopus_import: 1
status: public
title: The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface
proteins
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1853
year: '2015'
...
---
_id: '2030'
abstract:
- lang: eng
text: A hybrid-parallel direct-numerical-simulation method with application to turbulent
Taylor-Couette flow is presented. The Navier-Stokes equations are discretized
in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial
and azimuthal directions, and high-order finite differences in the radial direction.
Time is advanced by a second-order, semi-implicit projection scheme, which requires
the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders
very small slip velocities. Nonlinear terms are evaluated with the pseudospectral
method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared
with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node
communications and MPI overhead that become relevant at high processor-core counts,
and helps to contain the memory footprint. A strong scaling study shows that the
hybrid code maintains scalability up to more than 20,000 processor cores and thus
allows to perform simulations at higher resolutions than previously feasible.
In particular, it opens up the possibility to simulate turbulent Taylor-Couette
flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence
in Keplerian flows in experimentally relevant regimes.
author:
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Markus
full_name: Rampp, Markus
last_name: Rampp
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow. Computers
and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021
apa: Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel
implementation for pseudospectral simulations with application to Taylor-Couette
flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021
chicago: Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP
Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette
Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.
ieee: L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow,” Computers
and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.
ista: Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation
for pseudospectral simulations with application to Taylor-Couette flow. Computers
and Fluids. 106(1), 1–11.
mla: Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral
Simulations with Application to Taylor-Couette Flow.” Computers and Fluids,
vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.
short: L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.
date_created: 2018-12-11T11:55:18Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:51Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.compfluid.2014.09.021
intvolume: ' 106'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1311.2481
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 11
publication: Computers and Fluids
publication_status: published
publisher: Elsevier
publist_id: '5042'
quality_controlled: '1'
scopus_import: 1
status: public
title: A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations
with application to Taylor-Couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2015'
...
---
_id: '2034'
abstract:
- lang: eng
text: Opacity is a generic security property, that has been defined on (non-probabilistic)
transition systems and later on Markov chains with labels. For a secret predicate,
given as a subset of runs, and a function describing the view of an external observer,
the value of interest for opacity is a measure of the set of runs disclosing the
secret. We extend this definition to the richer framework of Markov decision processes,
where non-deterministicchoice is combined with probabilistic transitions, and
we study related decidability problems with partial or complete observation hypotheses
for the schedulers. We prove that all questions are decidable with complete observation
and ω-regular secrets. With partial observation, we prove that all quantitative
questions are undecidable but the question whether a system is almost surely non-opaquebecomes
decidable for a restricted class of ω-regular secrets, as well as for all ω-regular
secrets under finite-memory schedulers.
author:
- first_name: Béatrice
full_name: Bérard, Béatrice
last_name: Bérard
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathalie
full_name: Sznajder, Nathalie
last_name: Sznajder
citation:
ama: Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision
processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001
apa: Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity
for Markov decision processes. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2014.09.001
chicago: Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic
Opacity for Markov Decision Processes.” Information Processing Letters.
Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001.
ieee: B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov
decision processes,” Information Processing Letters, vol. 115, no. 1.
Elsevier, pp. 52–59, 2015.
ista: Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov
decision processes. Information Processing Letters. 115(1), 52–59.
mla: Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.”
Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59,
doi:10.1016/j.ipl.2014.09.001.
short: B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115
(2015) 52–59.
date_created: 2018-12-11T11:55:20Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:52Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ipl.2014.09.001
ec_funded: 1
intvolume: ' 115'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.4225
month: '01'
oa: 1
oa_version: Preprint
page: 52 - 59
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: ' Information Processing Letters'
publication_status: published
publisher: Elsevier
publist_id: '5025'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic opacity for Markov decision processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2015'
...
---
_id: '2035'
abstract:
- lang: eng
text: "Considering a continuous self-map and the induced endomorphism on homology,
we study the eigenvalues and eigenspaces of the latter. Taking a filtration of
representations, we define the persistence of the eigenspaces, effectively introducing
a hierarchical organization of the map. The algorithm that computes this information
for a finite sample is proved to be stable, and to give the correct answer for
a sufficiently dense sample. Results computed with an implementation of the algorithm
provide evidence of its practical utility.\r\n"
acknowledgement: This research is partially supported by the Toposys project FP7-ICT-318493-STREP,
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the Polish National Science Center under Grant
No. N201 419639.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Marian
full_name: Mrozek, Marian
last_name: Mrozek
citation:
ama: Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map.
Foundations of Computational Mathematics. 2015;15(5):1213-1244. doi:10.1007/s10208-014-9223-y
apa: Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2015). The persistent homology
of a self-map. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9223-y
chicago: Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent
Homology of a Self-Map.” Foundations of Computational Mathematics. Springer,
2015. https://doi.org/10.1007/s10208-014-9223-y.
ieee: H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of
a self-map,” Foundations of Computational Mathematics, vol. 15, no. 5.
Springer, pp. 1213–1244, 2015.
ista: Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a
self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.
mla: Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” Foundations
of Computational Mathematics, vol. 15, no. 5, Springer, 2015, pp. 1213–44,
doi:10.1007/s10208-014-9223-y.
short: H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics
15 (2015) 1213–1244.
date_created: 2018-12-11T11:55:20Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:54:53Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s10208-014-9223-y
ec_funded: 1
file:
- access_level: open_access
checksum: 3566f3a8b0c1bc550e62914a88c584ff
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:10Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4670'
file_name: IST-2016-486-v1+1_s10208-014-9223-y.pdf
file_size: 1317546
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '5'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1213 - 1244
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '5022'
pubrep_id: '486'
quality_controlled: '1'
scopus_import: 1
status: public
title: The persistent homology of a self-map
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: 15
year: '2015'
...
---
_id: '13392'
abstract:
- lang: eng
text: The chemical behaviour of molecules can be significantly modified by confinement
to volumes comparable to the dimensions of the molecules. Although such confined
spaces can be found in various nanostructured materials, such as zeolites, nanoporous
organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of
molecules in and out of these materials has greatly hampered studying the effect
of confinement on their physicochemical properties. Here, we show that this diffusion
limitation can be overcome by reversibly creating and destroying confined environments
by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals
functionalized with light-responsive ligands that readily self-assemble and trap
various molecules from the surrounding bulk solution. Once trapped, these molecules
can undergo chemical reactions with increased rates and with stereoselectivities
significantly different from those in bulk solution. Illumination with visible
light disassembles these nanoflasks, releasing the product in solution and thereby
establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying
chemical reactivities in confined environments and for synthesizing molecules
that are otherwise hard to achieve in bulk solution.
article_processing_charge: No
article_type: original
author:
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Soumyo
full_name: Sen, Soumyo
last_name: Sen
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Michał
full_name: Sawczyk, Michał
last_name: Sawczyk
- first_name: Kristina
full_name: Kučanda, Kristina
last_name: Kučanda
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Ji-Woong
full_name: Lee, Ji-Woong
last_name: Lee
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction
acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology.
2015;11:82-88. doi:10.1038/nnano.2015.256
apa: Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D.,
… Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically
self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256
chicago: Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda,
Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible
Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.”
Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256.
ieee: H. Zhao et al., “Reversible trapping and reaction acceleration within
dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11.
Springer Nature, pp. 82–88, 2015.
ista: Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK,
Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration
within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88.
mla: Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically
Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature,
2015, pp. 82–88, doi:10.1038/nnano.2015.256.
short: H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K.
Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.
date_created: 2023-08-01T09:44:04Z
date_published: 2015-11-23T00:00:00Z
date_updated: 2023-08-07T12:55:46Z
day: '23'
doi: 10.1038/nnano.2015.256
extern: '1'
external_id:
pmid:
- '26595335'
intvolume: ' 11'
keyword:
- Electrical and Electronic Engineering
- Condensed Matter Physics
- General Materials Science
- Biomedical Engineering
- Atomic and Molecular Physics
- and Optics
- Bioengineering
language:
- iso: eng
month: '11'
oa_version: None
page: 82-88
pmid: 1
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible trapping and reaction acceleration within dynamically self-assembling
nanoflasks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '13393'
abstract:
- lang: eng
text: Precise control of the self-assembly of selected components within complex
mixtures is a challenging goal whose realization is important for fabricating
novel nanomaterials. Herein we show that by decorating the surfaces of metallic
nanoparticles with differently substituted azobenzenes, it is possible to modulate
the wavelength of light at which the self-assembly of these nanoparticles is induced.
Exposing a mixture of two types of nanoparticles, each functionalized with a different
azobenzene, to UV or blue light induces the selective self-assembly of only one
type of nanoparticles. Irradiation with the other wavelength triggers the disassembly
of the aggregates, and the simultaneous self-assembly of nanoparticles of the
other type. By placing both types of azobenzenes on the same nanoparticles, we
created unique materials (“frustrated” nanoparticles) whose self-assembly is induced
irrespective of the wavelength of the incident light.
article_processing_charge: No
article_type: original
author:
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Thumu
full_name: Udayabhaskararao, Thumu
last_name: Udayabhaskararao
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly
of nanoparticles using differently substituted azobenzenes. Angewandte Chemie
International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419
apa: Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal
light-induced self-assembly of nanoparticles using differently substituted azobenzenes.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419
chicago: Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal
Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.”
Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419.
ieee: D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced
self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte
Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.
ista: Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced
self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte
Chemie International Edition. 54(42), 12394–12397.
mla: Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles
Using Differently Substituted Azobenzenes.” Angewandte Chemie International
Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419.
short: D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International
Edition 54 (2015) 12394–12397.
date_created: 2023-08-01T09:44:19Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2023-08-07T12:58:29Z
day: '01'
doi: 10.1002/anie.201502419
extern: '1'
external_id:
pmid:
- '25959725'
intvolume: ' 54'
issue: '42'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '10'
oa_version: None
page: 12394-12397
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Orthogonal light-induced self-assembly of nanoparticles using differently substituted
azobenzenes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...
---
_id: '13394'
abstract:
- lang: eng
text: The ability to guide the assembly of nanosized objects reversibly with external
stimuli, in particular light, is of fundamental importance, and it contributes
to the development of applications as diverse as nanofabrication and controlled
drug delivery. However, all the systems described to date are based on nanoparticles
(NPs) that are inherently photoresponsive, which makes their preparation cumbersome
and can markedly hamper their performance. Here we describe a conceptually new
methodology to assemble NPs reversibly using light that does not require the particles
to be functionalized with light-responsive ligands. Our strategy is based on the
use of a photoswitchable medium that responds to light in such a way that it modulates
the interparticle interactions. NP assembly proceeds quantitatively and without
apparent fatigue, both in solution and in gels. Exposing the gels to light in
a spatially controlled manner allowed us to draw images that spontaneously disappeared
after a specific period of time.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Ron
full_name: Leizrowice, Ron
last_name: Leizrowice
- first_name: Baruch
full_name: Margulis, Baruch
last_name: Margulis
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Martin
full_name: Börner, Martin
last_name: Börner
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of
non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303
apa: Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner,
M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive
nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303
chicago: Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao,
Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled
Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry.
Springer Nature, 2015. https://doi.org/10.1038/nchem.2303.
ieee: P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive
nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652,
2015.
ista: Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao
T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive
nanoparticles. Nature Chemistry. 7, 646–652.
mla: Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive
Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52,
doi:10.1038/nchem.2303.
short: P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T.
Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.
date_created: 2023-08-01T09:44:33Z
date_published: 2015-07-20T00:00:00Z
date_updated: 2023-08-07T13:00:15Z
day: '20'
doi: 10.1038/nchem.2303
extern: '1'
external_id:
pmid:
- '26201741'
intvolume: ' 7'
keyword:
- General Chemical Engineering
- General Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 646-652
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-controlled self-assembly of non-photoresponsive nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '13395'
abstract:
- lang: eng
text: Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive
ligands were prepared and shown to respond to these two types of stimuli reversibly
and in an orthogonal fashion. The composition of the coating could be tailored
to yield nanoparticles capable of aggregating exclusively when both UV and CO2
were applied at the same time, analogously to the behaviour of an AND logic gate.
article_processing_charge: No
article_type: original
author:
- first_name: Ji-Woong
full_name: Lee, Ji-Woong
last_name: Lee
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous
action of light and CO2. Chemical Communications. 2015;51(11):2036-2039.
doi:10.1039/c4cc08541h
apa: Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate
under the simultaneous action of light and CO2. Chemical Communications.
Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h
chicago: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate
under the Simultaneous Action of Light and CO2.” Chemical Communications.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h.
ieee: J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under
the simultaneous action of light and CO2,” Chemical Communications, vol.
51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.
ista: Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under
the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.
mla: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate
under the Simultaneous Action of Light and CO2.” Chemical Communications,
vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h.
short: J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.
date_created: 2023-08-01T09:44:48Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-08-07T13:01:53Z
day: '18'
doi: 10.1039/c4cc08541h
extern: '1'
external_id:
pmid:
- '25417754'
intvolume: ' 51'
issue: '11'
keyword:
- Materials Chemistry
- Metals and Alloys
- Surfaces
- Coatings and Films
- General Chemistry
- Ceramics and Composites
- Electronic
- Optical and Magnetic Materials
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C4CC08541H
month: '11'
oa: 1
oa_version: Published Version
page: 2036-2039
pmid: 1
publication: Chemical Communications
publication_identifier:
eissn:
- 1364-548X
issn:
- 1359-7345
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual-responsive nanoparticles that aggregate under the simultaneous action
of light and CO2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2015'
...
---
_id: '13396'
abstract:
- lang: eng
text: 'Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs)
is strongly affected by steric constraints and excitonic coupling between neighboring
chromophores. Therefore, control of the chromophore density is essential for enhancing
and manipulating the photoisomerization yield. We systematically compare two methods
to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate
SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates
and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual
decrease of the chromophore density and enable efficient photoswitching with low-power
light sources. X-ray spectroscopy reveals that coadsorption from solution yields
mixtures with tunable composition. The orientation of the chromophores with respect
to the surface normal changes from a tilted to an upright position with increasing
azobenzene density. For both systems, optical spectroscopy reveals a pronounced
excitonic shift that increases with the chromophore density. In spite of exciting
the optical transition of the monomer, the main spectral change in mixed SAMs
occurs in the excitonic band. In addition, the photoisomerization yield decreases
only slightly by increasing the azobenzene–alkanethiolate density, and we observed
photoswitching even with minor dilutions. Unlike in solution, azobenzene in the
planar SAM can be switched back almost completely by optical excitation from the
cis to the original trans state within a short time scale. These observations
indicate cooperativity in the photoswitching process of mixed SAMs.'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Moldt, Thomas
last_name: Moldt
- first_name: Daniel
full_name: Brete, Daniel
last_name: Brete
- first_name: Daniel
full_name: Przyrembel, Daniel
last_name: Przyrembel
- first_name: Sanjib
full_name: Das, Sanjib
last_name: Das
- first_name: Joel R.
full_name: Goldman, Joel R.
last_name: Goldman
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Cornelius
full_name: Gahl, Cornelius
last_name: Gahl
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Martin
full_name: Weinelt, Martin
last_name: Weinelt
citation:
ama: Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized
azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057.
doi:10.1021/la504291n
apa: Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K.,
… Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature. Langmuir. American Chemical
Society. https://doi.org/10.1021/la504291n
chicago: Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman,
Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the
Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface
Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n.
ieee: T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3.
American Chemical Society, pp. 1048–1057, 2015.
ista: Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn
R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.
mla: Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes
by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3,
American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n.
short: T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl,
R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057.
date_created: 2023-08-01T09:45:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2023-08-07T13:05:04Z
day: '27'
doi: 10.1021/la504291n
extern: '1'
external_id:
pmid:
- '25544061'
intvolume: ' 31'
issue: '3'
keyword:
- Electrochemistry
- Spectroscopy
- Surfaces and Interfaces
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '01'
oa_version: None
page: 1048-1057
pmid: 1
publication: Langmuir
publication_identifier:
eissn:
- 1520-5827
issn:
- 0743-7463
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution
and surface curvature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '13397'
abstract:
- lang: eng
text: Self-assembly of inorganic nanoparticles has been studied extensively for
particles having different sizes and compositions. However, relatively little
attention has been devoted to how the shape and surface chemistry of magnetic
nanoparticles affects their self-assembly properties. Here, we undertook a combined
experiment–theory study aimed at better understanding of the self-assembly of
cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental
parameters, such as the direction of the magnetic field and nanoparticle density,
a variety of superstructures can be obtained, including one-dimensional filaments
and helices, as well as C-shaped assemblies described here for the first time.
Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive
ligands. Using these modified nanoparticles, we were able to achieve orthogonal
control of self-assembly using a magnetic field and light.
article_processing_charge: No
article_type: original
author:
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Henry
full_name: Chan, Henry
last_name: Chan
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Elijah
full_name: Gelman, Elijah
last_name: Gelman
- first_name: Davide
full_name: Peddis, Davide
last_name: Peddis
- first_name: Artem
full_name: Baskin, Artem
last_name: Baskin
- first_name: Gregory
full_name: Leitus, Gregory
last_name: Leitus
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly
of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b
apa: Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin,
A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes.
Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b
chicago: Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide
Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced
Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society
of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b.
ieee: G. Singh et al., “Magnetic field-induced self-assembly of iron oxide
nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry,
pp. 403–421, 2015.
ista: Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus
G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes.
Faraday Discussions. 181, 403–421.
mla: Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide
Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry,
2015, pp. 403–21, doi:10.1039/c4fd00265b.
short: G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin,
G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.
date_created: 2023-08-01T09:45:17Z
date_published: 2015-01-02T00:00:00Z
date_updated: 2023-08-07T13:06:23Z
day: '02'
doi: 10.1039/c4fd00265b
extern: '1'
external_id:
pmid:
- '25920522'
intvolume: ' 181'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C4FD00265B
month: '01'
oa: 1
oa_version: Published Version
page: 403-421
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetic field-induced self-assembly of iron oxide nanocubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2015'
...
---
_id: '13398'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Yugang
full_name: Sun, Yugang
last_name: Sun
- first_name: Leonardo
full_name: Scarabelli, Leonardo
last_name: Scarabelli
- first_name: Nicholas
full_name: Kotov, Nicholas
last_name: Kotov
- first_name: Moritz
full_name: Tebbe, Moritz
last_name: Tebbe
- first_name: Xiao-Min
full_name: Lin, Xiao-Min
last_name: Lin
- first_name: Ward
full_name: Brullot, Ward
last_name: Brullot
- first_name: Lucio
full_name: Isa, Lucio
last_name: Isa
- first_name: Peter
full_name: Schurtenberger, Peter
last_name: Schurtenberger
- first_name: Helmuth
full_name: Moehwald, Helmuth
last_name: Moehwald
- first_name: Igor
full_name: Fedin, Igor
last_name: Fedin
- first_name: Orlin
full_name: Velev, Orlin
last_name: Velev
- first_name: Damien
full_name: Faivre, Damien
last_name: Faivre
- first_name: Christopher
full_name: Sorensen, Christopher
last_name: Sorensen
- first_name: Régine
full_name: Perzynski, Régine
last_name: Perzynski
- first_name: Munish
full_name: Chanana, Munish
last_name: Chanana
- first_name: Zhihai
full_name: Li, Zhihai
last_name: Li
- first_name: Fernando
full_name: Bresme, Fernando
last_name: Bresme
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Emre
full_name: Firlar, Emre
last_name: Firlar
- first_name: David
full_name: Schiffrin, David
last_name: Schiffrin
- first_name: Joao Batista
full_name: Souza Junior, Joao Batista
last_name: Souza Junior
- first_name: Andreas
full_name: Fery, Andreas
last_name: Fery
- first_name: Elena
full_name: Shevchenko, Elena
last_name: Shevchenko
- first_name: Ozgur
full_name: Tarhan, Ozgur
last_name: Tarhan
- first_name: Armand Paul
full_name: Alivisatos, Armand Paul
last_name: Alivisatos
- first_name: Sabrina
full_name: Disch, Sabrina
last_name: Disch
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Suvojit
full_name: Ghosh, Suvojit
last_name: Ghosh
citation:
ama: 'Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process:
General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g'
apa: 'Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., …
Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday
Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g'
chicago: 'Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min
Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General
Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.'
ieee: 'Y. Sun et al., “Field-assisted self-assembly process: General discussion,”
Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479,
2015.'
ista: 'Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger
P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M,
Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko
E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly
process: General discussion. Faraday Discussions. 181, 463–479.'
mla: 'Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.”
Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79,
doi:10.1039/c5fd90041g.'
short: Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa,
P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R.
Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B.
Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R.
Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.
date_created: 2023-08-01T09:45:29Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2023-08-08T07:16:20Z
day: '07'
doi: 10.1039/c5fd90041g
extern: '1'
external_id:
pmid:
- '26149295'
intvolume: ' 181'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 463-479
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Field-assisted self-assembly process: General discussion'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2015'
...
---
_id: '1383'
abstract:
- lang: eng
text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi
network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has
impeded our understanding of how the pH homeostasis within the plant TGN/EE controls
exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3
(det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly
impairing secretion and recycling of the brassinosteroid receptor and the cellulose
synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized
V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency
defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility.
Thus, our results provide strong evidence that acidification of the TGN/EE, but
not of the vacuole, is indispensable for functional secretion and recycling in
plants.
article_number: '15094'
article_processing_charge: No
article_type: original
author:
- first_name: Luo
full_name: Yu, Luo
last_name: Yu
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Anett
full_name: Doering, Anett
last_name: Doering
- first_name: Zhang
full_name: Yi, Zhang
last_name: Yi
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Lutz
full_name: Neumetzler, Lutz
last_name: Neumetzler
- first_name: Praveen
full_name: Krishnamoorthy, Praveen
last_name: Krishnamoorthy
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Volker
full_name: Bischoff, Volker
last_name: Bischoff
- first_name: Samantha
full_name: Vernhettes, Samantha
last_name: Vernhettes
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required
for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7).
doi:10.1038/nplants.2015.94
apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova,
E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94
chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone
Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required
for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2015. https://doi.org/10.1038/nplants.2015.94.
ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis
and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing
Group, 2015.
ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy
P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof
Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE
is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7),
15094.
mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis
and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature
Publishing Group, 2015, doi:10.1038/nplants.2015.94.
short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler,
P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne,
J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants
1 (2015).
date_created: 2018-12-11T11:51:42Z
date_published: 2015-07-06T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '06'
department:
- _id: JiFr
doi: 10.1038/nplants.2015.94
external_id:
pmid:
- '27250258'
intvolume: ' 1'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5827'
quality_controlled: '1'
scopus_import: 1
status: public
title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in
Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '1399'
abstract:
- lang: eng
text: This thesis is concerned with the computation and approximation of intrinsic
volumes. Given a smooth body M and a certain digital approximation of it, we develop
algorithms to approximate various intrinsic volumes of M using only measurements
taken from its digital approximations. The crucial idea behind our novel algorithms
is to link the recent theory of persistent homology to the theory of intrinsic
volumes via the Crofton formula from integral geometry and, in particular, via
Euler characteristic computations. Our main contributions are a multigrid convergent
digital algorithm to compute the first intrinsic volume of a solid body in R^n
as well as an appropriate integration pipeline to approximate integral-geometric
integrals defined over the Grassmannian manifold.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. On the approximation of intrinsic volumes. 2015.
apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute
of Science and Technology Austria.
chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute
of Science and Technology Austria, 2015.
ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science
and Technology Austria, 2015.
ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of
Science and Technology Austria.
mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute
of Science and Technology Austria, 2015.
short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
and Technology Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
language:
- iso: eng
month: '06'
oa_version: None
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5808'
related_material:
record:
- id: '1662'
relation: part_of_dissertation
status: public
- id: '1792'
relation: part_of_dissertation
status: public
- id: '2255'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: On the approximation of intrinsic volumes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...