---
_id: '8228'
abstract:
- lang: eng
text: "Background: Atopics have a lower risk for malignancies, and IgE targeted
to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or
adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective:
We aimed to investigate the effects of active and passive immunotherapy to the
tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor
expression affecting the levels of expressed IgE.\r\nMethods: We compared the
levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b,
IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic
domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1
mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated
serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2
mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle
control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated
with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults:
Overall, among the three strains of mice, HER-2 vaccination induced significantly
higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2
mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged
the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment
controls; active vaccination provided the highest benefit. Notably, untreated
high-IgE KN1 mice displayed the longest survival of all strains, which could not
be further extended by active or passive immunotherapy.\r\nConclusion: Active
and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice
engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit
following tumor challenge."
article_number: '100044'
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
orcid: 0000-0002-8701-2412
- first_name: Gertrude
full_name: Achatz-Straussberger, Gertrude
last_name: Achatz-Straussberger
- first_name: Anna
full_name: Bentley-Lukschal, Anna
last_name: Bentley-Lukschal
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Gernot
full_name: Achatz, Gernot
last_name: Achatz
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology:
High innate IgE levels are decisive for the survival of cancer-bearing mice. World
Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044'
apa: 'Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz,
G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High
innate IgE levels are decisive for the survival of cancer-bearing mice. World
Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044'
chicago: 'Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit
Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology:
High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.”
World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.'
ieee: 'J. Singer et al., “AllergoOncology: High innate IgE levels are decisive
for the survival of cancer-bearing mice,” World Allergy Organization Journal,
vol. 12, no. 7. Elsevier, 2019.'
ista: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G,
Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels
are decisive for the survival of cancer-bearing mice. World Allergy Organization
Journal. 12(7), 100044.'
mla: 'Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive
for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal,
vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.'
short: J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz,
S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).
date_created: 2020-08-10T11:50:54Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2021-01-12T08:17:36Z
day: '29'
doi: 10.1016/j.waojou.2019.100044
extern: '1'
intvolume: ' 12'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.waojou.2019.100044
month: '07'
oa: 1
oa_version: Published Version
publication: World Allergy Organization Journal
publication_identifier:
issn:
- 1939-4551
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing
mice'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2019'
...
---
_id: '8229'
abstract:
- lang: eng
text: Food proteins may get nitrated by various exogenous or endogenous mechanisms.
As individuals might get recurrently exposed to nitrated proteins via daily diet,
we aimed to investigate the effect of repeatedly ingested nitrated food proteins
on the subsequent immune response in non-allergic and allergic mice using the
milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model.
Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine
(3-NT) in extracts of different foods and in stomach content extracts of non-allergic
mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited
enhanced susceptibility to degradation in simulated gastric fluid experiments
compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased
interferon-γ and interleukin-10 release of stimulated spleen cells and led to
the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages
of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic
mice receiving BLGu. Regardless of the preceding immune status, non-allergic or
allergic, repeatedly ingested nitrated food proteins seem to considerably influence
the subsequent immune response.
article_number: '2463'
article_processing_charge: No
article_type: original
author:
- first_name: Anna S.
full_name: Ondracek, Anna S.
last_name: Ondracek
orcid: 0000-0001-7625-3651
- first_name: Denise
full_name: Heiden, Denise
last_name: Heiden
- first_name: Gertie J.
full_name: Oostingh, Gertie J.
last_name: Oostingh
- first_name: Elisabeth
full_name: Fuerst, Elisabeth
last_name: Fuerst
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Cornelia
full_name: Bergmayr, Cornelia
last_name: Bergmayr
- first_name: Johanna
full_name: Rohrhofer, Johanna
last_name: Rohrhofer
orcid: 0000-0002-2783-2099
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
orcid: 0000-0003-4019-5765
- first_name: Albert
full_name: Duschl, Albert
last_name: Duschl
orcid: 0000-0002-7034-9860
- first_name: Eva
full_name: Untersmayr, Eva
last_name: Untersmayr
orcid: 0000-0002-1963-499X
citation:
ama: Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food
allergen beta-lactoglobulin in an experimental food allergy model. Nutrients.
2019;11(10). doi:10.3390/nu11102463
apa: Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr,
C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin
in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463
chicago: Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst,
Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert
Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin
in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463.
ieee: A. S. Ondracek et al., “Immune effects of the nitrated food allergen
beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol.
11, no. 10. MDPI, 2019.
ista: Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer
J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated
food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients.
11(10), 2463.
mla: Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin
in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463,
MDPI, 2019, doi:10.3390/nu11102463.
short: A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr,
J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019).
date_created: 2020-08-10T11:51:04Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2021-01-12T08:17:36Z
day: '15'
doi: 10.3390/nu11102463
extern: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3390/nu11102463
month: '10'
oa: 1
oa_version: Published Version
publication: Nutrients
publication_identifier:
issn:
- 2072-6643
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental
food allergy model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2019'
...
---
_id: '8227'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Kristina M.
full_name: Ilieva, Kristina M.
last_name: Ilieva
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Heather J.
full_name: Bax, Heather J.
last_name: Bax
- first_name: Silvia
full_name: Crescioli, Silvia
last_name: Crescioli
- first_name: Laura
full_name: Montero‐Morales, Laura
last_name: Montero‐Morales
- first_name: Silvia
full_name: Mele, Silvia
last_name: Mele
- first_name: Heng Sheng
full_name: Sow, Heng Sheng
last_name: Sow
- first_name: Chara
full_name: Stavraka, Chara
last_name: Stavraka
- first_name: Debra H.
full_name: Josephs, Debra H.
last_name: Josephs
- first_name: James F.
full_name: Spicer, James F.
last_name: Spicer
- first_name: Herta
full_name: Steinkellner, Herta
last_name: Steinkellner
orcid: 0000-0003-4823-1505
- first_name: Erika
full_name: Jensen‐Jarolim, Erika
last_name: Jensen‐Jarolim
orcid: 0000-0003-4019-5765
- first_name: Andrew N. J.
full_name: Tutt, Andrew N. J.
last_name: Tutt
orcid: 0000-0001-8715-2901
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
orcid: 0000-0002-4100-7810
citation:
ama: 'Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development
and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989.
doi:10.1111/all.13818'
apa: 'Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L.,
Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development
and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley.
https://doi.org/10.1111/all.13818'
chicago: 'Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura
Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression
Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy.
Wiley, 2019. https://doi.org/10.1111/all.13818.'
ieee: 'K. M. Ilieva et al., “AllergoOncology: Expression platform development
and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74,
no. 10. Wiley, pp. 1985–1989, 2019.'
ista: 'Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow
HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt
ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and
functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989.'
mla: 'Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development
and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74,
no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.'
short: K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele,
H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim,
A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989.
date_created: 2020-08-10T11:50:42Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2021-01-12T08:17:35Z
day: '01'
doi: 10.1111/all.13818
extern: '1'
intvolume: ' 74'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/all.13818
month: '10'
oa: 1
oa_version: Published Version
page: 1985-1989
publication: Allergy
publication_identifier:
issn:
- 0105-4538
- 1398-9995
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'AllergoOncology: Expression platform development and functional profiling
of an anti‐HER2 IgE antibody'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2019'
...
---
_id: '8263'
abstract:
- lang: eng
text: "Background: The genus Streptococcus comprises pathogens that strongly influence
the health of humans and animals. Genome sequencing of multiple Streptococcus
strains demonstrated high variability in gene content and order even in closely
related strains of the same species and created a newly emerged object for genomic
analysis, the pan-genome. Here we analysed the genome evolution of 25 strains
of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of
Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique,
periphery, and universal genes differ in size, functional composition, the level
of nucleotide substitutions, and predisposition to horizontal gene transfer and
genomic rearrangements. The density of substitutions in intergenic regions appears
to be correlated with selection acting on adjacent genes, implying that more conserved
genes tend to have more conserved regulatory regions.\r\nThe total pan-genome
of the genus is open, but only due to strain-specific genes, whereas other pan-genome
fractions reach saturation. We have identified the set of genes with phylogenies
inconsistent with species and non-conserved location in the chromosome; these
genes are rare in at least one species and have likely experienced recent horizontal
transfer between species. The strain-specific fraction is enriched with mobile
elements and hypothetical proteins, but also contains a number of candidate virulence-related
genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping
the rearrangements to the phylogenetic tree revealed large parallel inversions
in all species. A parallel inversion of length 15 kB with breakpoints formed by
genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to
replacement of gene fragments that likely indicates the action of an antigen variation
mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic,
open pan-genome, that potentially confers them with the ability to adapt to changing
environmental conditions, i.e. antibiotic resistance or transmission between different
hosts. Hence, integrated analysis of all aspects of genome evolution is important
for the identification of potential pathogens and design of drugs and vaccines."
article_number: '83'
article_processing_charge: No
article_type: original
author:
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
orcid: 0000-0003-0120-9319
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Anna A.
full_name: Karan, Anna A.
last_name: Karan
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three
Streptococcus species: Selection, antigenic variation, and horizontal gene inflow.
BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6'
apa: 'Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019).
Micro-evolution of three Streptococcus species: Selection, antigenic variation,
and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature.
https://doi.org/10.1186/s12862-019-1403-6'
chicago: 'Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand.
“Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation,
and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature,
2019. https://doi.org/10.1186/s12862-019-1403-6.'
ieee: 'P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution
of three Streptococcus species: Selection, antigenic variation, and horizontal
gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.'
ista: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of
three Streptococcus species: Selection, antigenic variation, and horizontal gene
inflow. BMC Evolutionary Biology. 19, 83.'
mla: 'Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species:
Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary
Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.'
short: P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary
Biology 19 (2019).
date_created: 2020-08-15T11:04:07Z
date_published: 2019-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:54Z
day: '27'
doi: 10.1186/s12862-019-1403-6
extern: '1'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12862-019-1403-6
month: '03'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_identifier:
issn:
- 1471-2148
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Micro-evolution of three Streptococcus species: Selection, antigenic variation,
and horizontal gene inflow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2019'
...
---
_id: '8296'
abstract:
- lang: eng
text: While showing great promise, smart contracts are difficult to program correctly,
as they need a deep understanding of cryptography and distributed algorithms,
and offer limited functionality, as they have to be deterministic and cannot operate
on secret data. In this paper we present Protean, a general-purpose decentralized
computing platform that addresses these limitations by moving from a monolithic
execution model, where all participating nodes store all the state and execute
every computation, to a modular execution-model. Protean employs secure specialized
modules, called functional units, for building decentralized applications that
are currently insecure or impossible to implement with smart contracts. Each functional
unit is a distributed system that provides a special-purpose functionality by
exposing atomic transactions to the smart-contract developer. Combining these
transactions into arbitrarily-defined workflows, developers can build a larger
class of decentralized applications, such as provably-secure and fair lotteries
or e-voting.
article_processing_charge: No
author:
- first_name: Enis Ceyhun
full_name: Alp, Enis Ceyhun
last_name: Alp
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Georgia
full_name: Fragkouli, Georgia
last_name: Fragkouli
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose
decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating
Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448'
apa: 'Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking
general-purpose decentralized computing. In Proceedings of the Workshop on
Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448'
chicago: Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan
Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings
of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448.
ieee: E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose
decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating
Systems, Bertinoro, Italy, 2019, pp. 105–112.
ista: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose
decentralized computing. Proceedings of the Workshop on Hot Topics in Operating
Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.'
mla: Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.”
Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019,
pp. 105–12, doi:10.1145/3317550.3321448.
short: E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the
Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112.
conference:
end_date: 2019-05-15
location: Bertinoro, Italy
name: 'HotOS: Workshop on Hot Topics in Operating Systems'
start_date: 2019-05-13
date_created: 2020-08-26T11:45:45Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:56Z
day: '01'
doi: 10.1145/3317550.3321448
extern: '1'
language:
- iso: eng
month: '05'
oa_version: None
page: 105-112
publication: Proceedings of the Workshop on Hot Topics in Operating Systems
publication_identifier:
isbn:
- '9781450367271'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rethinking general-purpose decentralized computing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8304'
abstract:
- lang: eng
text: "Enabling secure communication across distributed systems is usually studied
under the assumption of trust between the different systems and an external adversary
trying to compromise the messages. With the appearance of distributed ledgers
or blockchains, numerous protocols have emerged, which attempt to achieve trustless
communication between distrusting ledgers and participants. Cross-chain communication
(CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding,
bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately,
existing proposals are designed ad-hoc for specific use-cases, making it hard
to gain confidence on their correctness and composability.\r\nWe provide the first
systematic exposition of protocols for CCC. First, we formalize the underlying
research problem and show that CCC is impossible without a trusted third party,
contrary to common beliefs in the blockchain community. We then develop a framework
to evaluate existing and to design new cross-chain protocols. The framework is
based on the use case, the trust model, and the security assumptions of interlinked
blockchains. Finally, we identify security and privacy challenges faced by protocols
in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers
a comprehensive guide for designing protocols bridging the numerous distributed
ledgers available today. It aims to facilitate clearer communication between academia
and industry in the field."
article_number: 2019/1128
article_processing_charge: No
author:
- first_name: Alexei
full_name: Zamyatin, Alexei
last_name: Zamyatin
- first_name: Mustafa
full_name: Al-Bassam, Mustafa
last_name: Al-Bassam
- first_name: Dionysis
full_name: Zindros, Dionysis
last_name: Zindros
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Pedro
full_name: Moreno-Sanchez, Pedro
last_name: Moreno-Sanchez
- first_name: Aggelos
full_name: Kiayias, Aggelos
last_name: Kiayias
- first_name: William J.
full_name: Knottenbelt, William J.
last_name: Knottenbelt
citation:
ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed
ledgers. Cryptology ePrint Archive.'
apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez,
P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed
ledgers. Cryptology ePrint Archive.'
chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris
Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK:
Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.'
ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,”
Cryptology ePrint Archive. .'
ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias
A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint
Archive, 2019/1128.'
mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.”
Cryptology EPrint Archive, 2019/1128.'
short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez,
A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.).
date_created: 2020-08-26T12:16:38Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2021-09-24T12:08:14Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://eprint.iacr.org/2019/1128 '
month: '10'
oa: 1
oa_version: Preprint
publication: Cryptology ePrint Archive
publication_status: submitted
status: public
title: 'SoK: Communication across distributed ledgers'
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8303'
abstract:
- lang: eng
text: 'ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol
used as a building block of many research and enterprise-level decentralized systems.
In this paper, we show that ByzCoin is unsuitable for deployment in an anopen,
adversarial network and instead introduceMOTOR. MOTORis designed as a secure,
robust, and scalable consensus suitable for permissionless sharded blockchains.
MOTORachieves these properties by making four key design choices: (a) it prioritizes
robustness in adversarial environments while maintaining adequate scalability,
(b) it employees provably correct cryptography that resists DoS attacks from individual
nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive
adversaries and prevents censorship, and (d) it creates an incentive compatible
reward mechanism. These choices are materialized as (a) a “rotating subleader”
communication pattern that balances the scalability needs with the robustness
requirements under failures, (b) deployment of provable secure BLS multi-signatures,
(c) use of deterministic thresh-old signatures as a source of randomness and (d)
careful design of the reward allocation mechanism. We have implemented MOTORand
compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an
at most2xoverhead whereas it maintains good performance even under high-percentage
of faults, unlike ByzCoin.'
article_number: 2019/676
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers.
Cryptology ePrint Archive.
apa: Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed
ledgers. Cryptology ePrint Archive.
chicago: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded
Distributed Ledgers.” Cryptology EPrint Archive, n.d.
ieee: E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed
ledgers,” Cryptology ePrint Archive. .
ista: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers.
Cryptology ePrint Archive, 2019/676.
mla: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed
Ledgers.” Cryptology EPrint Archive, 2019/676.
short: E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).
date_created: 2020-08-26T12:13:56Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2021-09-24T12:07:11Z
day: '06'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/676
month: '06'
oa: 1
oa_version: Preprint
publication: Cryptology ePrint Archive
publication_status: submitted
status: public
title: Robust and scalable consensus for sharded distributed ledgers
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8311'
abstract:
- lang: eng
text: 'One of the core promises of blockchain technology is that of enabling trustworthy
data dissemination in a trustless environment. What current blockchain systems
deliver, however, is slow dissemination of public data, rendering blockchain technology
unusable in settings where latency, transaction capacity, or data confidentiality
are important. In this thesis we focus on providing solutions on two of the most
pressing problems blockchain technology currently faces: scalability and data
confidentiality. To address the scalability issue, we present OMNILEDGER, a novel
scale-out distributed ledger that preserves long-term security under permissionless
operation. It ensures security and correctness by using a bias-resistant public-randomness
protocol for choosing large, statistically representative shards that process
transactions, and by introducing an efficient cross-shard commit protocol that
atomically handles transactions affecting multiple shards. To enable secure sharing
of confidential data we present CALYPSO, the first fully decentralized, auditable
access-control framework for secure blockchain-based data sharing which builds
upon two abstractions. First, on-chain secrets enable collective management of
(verifiably shared) secrets under a Byzantine adversary where an access-control
blockchain enforces user-specific access rules and a secret-management cothority
administers encrypted data. Second, skipchain-based identity and access management
enables efficient administration of dynamic, sovereign identities and access policies
and, in particular, permits clients to maintain long-term relationships with respect
to evolving user identities thanks to the trust-delegating forward links of skipchains.
In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient
decentralization, which are presented in Part II of this dissertation. These tools
can be used in decentralized and distributed systems to achieve (1) scalable consensus
(BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and
(3) relationship-keeping between independently updating communication endpoints
(SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they
can be (and already have been) used in a far wider scope.'
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: Kokoris Kogias E. Secure, confidential blockchains providing high throughput
and low latency. 2019. doi:10.5075/epfl-thesis-7101
apa: Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high
throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101
chicago: Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing
High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019.
https://doi.org/10.5075/epfl-thesis-7101.
ieee: E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput
and low latency,” École Polytechnique Fédérale de Lausanne, 2019.
ista: Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput
and low latency. École Polytechnique Fédérale de Lausanne.
mla: Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing
High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne,
2019, doi:10.5075/epfl-thesis-7101.
short: E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput
and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.
date_created: 2020-08-27T11:22:24Z
date_published: 2019-09-27T00:00:00Z
date_updated: 2021-12-20T15:30:47Z
day: '27'
degree_awarded: PhD
doi: 10.5075/epfl-thesis-7101
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.5075/epfl-thesis-7101
month: '09'
oa: 1
oa_version: Published Version
page: '244'
publication_status: published
publisher: École Polytechnique Fédérale de Lausanne
status: public
supervisor:
- first_name: Bryan Alexander
full_name: Ford, Bryan Alexander
last_name: Ford
title: Secure, confidential blockchains providing high throughput and low latency
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8314'
abstract:
- lang: eng
text: "Off-chain protocols (channels) are a promising solution to the scalability
and privacy challenges of blockchain payments. Current proposals, however, require
synchrony assumptions to preserve the safety of a channel, leaking to an adversary
the exact amount of time needed to control the network for a successful attack.
In this paper, we introduce Brick, the first payment channel that remains secure
under network asynchrony and concurrently provides correct incentives. The core
idea is to incorporate the conflict resolution process within the channel by introducing
a rational committee of external parties, called Wardens. Hence, if a party wants
to close a channel unilaterally, it can only get the committee's approval for
the last valid state. Brick provides sub-second latency because it does not employ
heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce
updates and close the channel, a light-weight abstraction that is powerful enough
to preserve safety and liveness to any rational parties. Furthermore, we consider
permissioned blockchains, where the additional property of auditability might
be desired for regulatory purposes. We introduce Brick+, an off-chain construction
that provides auditability on top of Brick without conflicting with its privacy
guarantees. We formally define the properties our payment channel construction
should fulfill, and prove that both Brick and Brick+ satisfy them. We also design
incentives for Brick such that honest and rational behavior aligns. Finally, we
provide a reference implementation of the smart contracts in Solidity."
article_number: '1905.11360'
article_processing_charge: No
author:
- first_name: Georgia
full_name: Avarikioti, Georgia
last_name: Avarikioti
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Roger
full_name: Wattenhofer, Roger
last_name: Wattenhofer
- first_name: Dionysis
full_name: Zindros, Dionysis
last_name: Zindros
citation:
ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous
payment channels. arXiv.'
apa: 'Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.).
Brick: Asynchronous payment channels. arXiv.'
chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and
Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.'
ieee: 'G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick:
Asynchronous payment channels,” arXiv. .'
ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous
payment channels. arXiv, 1905.11360.'
mla: 'Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv,
1905.11360.'
short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.).
date_created: 2020-08-27T11:36:54Z
date_published: 2019-05-27T00:00:00Z
date_updated: 2021-01-12T08:18:04Z
day: '27'
extern: '1'
external_id:
arxiv:
- '1905.11360'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.11360
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Brick: Asynchronous payment channels'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8315'
abstract:
- lang: eng
text: "Sharding distributed ledgers is the most promising on-chain solution for
scaling blockchain technology. In this work, we define and analyze the properties
a sharded distributed ledger should fulfill. More specifically, we show that a
sharded blockchain cannot be scalable under a fully adaptive adversary, but it
can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible
only if the distributed ledger creates succinct proofs of the valid state updates
at the end of each epoch. Our model builds upon and extends the Bitcoin backbone
protocol by defining consistency and\r\nscalability. Consistency encompasses the
need for atomic execution of cross-shard transactions to preserve safety, whereas
scalability encapsulates the speedup a sharded system can gain in comparison to
a non-sharded system. In\r\norder to show the power of our framework, we analyze
the most prominent sharded blockchains and either prove their correctness (OmniLedger,
RapidChain) under our model or pinpoint where they fail to balance the consistency
and\r\nscalability requirements (Elastico, Monoxide). "
article_number: '1910.10434'
article_processing_charge: No
author:
- first_name: Georgia
full_name: Avarikioti, Georgia
last_name: Avarikioti
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Roger
full_name: Wattenhofer, Roger
last_name: Wattenhofer
citation:
ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization
of distributed ledger sharding protocols. arXiv.'
apa: 'Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and
scale: Formalization of distributed ledger sharding protocols. arXiv.'
chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer.
“Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv,
n.d.'
ieee: 'G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale:
Formalization of distributed ledger sharding protocols,” arXiv. .'
ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization
of distributed ledger sharding protocols. arXiv, 1910.10434.'
mla: 'Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed
Ledger Sharding Protocols.” ArXiv, 1910.10434.'
short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.).
date_created: 2020-08-27T11:37:43Z
date_published: 2019-10-23T00:00:00Z
date_updated: 2021-01-12T08:18:05Z
day: '23'
extern: '1'
external_id:
arxiv:
- '1910.10434'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.10434
month: '10'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Divide and scale: Formalization of distributed ledger sharding protocols'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8313'
abstract:
- lang: eng
text: The present invention concerns a computer-implemented method for secure data
exchange between a sender (A) and a recipient (B), wherein the method is performed
by the sender (A) and comprises encrypting data using a symmetric key k, creating
a write transaction T W , wherein the write transaction T W comprises information
usable to derive the symmetric key k and an access policy identifying the recipient
(B) as being allowed to decrypt the encrypted data, providing the recipient (B)
access to the encrypted data, and sending the write transaction T W to a first
group of servers (AC) for being stored in a blockchain data structure maintained
by the first group of servers (AC).
applicant:
- 'École Polytechnique Fédérale De Lausanne '
article_processing_charge: No
author:
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Janovic, Philipp
last_name: Janovic
citation:
ama: Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure
data exchange. 2019.
apa: Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods
and systems for secure data exchange.
chicago: Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic.
“Methods and Systems for Secure Data Exchange,” 2019.
ieee: B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems
for secure data exchange.” 2019.
ista: Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for
secure data exchange.
mla: Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019.
short: B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019).
date_created: 2020-08-27T11:24:44Z
date_published: 2019-08-22T00:00:00Z
date_updated: 2022-01-05T14:00:32Z
day: '22'
extern: '1'
ipc: G06F21/62 ; H04L9/08 ; H04L9/32
ipn: WO2019158209 (A1)
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/WO2019158209A1
month: '08'
oa: 1
oa_version: Published Version
publication_date: 2019-08-22
status: public
title: Methods and systems for secure data exchange
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '8405'
abstract:
- lang: eng
text: Atomic-resolution structure determination is crucial for understanding protein
function. Cryo-EM and NMR spectroscopy both provide structural information, but
currently cryo-EM does not routinely give access to atomic-level structural data,
and, generally, NMR structure determination is restricted to small (<30 kDa) proteins.
We introduce an integrated structure determination approach that simultaneously
uses NMR and EM data to overcome the limits of each of these methods. The approach
enables structure determination of the 468 kDa large dodecameric aminopeptidase
TET2 to a precision and accuracy below 1 Å by combining secondary-structure information
obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large
subunits, distance restraints from backbone amides and ILV methyl groups, and
a 4.1 Å resolution EM map. The resulting structure exceeds current standards of
NMR and EM structure determination in terms of molecular weight and precision.
Importantly, the approach is successful even in cases where only medium-resolution
cryo-EM data are available.
article_number: '2697'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Leandro F.
full_name: Estrozi, Leandro F.
last_name: Estrozi
- first_name: Charles D.
full_name: Schwieters, Charles D.
last_name: Schwieters
- first_name: Gregory
full_name: Effantin, Gregory
last_name: Effantin
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Elena
full_name: Schmidt, Elena
last_name: Schmidt
- first_name: Rime
full_name: Kerfah, Rime
last_name: Kerfah
- first_name: Guillaume
full_name: Mas, Guillaume
last_name: Mas
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Peter
full_name: Güntert, Peter
last_name: Güntert
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Guy
full_name: Schoehn, Guy
last_name: Schoehn
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
citation:
ama: Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution
structure determination of a half-megadalton enzyme complex. Nature Communications.
2019;10. doi:10.1038/s41467-019-10490-9
apa: Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier,
R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-019-10490-9
chicago: Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin,
Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM
Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.”
Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.
ieee: D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen
AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G,
Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications. 10,
2697.
mla: Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure
Determination of a Half-Megadalton Enzyme Complex.” Nature Communications,
vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.
short: D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier,
A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A.
Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).
date_created: 2020-09-17T10:28:25Z
date_published: 2019-06-19T00:00:00Z
date_updated: 2021-01-12T08:19:03Z
day: '19'
doi: 10.1038/s41467-019-10490-9
extern: '1'
external_id:
pmid:
- '31217444'
intvolume: ' 10'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-019-10490-9
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton
enzyme complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2019'
...
---
_id: '8406'
abstract:
- lang: eng
text: Coordinated conformational transitions in oligomeric enzymatic complexes modulate
function in response to substrates and play a crucial role in enzyme inhibition
and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which
has emerged as a drug target against multiple pathogenic bacteria. Activation
of different ClpPs by inhibitors has been independently reported from drug development
efforts, but no rationale for inhibitor-induced activation has been hitherto proposed.
Using an integrated approach that includes x-ray crystallography, solid- and solution-state
nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration
calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP
active-site serine, mimicking a peptide substrate, and induces a concerted allosteric
activation of the complex. The bortezomib-activated conformation also exhibits
a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric
mechanism, where substrate binding to a single subunit locks ClpP into an active
conformation optimized for chaperone association and protein processive degradation.
article_number: eaaw3818
article_processing_charge: No
article_type: original
author:
- first_name: Jan
full_name: Felix, Jan
last_name: Felix
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Cecile
full_name: Morlot, Cecile
last_name: Morlot
- first_name: Olga
full_name: Abian, Olga
last_name: Abian
- first_name: Irina
full_name: Gutsche, Irina
last_name: Gutsche
- first_name: Adrian
full_name: Velazquez-Campoy, Adrian
last_name: Velazquez-Campoy
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
citation:
ama: Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation
of the ClpP protease machinery by substrates and active-site inhibitors. Science
Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818
apa: Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F.,
… Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease
machinery by substrates and active-site inhibitors. Science Advances. American
Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818
chicago: Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey
Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation
of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science
Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818.
ieee: J. Felix et al., “Mechanism of the allosteric activation of the ClpP
protease machinery by substrates and active-site inhibitors,” Science Advances,
vol. 5, no. 9. American Association for the Advancement of Science, 2019.
ista: Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian
O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric
activation of the ClpP protease machinery by substrates and active-site inhibitors.
Science Advances. 5(9), eaaw3818.
mla: Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease
Machinery by Substrates and Active-Site Inhibitors.” Science Advances,
vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science,
2019, doi:10.1126/sciadv.aaw3818.
short: J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot,
O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances
5 (2019).
date_created: 2020-09-17T10:28:36Z
date_published: 2019-09-04T00:00:00Z
date_updated: 2021-01-12T08:19:03Z
day: '04'
doi: 10.1126/sciadv.aaw3818
extern: '1'
intvolume: ' 5'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1126/sciadv.aaw3818'
month: '09'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Mechanism of the allosteric activation of the ClpP protease machinery by substrates
and active-site inhibitors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2019'
...
---
_id: '8413'
abstract:
- lang: eng
text: NMR relaxation dispersion methods provide a holistic way to observe microsecond
time-scale protein backbone motion both in solution and in the solid state. Different
nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell
and near-rotary-resonance) give complementary information about the amplitudes
and time scales of the conformational dynamics and provide comprehensive insights
into the mechanistic details of the structural rearrangements. In this paper,
we exemplify the benefits of the combination of various solution- and solid-state
relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain),
for which we are able to identify and model the functionally relevant conformational
rearrangements around the ligand recognition loop occurring on multiple microsecond
time scales. The observed loop motions suggest that the SH3 domain exists in a
binding-competent conformation in dynamic equilibrium with a sterically impaired
ground-state conformation both in solution and in crystalline form. This inherent
plasticity between the interconverting macrostates is compatible with a conformational-preselection
model and provides new insights into the recognition mechanisms of SH3 domains.
article_processing_charge: No
article_type: original
author:
- first_name: Petra
full_name: Rovó, Petra
last_name: Rovó
- first_name: Colin A.
full_name: Smith, Colin A.
last_name: Smith
- first_name: Diego
full_name: Gauto, Diego
last_name: Gauto
- first_name: Bert L.
full_name: de Groot, Bert L.
last_name: de Groot
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Rasmus
full_name: Linser, Rasmus
last_name: Linser
citation:
ama: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights
into microsecond time-scale motion of solid proteins using complementary 15N and
1H relaxation dispersion techniques. Journal of the American Chemical Society.
2019;141(2):858-869. doi:10.1021/jacs.8b09258
apa: Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser,
R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins
using complementary 15N and 1H relaxation dispersion techniques. Journal of
the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258
chicago: Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda,
and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of
Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.”
Journal of the American Chemical Society. American Chemical Society, 2019.
https://doi.org/10.1021/jacs.8b09258.
ieee: P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser,
“Mechanistic insights into microsecond time-scale motion of solid proteins using
complementary 15N and 1H relaxation dispersion techniques,” Journal of the
American Chemical Society, vol. 141, no. 2. American Chemical Society, pp.
858–869, 2019.
ista: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic
insights into microsecond time-scale motion of solid proteins using complementary
15N and 1H relaxation dispersion techniques. Journal of the American Chemical
Society. 141(2), 858–869.
mla: Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion
of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.”
Journal of the American Chemical Society, vol. 141, no. 2, American Chemical
Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258.
short: P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal
of the American Chemical Society 141 (2019) 858–869.
date_created: 2020-09-17T10:29:50Z
date_published: 2019-01-08T00:00:00Z
date_updated: 2021-01-12T08:19:07Z
day: '08'
doi: 10.1021/jacs.8b09258
extern: '1'
external_id:
pmid:
- '30620186'
intvolume: ' 141'
issue: '2'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '01'
oa_version: Submitted Version
page: 858-869
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Mechanistic insights into microsecond time-scale motion of solid proteins using
complementary 15N and 1H relaxation dispersion techniques
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2019'
...
---
_id: '8412'
abstract:
- lang: eng
text: Microsecond to millisecond timescale backbone dynamics of the amyloid core
residues in Y145Stop human prion protein (PrP) fibrils were investigated by using
15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance
spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled
the experimental relaxation dispersion profiles for most of the fibril core residues
to be modelled by using a two‐state exchange process with a common exchange rate
of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms,
and an excited‐state population of 2 %. We also found that the relaxation dispersion
profiles for several amino acids positioned near the edges of the most structured
regions of the amyloid core were better modelled by assuming somewhat higher excited‐state
populations (∼5–15 %) and faster exchange rate constants, corresponding to protein
backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of
the core residues were evaluated in the context of the structural model of human
Y145Stop PrP amyloid.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew D.
full_name: Shannon, Matthew D.
last_name: Shannon
- first_name: Theint
full_name: Theint, Theint
last_name: Theint
- first_name: Dwaipayan
full_name: Mukhopadhyay, Dwaipayan
last_name: Mukhopadhyay
- first_name: Krystyna
full_name: Surewicz, Krystyna
last_name: Surewicz
- first_name: Witold K.
full_name: Surewicz, Witold K.
last_name: Surewicz
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Christopher P.
full_name: Jaroniec, Christopher P.
last_name: Jaroniec
citation:
ama: Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the
core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR.
ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779
apa: Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K.,
Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human
Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem.
Wiley. https://doi.org/10.1002/cphc.201800779
chicago: Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz,
Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec.
“Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed
by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779.
ieee: M. D. Shannon et al., “Conformational dynamics in the core of human
Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem,
vol. 20, no. 2. Wiley, pp. 311–317, 2019.
ista: Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda
P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion
protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.
mla: Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop
Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem,
vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779.
short: M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D.
Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.
date_created: 2020-09-17T10:29:43Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:06Z
day: '21'
doi: 10.1002/cphc.201800779
extern: '1'
external_id:
pmid:
- '30276945'
intvolume: ' 20'
issue: '2'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '01'
oa_version: Submitted Version
page: 311-317
pmid: 1
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Conformational dynamics in the core of human Y145Stop prion protein amyloid
probed by relaxation dispersion NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '8411'
abstract:
- lang: eng
text: 'Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales
can provide important insight into protein function. In magic‐angle‐spinning (MAS)
NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion
experiments in different regimes of radio‐frequency field strengths: at low RF
field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type”
relaxation dispersion, while when the RF field approaches rotary resonance conditions
bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance
Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes
to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift
changes, populations and exchange kinetics. We use a numerical simulation procedure
to illustrate these effects and the potential of extracting exchange parameters,
and apply the methodology to the study of a previously described conformational
exchange process in microcrystalline ubiquitin.'
article_processing_charge: No
article_type: original
author:
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Karine
full_name: Giandoreggio-Barranco, Karine
last_name: Giandoreggio-Barranco
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond
protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion
MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935
apa: Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda,
P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance
R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935
chicago: Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco,
and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell
and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem.
Wiley, 2019. https://doi.org/10.1002/cphc.201800935.
ieee: D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda,
“Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance
R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley,
pp. 276–284, 2019.
ista: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond
protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion
MAS NMR. ChemPhysChem. 20(2), 276–284.
mla: Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell
and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem,
vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935.
short: D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem
20 (2019) 276–284.
date_created: 2020-09-17T10:29:36Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:06Z
day: '21'
doi: 10.1002/cphc.201800935
extern: '1'
external_id:
pmid:
- '30444575'
intvolume: ' 20'
issue: '2'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '01'
oa_version: Submitted Version
page: 276-284
pmid: 1
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance
R1p relaxation-dispersion MAS NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '8415'
abstract:
- lang: eng
text: 'We consider billiards obtained by removing three strictly convex obstacles
satisfying the non-eclipse condition on the plane. The restriction of the dynamics
to the set of non-escaping orbits is conjugated to a subshift on three symbols
that provides a natural labeling of all periodic orbits. We study the following
inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of
periodic orbits together with their labeling), determine the geometry of the billiard
table? We show that from the Marked Length Spectrum it is possible to recover
the curvature at periodic points of period two, as well as the Lyapunov exponent
of each periodic orbit.'
article_processing_charge: No
article_type: original
author:
- first_name: Péter
full_name: Bálint, Péter
last_name: Bálint
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Martin
full_name: Leguil, Martin
last_name: Leguil
citation:
ama: Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic
orbits and the geometry of open dispersing billiards. Communications in Mathematical
Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x
apa: Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length
spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications
in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x
chicago: Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked
Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.”
Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x.
ieee: P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum,
homoclinic orbits and the geometry of open dispersing billiards,” Communications
in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575,
2019.
ista: Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum,
homoclinic orbits and the geometry of open dispersing billiards. Communications
in Mathematical Physics. 374(3), 1531–1575.
mla: Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry
of Open Dispersing Billiards.” Communications in Mathematical Physics,
vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x.
short: P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical
Physics 374 (2019) 1531–1575.
date_created: 2020-09-17T10:41:27Z
date_published: 2019-05-09T00:00:00Z
date_updated: 2021-01-12T08:19:08Z
day: '09'
doi: 10.1007/s00220-019-03448-x
extern: '1'
external_id:
arxiv:
- '1809.08947'
intvolume: ' 374'
issue: '3'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.08947
month: '05'
oa: 1
oa_version: Preprint
page: 1531-1575
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Marked length spectrum, homoclinic orbits and the geometry of open dispersing
billiards
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 374
year: '2019'
...
---
_id: '8409'
abstract:
- lang: eng
text: The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer
that maintains the integrity of the bacterial cell. Due to its multi-gigadalton
size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex.
Solid-state NMR is an important technique to gain insight into its structure,
dynamics and interactions. Here, we explore the possibilities to study the PG
with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly
resolved spectra can be obtained, and show strategies to obtain site-specific
resonance assignments and distance information. We also explore the use of proton-proton
correlation experiments, thus opening the way for NMR studies of intact cell walls
without the need for isotope labeling.
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Bougault, Catherine
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial
peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal
of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009
apa: Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019).
Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at
100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009
chicago: Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre,
and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected
NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology.
Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.
ieee: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying
intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz
MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier,
pp. 66–72, 2019.
ista: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact
bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency.
Journal of Structural Biology. 206(1), 66–72.
mla: Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected
NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology,
vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009.
short: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of
Structural Biology 206 (2019) 66–72.
date_created: 2020-09-17T10:29:10Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:05Z
day: '01'
doi: 10.1016/j.jsb.2018.07.009
extern: '1'
external_id:
pmid:
- '30031884'
intvolume: ' 206'
issue: '1'
keyword:
- Structural Biology
language:
- iso: eng
month: '04'
oa_version: Submitted Version
page: 66-72
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy
at 100 kHz MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 206
year: '2019'
...
---
_id: '8407'
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Schanda P. Relaxing with liquids and solids – A perspective on biomolecular
dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025
apa: Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular
dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025
chicago: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular
Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025.
ieee: P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular
dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186,
2019.
ista: Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular
dynamics. Journal of Magnetic Resonance. 306, 180–186.
mla: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular
Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp.
180–86, doi:10.1016/j.jmr.2019.07.025.
short: P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.
date_created: 2020-09-17T10:28:47Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2021-01-12T08:19:04Z
day: '01'
doi: 10.1016/j.jmr.2019.07.025
extern: '1'
external_id:
pmid:
- '31350165'
intvolume: ' 306'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '09'
oa_version: Submitted Version
page: 180-186
pmid: 1
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Relaxing with liquids and solids – A perspective on biomolecular dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 306
year: '2019'
...
---
_id: '8410'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Eduard Y.
full_name: Chekmenev, Eduard Y.
last_name: Chekmenev
citation:
ama: Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177.
doi:10.1002/cphc.201801100
apa: Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem.
Wiley. https://doi.org/10.1002/cphc.201801100
chicago: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem.
Wiley, 2019. https://doi.org/10.1002/cphc.201801100.
ieee: P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem,
vol. 20, no. 2. Wiley, pp. 177–177, 2019.
ista: Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2),
177–177.
mla: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem,
vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100.
short: P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177.
date_created: 2020-09-17T10:29:26Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:05Z
day: '21'
doi: 10.1002/cphc.201801100
extern: '1'
external_id:
pmid:
- '30556633'
intvolume: ' 20'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/cphc.201801100
month: '01'
oa: 1
oa_version: Published Version
page: 177-177
pmid: 1
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: NMR for Biological Systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '8570'
abstract:
- lang: eng
text: 'This report presents the results of a friendly competition for formal verification
of continuous and hybrid systems with linear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been
applied to solve six different benchmark problems in the category for linear continuous
dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx,
and XSpeed. This report is a snapshot of the current landscape of tools and the
types of benchmarks they are particularly suited for. Due to the diversity of
problems, we are not ranking tools, yet the presented results provide one of the
most complete assessments of tools for the safety verification of continuous and
hybrid systems with linear continuous dynamics up to this date.'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Stefan
full_name: Schupp, Stefan
last_name: Schupp
citation:
ama: 'Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w'
apa: 'Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp,
S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40).
Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w'
chicago: 'Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper,
Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report:
Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series
in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.'
ieee: 'M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with linear continuous dynamics,” in EPiC Series in Computing,
Montreal, Canada, 2019, vol. 61, pp. 14–40.'
ista: 'Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp
S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on
Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.'
mla: 'Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol.
61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.'
short: M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling,
S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2020-09-26T14:23:54Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '25'
department:
- _id: ToHe
doi: 10.29007/bj1w
intvolume: ' 61'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://easychair.org/publications/open/1gbP
month: '05'
oa: 1
oa_version: Published Version
page: 14-40
publication: EPiC Series in Computing
publication_identifier:
eissn:
- '23987340'
publication_status: published
publisher: EasyChair
quality_controlled: '1'
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '9016'
abstract:
- lang: eng
text: Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein
interaction (PPI) represents a potential approach for treating numerous cancers.
As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135)
is a strategy through which chemical probes might be elaborated to test this hypothesis.
In this work, variant H3118–135 peptides bearing pentenylglycine residues at the
i and i+4 positions were constrained by olefin metathesis. Biophysical analyses
revealed that promotion of a bioactive helical conformation depends on the position
at which the constraint is introduced, but that the potency of binding towards
ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation
occurs.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Silvia
full_name: Rodriguez‐Marin, Silvia
last_name: Rodriguez‐Marin
- first_name: Zsófia
full_name: Hegedüs, Zsófia
last_name: Hegedüs
- first_name: Marie E.
full_name: Perrin, Marie E.
last_name: Perrin
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
- first_name: Andrew J.
full_name: Wilson, Andrew J.
last_name: Wilson
citation:
ama: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
2019;20(7):891-895. doi:10.1002/cbic.201800633
apa: Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein,
F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained
peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633
chicago: Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin,
Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.
ieee: M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein,
and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,”
ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.
ista: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
20(7), 891–895.
mla: Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.
short: M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein,
A.J. Wilson, ChemBioChem 20 (2019) 891–895.
date_created: 2021-01-19T10:59:14Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-02-23T13:46:48Z
day: '01'
doi: 10.1002/cbic.201800633
extern: '1'
intvolume: ' 20'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1002/cbic.201800633'
month: '04'
oa: 1
oa_version: Published Version
page: 891-895
publication: ChemBioChem
publication_identifier:
issn:
- 1439-4227
- 1439-7633
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Recognition of ASF1 by using hydrocarbon‐constrained peptides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '9060'
abstract:
- lang: eng
text: Molecular motors are essential to the living, generating fluctuations that
boost transport and assist assembly. Active colloids, that consume energy to move,
hold similar potential for man-made materials controlled by forces generated from
within. Yet, their use as a powerhouse in materials science lacks. Here we show
a massive acceleration of the annealing of a monolayer of passive beads by moderate
addition of self-propelled microparticles. We rationalize our observations with
a model of collisions that drive active fluctuations and activate the annealing.
The experiment is quantitatively compared with Brownian dynamic simulations that
further unveil a dynamical transition in the mechanism of annealing. Active dopants
travel uniformly in the system or co-localize at the grain boundaries as a result
of the persistence of their motion. Our findings uncover the potential of internal
activity to control materials and lay the groundwork for the rise of materials
science beyond equilibrium.
article_number: '3380'
article_processing_charge: No
article_type: original
author:
- first_name: Sophie
full_name: Ramananarivo, Sophie
last_name: Ramananarivo
- first_name: Etienne
full_name: Ducrot, Etienne
last_name: Ducrot
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal
monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y
apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled
annealing of colloidal monolayers. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-11362-y
chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled
Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature,
2019. https://doi.org/10.1038/s41467-019-11362-y.
ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing
of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer
Nature, 2019.
ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing
of colloidal monolayers. Nature Communications. 10(1), 3380.
mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.”
Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.
short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).
date_created: 2021-02-02T13:43:36Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-02-23T13:47:59Z
day: '29'
ddc:
- '530'
doi: 10.1038/s41467-019-11362-y
extern: '1'
external_id:
arxiv:
- '1909.07382'
pmid:
- '31358762'
file:
- access_level: open_access
checksum: 70c6e5d6fbea0932b0669505ab6633ec
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:47:21Z
date_updated: 2021-02-02T13:47:21Z
file_id: '9061'
file_name: 2019_NatureComm_Ramananarivo.pdf
file_size: 2820337
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:47:21Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Activity-controlled annealing of colloidal monolayers
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2019'
...
---
_id: '9460'
abstract:
- lang: eng
text: Epigenetic reprogramming is required for proper regulation of gene expression
in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for
seed viability, pollen function, and successful reproduction. The DEMETER (DME)
DNA glycosylase initiates localized DNA demethylation in vegetative and central
cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively.
In rice, the central cell genome displays local DNA hypomethylation, suggesting
that active DNA demethylation also occurs in rice; however, the enzyme responsible
for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING
1a (ROS1a) gene, which is related to DME and is essential for rice seed viability
and pollen function. Here, we report genome-wide analyses of DNA methylation in
wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative
cell genome is locally hypomethylated compared with sperm by a process that requires
ROS1a activity. We show that many ROS1a target sequences in the vegetative cell
are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates
the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation
is indirectly promoted by DNA demethylation in the vegetative cell. These results
reveal that DNA glycosylase-mediated DNA demethylation processes are conserved
in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally,
although global non-CG methylation levels of sperm and egg differ, the maternal
and paternal embryo genomes show similar non-CG methylation levels, suggesting
that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell
fusion.
article_processing_charge: No
article_type: original
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Akemi
full_name: Ono, Akemi
last_name: Ono
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative
cells promotes methylation in sperm. Proceedings of the National Academy of
Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T.,
& Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116
chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman,
Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative
Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm,” Proceedings of the National Academy of Sciences,
vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.
ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL.
2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation
in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.
mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells
Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences,
vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.
short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L.
Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
date_created: 2021-06-04T12:38:20Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2021-12-14T07:52:30Z
day: '07'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1821435116
extern: '1'
external_id:
pmid:
- '31000601'
file:
- access_level: open_access
checksum: 5b0ae3779b8b21b5223bd2d3cceede3a
content_type: application/pdf
creator: asandaue
date_created: 2021-06-04T12:50:47Z
date_updated: 2021-06-04T12:50:47Z
file_id: '9461'
file_name: 2019_PNAS_Kim.pdf
file_size: 1142540
relation: main_file
success: 1
file_date_updated: 2021-06-04T12:50:47Z
has_accepted_license: '1'
intvolume: ' 116'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 9652-9657
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in
sperm
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2019'
...
---
_id: '9689'
abstract:
- lang: eng
text: A central goal of computational physics and chemistry is to predict material
properties by using first-principles methods based on the fundamental laws of
quantum mechanics. However, the high computational costs of these methods typically
prevent rigorous predictions of macroscopic quantities at finite temperatures,
such as heat capacity, density, and chemical potential. Here, we enable such predictions
by marrying advanced free-energy methods with data-driven machine-learning interatomic
potentials. We show that, for the ubiquitous and technologically essential system
of water, a first-principles thermodynamic description not only leads to excellent
agreement with experiments, but also reveals the crucial role of nuclear quantum
fluctuations in modulating the thermodynamic stabilities of different phases of
water.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Edgar A.
full_name: Engel, Edgar A.
last_name: Engel
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences.
2019;116(4):1110-1115. doi:10.1073/pnas.1815117116
apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019).
Ab initio thermodynamics of liquid and solid water. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116
chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele
Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.
ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio
thermodynamics of liquid and solid water,” Proceedings of the National Academy
of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115,
2019.
ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4),
1110–1115.
mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.”
Proceedings of the National Academy of Sciences, vol. 116, no. 4, National
Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.
short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of
the National Academy of Sciences 116 (2019) 1110–1115.
date_created: 2021-07-19T10:17:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-02-23T14:05:08Z
day: '22'
doi: 10.1073/pnas.1815117116
extern: '1'
external_id:
arxiv:
- '1811.08630'
pmid:
- '30610171'
intvolume: ' 116'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1815117116
month: '01'
oa: 1
oa_version: Published Version
page: 1110-1115
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ab initio thermodynamics of liquid and solid water
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 116
year: '2019'
...
---
_id: '6819'
abstract:
- lang: eng
text: Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations
have been shown to exert toxicity via various mechanisms. It has been asserted
that glyphosate substitutes for glycine in polypeptide chains leading to protein
misfolding and toxicity. However, as no direct evidence exists for glycine to
glyphosate substitution in proteins, including in mammalian organisms, we tested
this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer
cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts
from three treated and three untreated cell cultures were analysed as one TMT-6plex
labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities
for peptides bearing true glyphosate treatment induced-post translational modifications
as well as allowing an investigation of the total proteome.
article_number: '494'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate
does not substitute for glycine in proteins of actively dividing mammalian cells.
BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine
in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes.
BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate
does not substitute for glycine in proteins of actively dividing mammalian cells.
BMC Research Notes. 12, 494.
mla: Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in
Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol.
12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
BMC Research Notes 12 (2019).
date_created: 2019-08-18T22:00:39Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2023-02-23T14:08:14Z
day: '08'
ddc:
- '570'
department:
- _id: LifeSc
doi: 10.1186/s13104-019-4534-3
external_id:
pmid:
- '31395095'
file:
- access_level: open_access
checksum: 4a2bb7994b7f2c432bf44f5127ea3102
content_type: application/pdf
creator: dernst
date_created: 2019-08-23T11:10:35Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6829'
file_name: 2019_BMC_Antoniou.pdf
file_size: 1177482
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Research Notes
publication_identifier:
eissn:
- 1756-0500
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
related_material:
record:
- id: '9784'
relation: research_data
status: public
scopus_import: 1
status: public
title: Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2019'
...
---
_id: '9784'
abstract:
- lang: eng
text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either
the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1
of seeding flasks and following 6-days of continuous culture. Note: no differences
in cell numbers were observed between negative control and glyphosate treated
cultures.'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of
Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells. 2019. doi:10.6084/m9.figshare.9411761.v1
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins
of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute
for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature,
2019. https://doi.org/10.6084/m9.figshare.9411761.v1.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells.” Springer Nature, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1
of Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.
mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for
Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature,
2019, doi:10.6084/m9.figshare.9411761.v1.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
(2019).
date_created: 2021-08-06T08:14:05Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2023-02-23T12:52:29Z
day: '09'
department:
- _id: LifeSc
doi: 10.6084/m9.figshare.9411761.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9411761.v1
month: '08'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6819'
relation: used_in_publication
status: public
status: public
title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9839'
abstract:
- lang: eng
text: 'More than 100 years after Grigg’s influential analysis of species’ borders,
the causes of limits to species’ ranges still represent a puzzle that has never
been understood with clarity. The topic has become especially important recently
as many scientists have become interested in the potential for species’ ranges
to shift in response to climate change—and yet nearly all of those studies fail
to recognise or incorporate evolutionary genetics in a way that relates to theoretical
developments. I show that range margins can be understood based on just two measurable
parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and
(ii) the strength of genetic drift, which reduces genetic diversity. Together,
these two parameters define an ‘expansion threshold’: adaptation fails when genetic
drift reduces genetic diversity below that required for adaptation to a heterogeneous
environment. When the key parameters drop below this expansion threshold locally,
a sharp range margin forms. When they drop below this threshold throughout the
species’ range, adaptation collapses everywhere, resulting in either extinction
or formation of a fragmented metapopulation. Because the effects of dispersal
differ fundamentally with dimension, the second parameter—the strength of genetic
drift—is qualitatively different compared to a linear habitat. In two-dimensional
habitats, genetic drift becomes effectively independent of selection. It decreases
with ‘neighbourhood size’—the number of individuals accessible by dispersal within
one generation. Moreover, in contrast to earlier predictions, which neglected
evolution of genetic variance and/or stochasticity in two dimensions, dispersal
into small marginal populations aids adaptation. This is because the reduction
of both genetic and demographic stochasticity has a stronger effect than the cost
of dispersal through increased maladaptation. The expansion threshold thus provides
a novel, theoretically justified, and testable prediction for formation of the
range margin and collapse of the species’ range.'
article_processing_charge: No
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: 'Polechova J. Data from: Is the sky the limit? On the expansion threshold of
a species’ range. 2019. doi:10.5061/dryad.5vv37'
apa: 'Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold
of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37'
chicago: 'Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold
of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.'
ieee: 'J. Polechova, “Data from: Is the sky the limit? On the expansion threshold
of a species’ range.” Dryad, 2019.'
ista: 'Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold
of a species’ range, Dryad, 10.5061/dryad.5vv37.'
mla: 'Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold
of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.'
short: J. Polechova, (2019).
date_created: 2021-08-09T13:07:28Z
date_published: 2019-06-22T00:00:00Z
date_updated: 2023-02-23T11:14:30Z
day: '22'
department:
- _id: NiBa
doi: 10.5061/dryad.5vv37
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.5vv37
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '315'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is the sky the limit? On the expansion threshold of a species''
range'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '8408'
abstract:
- lang: eng
text: Aromatic residues are located at structurally important sites of many proteins.
Probing their interactions and dynamics can provide important functional insight
but is challenging in large proteins. Here, we introduce approaches to characterize
dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning
(MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields
isolated two-spin systems that are ideally suited for artefact-free dynamics measurements,
and allows probing motions effectively without molecular-weight limitations. The
application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest
protein assigned by MAS NMR, provides insights into motions occurring on a wide
range of time scales (ps-ms). We quantitatively probe ring flip motions, and show
the temperature dependence by MAS NMR measurements down to 100 K. Interestingly,
favorable line widths are observed down to 100 K, with potential implications
for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion
measurements and detect structural excursions occurring on a microsecond time
scale in the entry pore to the catalytic chamber and at a trimer interface that
was proposed as exit pore. We show that the labeling scheme with deuteration at
ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments
with protonated, uniformly 13C-labeled samples.
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Alessandro
full_name: Barducci, Alessandro
last_name: Barducci
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Tsutomu
full_name: Terauchi, Tsutomu
last_name: Terauchi
- first_name: David
full_name: Gajan, David
last_name: Gajan
- first_name: Yohei
full_name: Miyanoiri, Yohei
last_name: Miyanoiri
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Masatsune
full_name: Kainosho, Masatsune
last_name: Kainosho
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation,
and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and
fast magic-angle spinning NMR. Journal of the American Chemical Society.
2019;141(28):11183-11195. doi:10.1021/jacs.9b04219
apa: Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T.,
… Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient
conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle
spinning NMR. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.9b04219
chicago: Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel,
Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation,
and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and
Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society.
American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b04219.
ieee: D. F. Gauto et al., “Aromatic ring dynamics, thermal activation, and
transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast
magic-angle spinning NMR,” Journal of the American Chemical Society, vol.
141, no. 28. American Chemical Society, pp. 11183–11195, 2019.
ista: Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri
Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics,
thermal activation, and transient conformations of a 468 kDa enzyme by specific
1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical
Society. 141(28), 11183–11195.
mla: Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient
Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle
Spinning NMR.” Journal of the American Chemical Society, vol. 141, no.
28, American Chemical Society, 2019, pp. 11183–95, doi:10.1021/jacs.9b04219.
short: D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan,
Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal
of the American Chemical Society 141 (2019) 11183–11195.
date_created: 2020-09-17T10:29:00Z
date_published: 2019-06-14T00:00:00Z
date_updated: 2021-01-12T08:19:04Z
day: '14'
doi: 10.1021/jacs.9b04219
extern: '1'
external_id:
pmid:
- '31199882'
intvolume: ' 141'
issue: '28'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '06'
oa_version: Submitted Version
page: 11183-11195
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Aromatic ring dynamics, thermal activation, and transient conformations of
a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2019'
...
---
_id: '8418'
abstract:
- lang: eng
text: For the Restricted Circular Planar 3 Body Problem, we show that there exists
an open set U in phase space of fixed measure, where the set of initial points
which lead to collision is O(μ120) dense as μ→0.
article_processing_charge: No
article_type: original
author:
- first_name: Marcel
full_name: Guardia, Marcel
last_name: Guardia
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Jianlu
full_name: Zhang, Jianlu
last_name: Zhang
citation:
ama: Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the
Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and
Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7
apa: Guardia, M., Kaloshin, V., & Zhang, J. (2019). Asymptotic density of collision
orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational
Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7
chicago: Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density
of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive
for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7.
ieee: M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits
in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics
and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.
ista: Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits
in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics
and Analysis. 233(2), 799–836.
mla: Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted
Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis,
vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7.
short: M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis
233 (2019) 799–836.
date_created: 2020-09-17T10:41:51Z
date_published: 2019-03-12T00:00:00Z
date_updated: 2021-01-12T08:19:09Z
day: '12'
doi: 10.1007/s00205-019-01368-7
extern: '1'
intvolume: ' 233'
issue: '2'
keyword:
- Mechanical Engineering
- Mathematics (miscellaneous)
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00205-019-01368-7
month: '03'
oa: 1
oa_version: Published Version
page: 799-836
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
issn:
- 0003-9527
- 1432-0673
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Asymptotic density of collision orbits in the Restricted Circular Planar 3
Body Problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 233
year: '2019'
...
---
_id: '8416'
abstract:
- lang: eng
text: In this paper, we show that any smooth one-parameter deformations of a strictly
convex integrable billiard table Ω0 preserving the integrability near the boundary
have to be tangent to a finite dimensional space passing through Ω0.
article_processing_charge: No
article_type: original
author:
- first_name: Guan
full_name: Huang, Guan
last_name: Huang
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Huang G, Kaloshin V. On the finite dimensionality of integrable deformations
of strictly convex integrable billiard tables. Moscow Mathematical Journal.
2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327
apa: Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable
deformations of strictly convex integrable billiard tables. Moscow Mathematical
Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327
chicago: Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable
Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical
Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327.
ieee: G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations
of strictly convex integrable billiard tables,” Moscow Mathematical Journal,
vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.
ista: Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations
of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2),
307–327.
mla: Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable
Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical
Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27,
doi:10.17323/1609-4514-2019-19-2-307-327.
short: G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.
date_created: 2020-09-17T10:41:36Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:08Z
day: '01'
doi: 10.17323/1609-4514-2019-19-2-307-327
extern: '1'
external_id:
arxiv:
- '1809.09341'
intvolume: ' 19'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.09341
month: '04'
oa: 1
oa_version: Preprint
page: 307-327
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-4514
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: On the finite dimensionality of integrable deformations of strictly convex
integrable billiard tables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2019'
...
---
_id: '8693'
abstract:
- lang: eng
text: We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s
Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation
in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp”
asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation).
All constants involved are explicitly computed.
article_processing_charge: No
article_type: original
author:
- first_name: Luigi
full_name: Chierchia, Luigi
last_name: Chierchia
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
citation:
ama: Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular
and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017
apa: Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem.
Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017
chicago: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM
Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017.
ieee: L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular
and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.
ista: Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular
and Chaotic Dynamics. 24, 583–606.
mla: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.”
Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017.
short: L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.
date_created: 2020-10-21T15:25:45Z
date_published: 2019-12-10T00:00:00Z
date_updated: 2021-01-12T08:20:34Z
day: '10'
doi: 10.1134/S1560354719060017
extern: '1'
external_id:
arxiv:
- '1908.02523'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.02523
month: '12'
oa: 1
oa_version: Preprint
page: 583–606
publication: Regular and Chaotic Dynamics
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: V. I. Arnold’s “pointwise” KAM theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2019'
...
---
_id: '9018'
abstract:
- lang: eng
text: Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved
in histone dynamics during replication, transcription, and DNA repair. Overexpressed
in proliferating tissues including many tumors, ASF1 has emerged as a promising
therapeutic target. Here, we combine structural, computational, and biochemical
approaches to design peptides that inhibit the ASF1-histone interaction. Starting
from the structure of the human ASF1-histone complex, we developed a rational
design strategy combining epitope tethering and optimization of interface contacts
to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When
introduced into cultured cells, the inhibitors impair cell proliferation, perturb
cell-cycle progression, and reduce cell migration and invasion in a manner commensurate
with their affinity for ASF1. Finally, we find that direct injection of the most
potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results
open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: Jessica
full_name: Andreani, Jessica
last_name: Andreani
- first_name: Gwenaëlle
full_name: Moal, Gwenaëlle
last_name: Moal
- first_name: Guillaume
full_name: Pinna, Guillaume
last_name: Pinna
- first_name: Ekaterina
full_name: Boyarchuk, Ekaterina
last_name: Boyarchuk
- first_name: Marie-Cécile
full_name: Gaillard, Marie-Cécile
last_name: Gaillard
- first_name: Regis
full_name: Courbeyrette, Regis
last_name: Courbeyrette
- first_name: Carl
full_name: Mann, Carl
last_name: Mann
- first_name: Jean-Yves
full_name: Thuret, Jean-Yves
last_name: Thuret
- first_name: Bérengère
full_name: Guichard, Bérengère
last_name: Guichard
- first_name: Brice
full_name: Murciano, Brice
last_name: Murciano
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Adeline
full_name: Poitou, Adeline
last_name: Poitou
- first_name: Claire
full_name: Frederic, Claire
last_name: Frederic
- first_name: Marie-Hélène
full_name: Le Du, Marie-Hélène
last_name: Le Du
- first_name: Morgane
full_name: Agez, Morgane
last_name: Agez
- first_name: Caroline
full_name: Roelants, Caroline
last_name: Roelants
- first_name: Zachary A.
full_name: Gurard-Levin, Zachary A.
last_name: Gurard-Levin
- first_name: Geneviève
full_name: Almouzni, Geneviève
last_name: Almouzni
- first_name: Nadia
full_name: Cherradi, Nadia
last_name: Cherradi
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity
peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology.
2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002
apa: Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E.,
… Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides
inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier.
https://doi.org/10.1016/j.chembiol.2019.09.002
chicago: Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume
Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational
Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell
Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.
ieee: M. M. Bakail et al., “Design on a rational basis of high-affinity peptides
inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26,
no. 11. Elsevier, p. 1573–1585.e10, 2019.
ista: Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C,
Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A,
Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi
N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity
peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11),
1573–1585.e10.
mla: Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides
Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26,
no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.
short: M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C.
Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N.
Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin,
G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26
(2019) 1573–1585.e10.
date_created: 2021-01-19T11:04:50Z
date_published: 2019-11-21T00:00:00Z
date_updated: 2023-02-23T13:46:53Z
day: '21'
doi: 10.1016/j.chembiol.2019.09.002
extern: '1'
external_id:
pmid:
- '31543461'
intvolume: ' 26'
issue: '11'
keyword:
- Clinical Biochemistry
- Molecular Medicine
- Biochemistry
- Molecular Biology
- Pharmacology
- Drug Discovery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chembiol.2019.09.002
month: '11'
oa: 1
oa_version: Published Version
page: 1573-1585.e10
pmid: 1
publication: Cell Chemical Biology
publication_identifier:
issn:
- 2451-9456
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Design on a rational basis of high-affinity peptides inhibiting the histone
chaperone ASF1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2019'
...
---
_id: '9530'
abstract:
- lang: eng
text: "Background\r\nDNA methylation of active genes, also known as gene body methylation,
is found in many animal and plant genomes. Despite this, the transcriptional and
developmental role of such methylation remains poorly understood. Here, we explore
the dynamic range of DNA methylation in honey bee, a model organism for gene body
methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies
globally fluctuates during honey bee development. However, these changes cause
no gene expression alterations. Intriguingly, despite the global alterations,
tissue-specific CG methylation patterns of complete genes or exons are rare, implying
robust maintenance of genic methylation during development. Additionally, we show
that CG methylation maintenance fluctuates in somatic cells, while reaching maximum
fidelity in sperm cells. Finally, unlike universally present CG methylation, we
discovered non-CG methylation specifically in bee heads that resembles such methylation
in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose
that gene body CG methylation can oscillate during development if it is kept to
a level adequate to preserve function. Additionally, our data suggest that heightened
non-CG methylation is a conserved regulator of animal nervous systems."
article_number: '62'
article_processing_charge: No
article_type: original
author:
- first_name: Keith D.
full_name: Harris, Keith D.
last_name: Harris
- first_name: James P. B.
full_name: Lloyd, James P. B.
last_name: Lloyd
- first_name: Katherine
full_name: Domb, Katherine
last_name: Domb
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
citation:
ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained
with high fidelity in the honey bee germline and exhibits global non-functional
fluctuations during somatic development. Epigenetics and Chromatin. 2019;12.
doi:10.1186/s13072-019-0307-4
apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019).
DNA methylation is maintained with high fidelity in the honey bee germline and
exhibits global non-functional fluctuations during somatic development. Epigenetics
and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4
chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman,
and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey
Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.”
Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.
ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development,” Epigenetics and Chromatin,
vol. 12. Springer Nature, 2019.
ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development. Epigenetics and Chromatin.
12, 62.
mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity
in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during
Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer
Nature, 2019, doi:10.1186/s13072-019-0307-4.
short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics
and Chromatin 12 (2019).
date_created: 2021-06-08T09:21:51Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2021-12-14T07:53:00Z
day: '10'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13072-019-0307-4
extern: '1'
external_id:
pmid:
- '31601251'
file:
- access_level: open_access
checksum: 86ff50a7517891511af2733c76c81b67
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:29:19Z
date_updated: 2021-06-08T09:29:19Z
file_id: '9531'
file_name: 2019_EpigeneticsAndChromatin_Harris.pdf
file_size: 3221067
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:29:19Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Epigenetics and Chromatin
publication_identifier:
eissn:
- 1756-8935
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation is maintained with high fidelity in the honey bee germline
and exhibits global non-functional fluctuations during somatic development
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2019'
...
---
_id: '9586'
abstract:
- lang: eng
text: "Consider integers \U0001D458,ℓ such that 0⩽ℓ⩽(\U0001D4582) . Given a large
graph \U0001D43A , what is the fraction of \U0001D458 -vertex subsets of \U0001D43A
\ which span exactly ℓ edges? When \U0001D43A is empty or complete, and ℓ
\ is zero or (\U0001D4582) , this fraction can be exactly 1. On the other hand,
if ℓ is far from these extreme values, one might expect that this fraction is
substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich,
and Tyomkyn who initiated the systematic study of this question and proposed several
natural conjectures.\r\nLet ℓ∗=min{ℓ,(\U0001D4582)−ℓ} . Our main result is that
for any \U0001D458 and ℓ , the fraction of \U0001D458 -vertex subsets that
span ℓ edges is at most log\U0001D442(1)(ℓ∗/\U0001D458)√ \U0001D458/ℓ∗, which
is best-possible up to the logarithmic factor. This improves on multiple results
of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures.
In addition, we also make some first steps towards some analogous questions for
hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of
different probabilistic tools, such as polynomial anticoncentration inequalities,
hypercontractivity, and a coupling trick for random variables defined on a ‘slice’
of the Boolean hypercube."
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
- first_name: Tuan
full_name: Tran, Tuan
last_name: Tran
citation:
ama: Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal
of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192
apa: Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph
statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192
chicago: Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for
Subgraph Statistics.” Journal of the London Mathematical Society. Wiley,
2019. https://doi.org/10.1112/jlms.12192.
ieee: M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,”
Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp.
757–777, 2019.
ista: Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics.
Journal of the London Mathematical Society. 99(3), 757–777.
mla: Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal
of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77,
doi:10.1112/jlms.12192.
short: M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society
99 (2019) 757–777.
date_created: 2021-06-22T09:46:03Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2023-02-23T14:01:53Z
day: '03'
doi: 10.1112/jlms.12192
extern: '1'
external_id:
arxiv:
- '1807.05202'
intvolume: ' 99'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05202
month: '05'
oa: 1
oa_version: Preprint
page: 757-777
publication: Journal of the London Mathematical Society
publication_identifier:
eissn:
- 1469-7750
issn:
- 0024-6107
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anticoncentration for subgraph statistics
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 99
year: '2019'
...
---
_id: '9580'
abstract:
- lang: eng
text: An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H
into r parts and the size of the cut is the number of edges which have a vertex
in each part. A classical result of Edwards says that every m-edge graph has a
2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts
which exceed the expected size of a random cut by some multiple of the standard
deviation. We study analogues of this and related results in hypergraphs. First,
we observe that similarly to graphs, every m-edge k-uniform hypergraph has an
r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover,
in the case where k = 3 and r = 2 this bound is best possible and is attained
by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥
4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose
size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant
difference in behaviour, since the amount by which the size of the largest cut
exceeds the expected size of a random cut is now considerably larger than the
standard deviation.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Conlon, David
last_name: Conlon
- first_name: Jacob
full_name: Fox, Jacob
last_name: Fox
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel
Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z
apa: Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts
above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z
chicago: Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph
Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019.
https://doi.org/10.1007/s11856-019-1897-z.
ieee: D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the
average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp.
67–111, 2019.
ista: Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average.
Israel Journal of Mathematics. 233(1), 67–111.
mla: Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal
of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.
short: D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233
(2019) 67–111.
date_created: 2021-06-21T13:36:02Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-02-23T14:01:41Z
day: '01'
doi: 10.1007/s11856-019-1897-z
extern: '1'
external_id:
arxiv:
- '1803.08462'
intvolume: ' 233'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08462
month: '08'
oa: 1
oa_version: Preprint
page: 67-111
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hypergraph cuts above the average
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 233
year: '2019'
...
---
_id: '9585'
abstract:
- lang: eng
text: An n-vertex graph is called C-Ramsey if it has no clique or independent set
of size C log n. All known constructions of Ramsey graphs involve randomness in
an essential way, and there is an ongoing line of research towards showing that
in fact all Ramsey graphs must obey certain “richness” properties characteristic
of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that
in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have
the same numbers of vertices and edges. Improving on earlier results of Alon,
Balogh, Kostochka and Samotij, in this paper we prove this conjecture.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs.
Transactions of the American Mathematical Society. 2019;372(8):5571-5594.
doi:10.1090/tran/7729
apa: Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs
of Ramsey graphs. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/7729
chicago: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced
Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society.
American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.
ieee: M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of
Ramsey graphs,” Transactions of the American Mathematical Society, vol.
372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.
ista: Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey
graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.
mla: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs
of Ramsey Graphs.” Transactions of the American Mathematical Society, vol.
372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729.
short: M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society
372 (2019) 5571–5594.
date_created: 2021-06-22T09:31:45Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-02-23T14:01:50Z
day: '15'
doi: 10.1090/tran/7729
extern: '1'
external_id:
arxiv:
- '1712.05656'
intvolume: ' 372'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1090/tran/7729
month: '10'
oa: 1
oa_version: Submitted Version
page: 5571-5594
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6850
issn:
- 0002-9947
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proof of a conjecture on induced subgraphs of Ramsey graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 372
year: '2019'
...
---
_id: '9677'
abstract:
- lang: eng
text: Progress in the atomic-scale modeling of matter over the past decade has been
tremendous. This progress has been brought about by improvements in methods for
evaluating interatomic forces that work by either solving the electronic structure
problem explicitly, or by computing accurate approximations of the solution and
by the development of techniques that use the Born–Oppenheimer (BO) forces to
move the atoms on the BO potential energy surface. As a consequence of these developments
it is now possible to identify stable or metastable states, to sample configurations
consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics
of reactions and phase transitions. All too often, however, progress is slowed
down by the bottleneck associated with implementing new optimization algorithms
and/or sampling techniques into the many existing electronic-structure and empirical-potential
codes. To address this problem, we are thus releasing a new version of the i-PI
software. This piece of software is an easily extensible framework for implementing
advanced atomistic simulation techniques using interatomic potentials and forces
calculated by an external driver code. While the original version of the code
(Ceriotti et al., 2014) was developed with a focus on path integral molecular
dynamics techniques, this second release of i-PI not only includes several new
advanced path integral methods, but also offers other classes of algorithms. In
other words, i-PI is moving towards becoming a universal force engine that is
both modular and tightly coupled to the driver codes that evaluate the potential
energy surface and its derivatives.
article_processing_charge: No
article_type: original
author:
- first_name: Venkat
full_name: Kapil, Venkat
last_name: Kapil
- first_name: Mariana
full_name: Rossi, Mariana
last_name: Rossi
- first_name: Ondrej
full_name: Marsalek, Ondrej
last_name: Marsalek
- first_name: Riccardo
full_name: Petraglia, Riccardo
last_name: Petraglia
- first_name: Yair
full_name: Litman, Yair
last_name: Litman
- first_name: Thomas
full_name: Spura, Thomas
last_name: Spura
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alice
full_name: Cuzzocrea, Alice
last_name: Cuzzocrea
- first_name: Robert H.
full_name: Meißner, Robert H.
last_name: Meißner
- first_name: David M.
full_name: Wilkins, David M.
last_name: Wilkins
- first_name: Benjamin A.
full_name: Helfrecht, Benjamin A.
last_name: Helfrecht
- first_name: Przemysław
full_name: Juda, Przemysław
last_name: Juda
- first_name: Sébastien P.
full_name: Bienvenue, Sébastien P.
last_name: Bienvenue
- first_name: Wei
full_name: Fang, Wei
last_name: Fang
- first_name: Jan
full_name: Kessler, Jan
last_name: Kessler
- first_name: Igor
full_name: Poltavsky, Igor
last_name: Poltavsky
- first_name: Steven
full_name: Vandenbrande, Steven
last_name: Vandenbrande
- first_name: Jelle
full_name: Wieme, Jelle
last_name: Wieme
- first_name: Clemence
full_name: Corminboeuf, Clemence
last_name: Corminboeuf
- first_name: Thomas D.
full_name: Kühne, Thomas D.
last_name: Kühne
- first_name: David E.
full_name: Manolopoulos, David E.
last_name: Manolopoulos
- first_name: Thomas E.
full_name: Markland, Thomas E.
last_name: Markland
- first_name: Jeremy O.
full_name: Richardson, Jeremy O.
last_name: Richardson
- first_name: Alexandre
full_name: Tkatchenko, Alexandre
last_name: Tkatchenko
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Veronique
full_name: Van Speybroeck, Veronique
last_name: Van Speybroeck
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for
advanced molecular simulations. Computer Physics Communications. 2019;236:214-223.
doi:10.1016/j.cpc.2018.09.020'
apa: 'Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T.,
… Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular
simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020'
chicago: 'Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair
Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine
for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier,
2019. https://doi.org/10.1016/j.cpc.2018.09.020.'
ieee: 'V. Kapil et al., “i-PI 2.0: A universal force engine for advanced
molecular simulations,” Computer Physics Communications, vol. 236. Elsevier,
pp. 214–223, 2019.'
ista: 'Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea
A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler
J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos
DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti
M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations.
Computer Physics Communications. 236, 214–223.'
mla: 'Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular
Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019,
pp. 214–23, doi:10.1016/j.cpc.2018.09.020.'
short: V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng,
A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue,
W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf,
T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko,
G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications
236 (2019) 214–223.
date_created: 2021-07-16T08:53:01Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2021-08-09T12:37:16Z
day: '01'
doi: 10.1016/j.cpc.2018.09.020
extern: '1'
external_id:
arxiv:
- '1808.03824'
intvolume: ' 236'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.03824
month: '03'
oa: 1
oa_version: Preprint
page: 214-223
publication: Computer Physics Communications
publication_identifier:
issn:
- 0010-4655
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'i-PI 2.0: A universal force engine for advanced molecular simulations'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 236
year: '2019'
...
---
_id: '9680'
abstract:
- lang: eng
text: Atomistic modeling of phase transitions, chemical reactions, or other rare
events that involve overcoming high free energy barriers usually entails prohibitively
long simulation times. Introducing a bias potential as a function of an appropriately
chosen set of collective variables can significantly accelerate the exploration
of phase space, albeit at the price of distorting the distribution of microstates.
Efficient reweighting to recover the unbiased distribution can be nontrivial when
employing adaptive sampling techniques such as metadynamics, variationally enhanced
sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium
manner under a time-dependent bias. We introduce an iterative unbiasing scheme
that makes efficient use of all the trajectory data and that does not require
the distribution to be evaluated on a grid. The method can thus be used even when
the bias has a high dimensionality. We benchmark this approach against some of
the existing schemes on model systems with different complexity and dimensionality.
article_processing_charge: No
article_type: original
author:
- first_name: F.
full_name: Giberti, F.
last_name: Giberti
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: G. A.
full_name: Tribello, G. A.
last_name: Tribello
- first_name: M.
full_name: Ceriotti, M.
last_name: Ceriotti
citation:
ama: Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium
sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107.
doi:10.1021/acs.jctc.9b00907
apa: Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative
unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907
chicago: Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative
Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation.
American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907.
ieee: F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing
of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation,
vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.
ista: Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of
quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1),
100–107.
mla: Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal
of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society,
2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.
short: F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory
and Computation 16 (2019) 100–107.
date_created: 2021-07-19T06:56:45Z
date_published: 2019-01-14T00:00:00Z
date_updated: 2021-08-09T12:37:37Z
day: '14'
doi: 10.1021/acs.jctc.9b00907
extern: '1'
external_id:
arxiv:
- '1911.01140'
pmid:
- '31743021'
intvolume: ' 16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.01140
month: '01'
oa: 1
oa_version: Preprint
page: 100-107
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterative unbiasing of quasi-equilibrium sampling
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 16
year: '2019'
...
---
_id: '12600'
abstract:
- lang: eng
text: The snow cover dynamics of High Mountain Asia are usually assessed at spatial
resolutions of 250 m or greater, but this scale is too coarse to clearly represent
the rugged topography common to the region. Higher-resolution measurement of snow-covered
area often results in biased sampling due to cloud cover and deep shadows. We
therefore develop a Normalized Difference Snow Index-based workflow to delineate
snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and
apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning
1999 to 2013. For each scene, we determine the spatial distribution of snow line
altitudes (SLAs) with respect to aspect and across six subcatchments. Our results
show that the mean SLA exhibits distinct seasonal behavior based on aspect and
subcatchment position. We find that SLA dynamics respond to spatial and seasonal
trade-offs in precipitation, temperature, and solar radiation, which act as primary
controls. We identify two SLA spatial gradients, which we attribute to the effect
of spatially variable precipitation. Our results also reveal that aspect-related
SLA differences vary seasonally and are influenced by solar radiation. In terms
of seasonal dominant controls, we demonstrate that the snow line is controlled
by snow precipitation in winter, melt in premonsoon, a combination of both in
postmonsoon, and temperature in monsoon, explaining to a large extent the spatial
and seasonal variability of the SLA in the upper Langtang Valley. We conclude
that while SLA and snow-covered area are complementary metrics, the SLA has a
strong potential for understanding local-scale snow cover dynamics and their controlling
mechanisms.
article_processing_charge: No
article_type: original
author:
- first_name: Marc
full_name: Girona‐Mata, Marc
last_name: Girona‐Mata
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Silvan
full_name: Ragettli, Silvan
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline
delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment.
Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935
apa: Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019).
High‐resolution snowline delineation from Landsat imagery to infer snow cover
controls in a Himalayan catchment. Water Resources Research. American Geophysical
Union. https://doi.org/10.1029/2019wr024935
chicago: Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti.
“High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover
Controls in a Himalayan Catchment.” Water Resources Research. American
Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935.
ieee: M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution
snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan
catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical
Union, pp. 6754–6772, 2019.
ista: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution
snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan
catchment. Water Resources Research. 55(8), 6754–6772.
mla: Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat
Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources
Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935.
short: M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources
Research 55 (2019) 6754–6772.
date_created: 2023-02-20T08:12:59Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-02-28T12:14:18Z
day: '01'
doi: 10.1029/2019wr024935
extern: '1'
intvolume: ' 55'
issue: '8'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2019WR024935
month: '08'
oa: 1
oa_version: Published Version
page: 6754-6772
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: High‐resolution snowline delineation from Landsat imagery to infer snow cover
controls in a Himalayan catchment
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '12602'
abstract:
- lang: eng
text: 'This study aims at developing and applying a spatially-distributed coupled
glacier mass balance and ice-flow model to attribute the response of glaciers
to natural and anthropogenic climate change. We focus on two glaciers with contrasting
surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal)
and a clean-ice glacier (Hintereisferner in Austria). The model is applied from
the end of the Little Ice Age (1850) to the present-day (2016) and is forced with
four bias-corrected General Circulation Models (GCMs) from the historical experiment
of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet,
cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic
climate change on glacier mass balance and flow runs from these GCMs with and
without further anthropogenic forcing after 1970 until 2016 are selected. The
outcomes indicate that both glaciers experience the largest reduction in area
and volume under warm climate conditions, whereas area and volume reductions are
smaller under cold climate conditions. Simultaneously with changes in glacier
area and volume, surface velocities generally decrease over time. Without further
anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier
area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in
glacier area (volume) for the clean-ice glacier. The difference in the magnitude
between the two glaciers can mainly be attributed to differences in the response
time of the glaciers, where the clean-ice glacier shows a much faster response
to climate change. We conclude that the response of the two glaciers can mainly
be attributed to anthropogenic climate change and that the impact is larger on
the clean-ice glacier. The outcomes show that the model performs well under different
climate conditions and that the developed approach can be used for regional-scale
glacio-hydrological modeling.'
article_number: '143'
article_processing_charge: No
article_type: original
author:
- first_name: René R.
full_name: Wijngaard, René R.
last_name: Wijngaard
- first_name: Jakob F.
full_name: Steiner, Jakob F.
last_name: Steiner
- first_name: Philip D. A.
full_name: Kraaijenbrink, Philip D. A.
last_name: Kraaijenbrink
- first_name: Christoph
full_name: Klug, Christoph
last_name: Klug
- first_name: Surendra
full_name: Adhikari, Surendra
last_name: Adhikari
- first_name: Argha
full_name: Banerjee, Argha
last_name: Banerjee
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Ludovicus P. H.
full_name: van Beek, Ludovicus P. H.
last_name: van Beek
- first_name: Marc F. P.
full_name: Bierkens, Marc F. P.
last_name: Bierkens
- first_name: Arthur F.
full_name: Lutz, Arthur F.
last_name: Lutz
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
citation:
ama: Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of
the Langtang Glacier and the Hintereisferner to a changing climate since the Little
Ice Age. Frontiers in Earth Science. 2019;7. doi:10.3389/feart.2019.00143
apa: Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari,
S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang
Glacier and the Hintereisferner to a changing climate since the Little Ice Age.
Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2019.00143
chicago: Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph
Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling
the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate
since the Little Ice Age.” Frontiers in Earth Science. Frontiers Media,
2019. https://doi.org/10.3389/feart.2019.00143.
ieee: R. R. Wijngaard et al., “Modeling the response of the Langtang Glacier
and the Hintereisferner to a changing climate since the Little Ice Age,” Frontiers
in Earth Science, vol. 7. Frontiers Media, 2019.
ista: Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee
A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling
the response of the Langtang Glacier and the Hintereisferner to a changing climate
since the Little Ice Age. Frontiers in Earth Science. 7, 143.
mla: Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and
the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers
in Earth Science, vol. 7, 143, Frontiers Media, 2019, doi:10.3389/feart.2019.00143.
short: R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari,
A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W.
Immerzeel, Frontiers in Earth Science 7 (2019).
date_created: 2023-02-20T08:13:08Z
date_published: 2019-06-04T00:00:00Z
date_updated: 2023-02-28T12:04:48Z
day: '04'
doi: 10.3389/feart.2019.00143
extern: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3389/feart.2019.00143
month: '06'
oa: 1
oa_version: Published Version
publication: Frontiers in Earth Science
publication_identifier:
issn:
- 2296-6463
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling the response of the Langtang Glacier and the Hintereisferner to a
changing climate since the Little Ice Age
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2019'
...
---
_id: '12601'
abstract:
- lang: eng
text: Ice cliffs and ponds on debris-covered glaciers have received increased attention
due to their role in amplifying local melt. However, very few studies have looked
at these features on the catchment scale to determine their patterns and changes
in space and time. We have compiled a detailed inventory of cliffs and ponds in
the Langtang catchment, central Himalaya, from six high-resolution satellite orthoimages
and DEMs between 2006 and 2015, and a historic orthophoto from 1974. Cliffs cover
between 1.4% (± 0.4%) in the dry and 3.4% (± 0.9%) in the wet seasons and ponds
between 0.6% (± 0.1%) and 1.6% (± 0.3%) of the total debris-covered tongues. We
find large variations between seasons, as cliffs and ponds tend to grow in the
wetter monsoon period, but there is no obvious trend in total area over the study
period. The inventory further shows that cliffs are predominately north-facing
irrespective of the glacier flow direction. Both cliffs and ponds appear in higher
densities several hundred metres from the terminus in areas where tributaries
reach the main glacier tongue. On the largest glacier in the catchment ~10% of
all cliffs and ponds persisted over nearly a decade.
article_processing_charge: No
article_type: original
author:
- first_name: JAKOB F.
full_name: STEINER, JAKOB F.
last_name: STEINER
- first_name: PASCAL
full_name: BURI, PASCAL
last_name: BURI
- first_name: EVAN S.
full_name: MILES, EVAN S.
last_name: MILES
- first_name: SILVAN
full_name: RAGETTLI, SILVAN
last_name: RAGETTLI
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: 'STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. Supraglacial ice
cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and
characteristics. Journal of Glaciology. 2019;65(252):617-632. doi:10.1017/jog.2019.40'
apa: 'STEINER, J. F., BURI, P., MILES, E. S., RAGETTLI, S., & Pellicciotti,
F. (2019). Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal
distribution and characteristics. Journal of Glaciology. Cambridge University
Press. https://doi.org/10.1017/jog.2019.40'
chicago: 'STEINER, JAKOB F., PASCAL BURI, EVAN S. MILES, SILVAN RAGETTLI, and Francesca
Pellicciotti. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal
Distribution and Characteristics.” Journal of Glaciology. Cambridge University
Press, 2019. https://doi.org/10.1017/jog.2019.40.'
ieee: 'J. F. STEINER, P. BURI, E. S. MILES, S. RAGETTLI, and F. Pellicciotti, “Supraglacial
ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution
and characteristics,” Journal of Glaciology, vol. 65, no. 252. Cambridge
University Press, pp. 617–632, 2019.'
ista: 'STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. 2019. Supraglacial
ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution
and characteristics. Journal of Glaciology. 65(252), 617–632.'
mla: 'STEINER, JAKOB F., et al. “Supraglacial Ice Cliffs and Ponds on Debris-Covered
Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology,
vol. 65, no. 252, Cambridge University Press, 2019, pp. 617–32, doi:10.1017/jog.2019.40.'
short: J.F. STEINER, P. BURI, E.S. MILES, S. RAGETTLI, F. Pellicciotti, Journal
of Glaciology 65 (2019) 617–632.
date_created: 2023-02-20T08:13:03Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-02-28T12:11:07Z
day: '01'
doi: 10.1017/jog.2019.40
extern: '1'
intvolume: ' 65'
issue: '252'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/jog.2019.40
month: '08'
oa: 1
oa_version: Published Version
page: 617-632
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal
distribution and characteristics'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 65
year: '2019'
...
---
_id: '12192'
abstract:
- lang: eng
text: Transposable elements (TEs), the movement of which can damage the genome,
are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in
the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis
thaliana. However, the extent and mechanism of this activation are unknown. Here
we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed
DNA demethylation. We further demonstrate that DEMETER access to some of these
TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically
expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent
mechanism. We demonstrate that H1 is required for heterochromatin condensation
in plant cells and show that H1 overexpression creates heterochromatic foci in
the VC progenitor cell. Taken together, our results demonstrate that the natural
depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation,
heterochromatin relaxation, and TE activation.
acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP
vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder)
for their assistance with microscopy, and the Norwich BioScience Institute Partnership
Computing infrastructure for Science Group for High Performance Computing resources.
This work was funded by a Biotechnology and Biological Sciences Research Council
(BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research
Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers
by the Gatsby Charitable Foundation (SH and XF).
article_number: '42530'
article_processing_charge: No
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells
causes DNA demethylation, heterochromatin decondensation and transposon activation.
eLife. 2019;8. doi:10.7554/elife.42530
apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of
histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation
and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530
chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion
of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation
and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019.
https://doi.org/10.7554/elife.42530.
ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1
in sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.
ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in
sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation. eLife. 8, 42530.
mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA
Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife,
vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.
short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).
date_created: 2023-01-16T09:17:21Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2023-05-08T10:54:12Z
day: '28'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.7554/elife.42530
extern: '1'
external_id:
unknown:
- '31135340'
file:
- access_level: open_access
checksum: ea6b89c20d59e5eb3646916fe5d568ad
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T09:42:46Z
date_updated: 2023-02-07T09:42:46Z
file_id: '12525'
file_name: 2019_elife_He.pdf
file_size: 2493837
relation: main_file
success: 1
file_date_updated: 2023-02-07T09:42:46Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/
month: '05'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications, Ltd
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin
decondensation and transposon activation
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: 8
year: '2019'
...
---
_id: '12190'
abstract:
- lang: eng
text: Meiotic crossover frequency varies within genomes, which influences genetic
diversity and adaptation. In turn, genetic variation within populations can act
to modify crossover frequency in cis and trans. To identify genetic variation
that controls meiotic crossover frequency, we screened Arabidopsis accessions
using fluorescent recombination reporters. We mapped a genetic modifier of crossover
frequency in Col × Bur populations of Arabidopsis to a premature stop codon within
TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase
II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare
variant found in the British Isles, originating in South-West Ireland. Using genetics,
genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers,
with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq)
from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas
its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting
gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread
transcriptional changes, including in genes that regulate the meiotic cell cycle
and recombination. Therefore, TAF4b duplication is associated with acquisition
of meiocyte-specific expression and promotion of germline transcription, which
act directly or indirectly to elevate crossovers. This identifies a novel mode
of meiotic recombination control via a general transcription factor.
acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham
Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for
FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash
University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon
(INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for
access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.),
European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’
(BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and
X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.;
StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Emma J.
full_name: Lawrence, Emma J.
last_name: Lawrence
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Andrew J.
full_name: Tock, Andrew J.
last_name: Tock
- first_name: Christophe
full_name: Lambing, Christophe
last_name: Lambing
- first_name: Alexander R.
full_name: Blackwell, Alexander R.
last_name: Blackwell
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Ian R.
full_name: Henderson, Ian R.
last_name: Henderson
citation:
ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084
apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng,
X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084
chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander
R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED
FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.”
Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084.
ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis,” Current
Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.
ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR.
2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover
and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.
mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls
Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology,
vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.
short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R.
Henderson, Current Biology 29 (2019) 2676–2686.e3.
date_created: 2023-01-16T09:16:33Z
date_published: 2019-08-19T00:00:00Z
date_updated: 2023-05-08T10:54:54Z
day: '19'
department:
- _id: XiFe
doi: 10.1016/j.cub.2019.06.084
extern: '1'
external_id:
pmid:
- '31378616'
intvolume: ' 29'
issue: '16'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2676-2686.e3
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and
germline transcription in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
_id: '8305'
abstract:
- lang: eng
text: In this paper, we present the first fully asynchronous distributed key generation
(ADKG) algorithm as well as the first distributed key generation algorithm that
can create keys with a dual (f,2f+1)−threshold that are necessary for scalable
consensus (which so far needs a trusted dealer assumption). In order to create
a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open
question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds
f+1Cryptology
ePrint Archive.'
apa: 'Kokoris Kogias, E., Spiegelman, A., Malkhi, D., & Abraham, I. (n.d.).
Bootstrapping consensus without trusted setup: fully asynchronous distributed
key generation. Cryptology ePrint Archive.'
chicago: 'Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and
Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous
Distributed Key Generation.” Cryptology EPrint Archive, n.d.'
ieee: 'E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping
consensus without trusted setup: fully asynchronous distributed key generation,”
Cryptology ePrint Archive. .'
ista: 'Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus
without trusted setup: fully asynchronous distributed key generation. Cryptology
ePrint Archive, 2019/1015.'
mla: 'Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted
Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive,
2019/1015.'
short: E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint
Archive (n.d.).
date_created: 2020-08-26T12:18:00Z
date_published: 2019-09-10T00:00:00Z
date_updated: 2023-05-10T09:27:54Z
day: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/1015
month: '09'
oa: 1
oa_version: Preprint
publication: Cryptology ePrint Archive
publication_status: submitted
status: public
title: 'Bootstrapping consensus without trusted setup: fully asynchronous distributed
key generation'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '12901'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Janos
full_name: Kiss, Janos
id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87
last_name: Kiss
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
citation:
ama: 'Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster?
In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches
Rechnen der Universität Graz; 2019:25.'
apa: 'Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running
an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee,
Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität
Graz.'
chicago: Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for
Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut
für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.
ieee: A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC
Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria,
2019, p. 25.
ista: 'Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC
Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.'
mla: Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19
- Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches
Rechnen der Universität Graz, 2019, p. 25.
short: A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019
, Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz,
2019, p. 25.
conference:
end_date: 2019-02-27
location: Grundlsee, Austria
name: 'AHPC: Austrian HPC Meeting'
start_date: 2019-02-25
date_created: 2023-05-05T12:48:48Z
date_published: 2019-02-27T00:00:00Z
date_updated: 2023-05-16T07:29:32Z
day: '27'
ddc:
- '000'
department:
- _id: ScienComp
file:
- access_level: open_access
checksum: acc8272027faaf30709c51ac5c58ffa4
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:27:09Z
date_updated: 2023-05-16T07:27:09Z
file_id: '12970'
file_name: 2019_AHPC_Schloegl.pdf
file_size: 1097603
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:27:09Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf
month: '02'
oa: 1
oa_version: Published Version
page: '25'
publication: 'AHPC19 - Austrian HPC Meeting 2019 '
publication_status: published
publisher: Institut für Mathematik und wissenschaftliches Rechnen der Universität
Graz
status: public
title: Is Debian suitable for running an HPC Cluster?
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '11060'
abstract:
- lang: eng
text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum
(ER) that is gated by the nuclear pore complex. It is unknown whether proteins
of the INM and ER are degraded through shared or distinct pathways in mammalian
cells. We applied dynamic proteomics to profile protein half-lives and report
that INM and ER residents turn over at similar rates, indicating that the INM’s
unique topology is not a barrier to turnover. Using a microscopy approach, we
observed that the proteasome can degrade INM proteins in situ. However, we also
uncovered evidence for selective, vesicular transport-mediated turnover of a single
INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared
from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular
trafficking to lysosomes. This work demonstrates that the INM can be dynamically
remodeled in response to environmental inputs.
article_number: e49796
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Hsiao
full_name: Tsai, Hsiao
last_name: Tsai
- first_name: Juliana
full_name: Capitanio, Juliana
last_name: Capitanio
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance
of the inner nuclear membrane protein emerin by vesicular transport during ER
stress. eLife. 2019;8. doi:10.7554/elife.49796
apa: Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019).
Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796
chicago: Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and
Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin
by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/elife.49796.
ieee: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective
clearance of the inner nuclear membrane protein emerin by vesicular transport
during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance
of the inner nuclear membrane protein emerin by vesicular transport during ER
stress. eLife. 8, e49796.
mla: Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane
Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8,
e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796.
short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).
date_created: 2022-04-07T07:45:02Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-05-31T06:36:22Z
day: '10'
ddc:
- '570'
doi: 10.7554/elife.49796
extern: '1'
external_id:
pmid:
- '31599721'
file:
- access_level: open_access
checksum: 1e8672a1e9c3dc0a2d3d0dad89673616
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T08:18:01Z
date_updated: 2022-04-08T08:18:01Z
file_id: '11138'
file_name: 2019_eLife_Buchwalter.pdf
file_size: 6984654
relation: main_file
success: 1
file_date_updated: 2022-04-08T08:18:01Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '13079'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress
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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2019'
...
---
_id: '13079'
abstract:
- lang: eng
text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum
(ER) that is gated by the nuclear pore complex. It is unknown whether proteins
of the INM and ER are degraded through shared or distinct pathways in mammalian
cells. We applied dynamic proteomics to profile protein half-lives and report
that INM and ER residents turn over at similar rates, indicating that the INM’s
unique topology is not a barrier to turnover. Using a microscopy approach, we
observed that the proteasome can degrade INM proteins in situ. However, we also
uncovered evidence for selective, vesicular transport-mediated turnover of a single
INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared
from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular
trafficking to lysosomes. This work demonstrates that the INM can be dynamically
remodeled in response to environmental inputs.
article_processing_charge: No
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Hsiao
full_name: Tsai, Hsiao
last_name: Tsai
- first_name: Juliana
full_name: Capitanio, Juliana
last_name: Capitanio
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: 'Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Data from: Selective
clearance of the inner nuclear membrane protein emerin by vesicular transport
during ER stress. 2019. doi:10.5061/DRYAD.N0R525H'
apa: 'Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019).
Data from: Selective clearance of the inner nuclear membrane protein emerin by
vesicular transport during ER stress. Dryad. https://doi.org/10.5061/DRYAD.N0R525H'
chicago: 'Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and
Martin Hetzer. “Data from: Selective Clearance of the Inner Nuclear Membrane Protein
Emerin by Vesicular Transport during ER Stress.” Dryad, 2019. https://doi.org/10.5061/DRYAD.N0R525H.'
ieee: 'A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Data from:
Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress.” Dryad, 2019.'
ista: 'Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Data from:
Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress, Dryad, 10.5061/DRYAD.N0R525H.'
mla: 'Buchwalter, Abigail, et al. Data from: Selective Clearance of the Inner
Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress. Dryad,
2019, doi:10.5061/DRYAD.N0R525H.'
short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, (2019).
date_created: 2023-05-23T17:09:30Z
date_published: 2019-10-28T00:00:00Z
date_updated: 2023-05-31T06:36:23Z
day: '28'
ddc:
- '570'
doi: 10.5061/DRYAD.N0R525H
extern: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.n0r525h
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '11060'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selective clearance of the inner nuclear membrane protein emerin
by vesicular transport during ER stress'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6989'
abstract:
- lang: eng
text: 'When can a polyomino piece of paper be folded into a unit cube? Prior work
studied tree-like polyominoes, but polyominoes with holes remain an intriguing
open problem. We present sufficient conditions for a polyomino with hole(s) to
fold into a cube, and conditions under which cube folding is impossible. In particular,
we show that all but five special simple holes guarantee foldability. '
acknowledgement: This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank
all other participants for a fruitful atmosphere.
article_processing_charge: No
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Hugo A
full_name: Akitaya, Hugo A
last_name: Akitaya
- first_name: Kenneth C
full_name: Cheung, Kenneth C
last_name: Cheung
- first_name: Erik D
full_name: Demaine, Erik D
last_name: Demaine
- first_name: Martin L
full_name: Demaine, Martin L
last_name: Demaine
- first_name: Sandor P
full_name: Fekete, Sandor P
last_name: Fekete
- first_name: Linda
full_name: Kleist, Linda
last_name: Kleist
- first_name: Irina
full_name: Kostitsyna, Irina
last_name: Kostitsyna
- first_name: Maarten
full_name: Löffler, Maarten
last_name: Löffler
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Klara
full_name: Mundilova, Klara
last_name: Mundilova
- first_name: Christiane
full_name: Schmidt, Christiane
last_name: Schmidt
citation:
ama: 'Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes
into a cube. In: Proceedings of the 31st Canadian Conference on Computational
Geometry. Canadian Conference on Computational Geometry; 2019:164-170.'
apa: 'Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M.
L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a
cube. In Proceedings of the 31st Canadian Conference on Computational Geometry
(pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.'
chicago: Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin
L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes
into a Cube.” In Proceedings of the 31st Canadian Conference on Computational
Geometry, 164–70. Canadian Conference on Computational Geometry, 2019.
ieee: O. Aichholzer et al., “Folding polyominoes with holes into a cube,”
in Proceedings of the 31st Canadian Conference on Computational Geometry,
Edmonton, Canada, 2019, pp. 164–170.
ista: 'Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist
L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding
polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference
on Computational Geometry. CCCG: Canadian Conference in Computational Geometry,
164–170.'
mla: Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings
of the 31st Canadian Conference on Computational Geometry, Canadian Conference
on Computational Geometry, 2019, pp. 164–70.
short: O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P.
Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt,
in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian
Conference on Computational Geometry, 2019, pp. 164–170.
conference:
end_date: 2019-08-10
location: Edmonton, Canada
name: 'CCCG: Canadian Conference in Computational Geometry'
start_date: 2019-08-08
date_created: 2019-11-04T16:46:11Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-04T10:57:42Z
day: '01'
department:
- _id: HeEd
external_id:
arxiv:
- '1910.09917'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://cccg.ca/proceedings/2019/proceedings.pdf
month: '08'
oa: 1
oa_version: Published Version
page: 164-170
publication: Proceedings of the 31st Canadian Conference on Computational Geometry
publication_status: published
publisher: Canadian Conference on Computational Geometry
quality_controlled: '1'
related_material:
record:
- id: '8317'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: Folding polyominoes with holes into a cube
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2019'
...
---
_id: '13366'
abstract:
- lang: eng
text: The ability to reversibly assemble nanoparticles using light is both fundamentally
interesting and important for applications ranging from reversible data storage
to controlled drug delivery. Here, the diverse approaches that have so far been
developed to control the self-assembly of nanoparticles using light are reviewed
and compared. These approaches include functionalizing nanoparticles with monolayers
of photoresponsive molecules, placing them in photoresponsive media capable of
reversibly protonating the particles under light, and decorating plasmonic nanoparticles
with thermoresponsive polymers, to name just a few. The applicability of these
methods to larger, micrometer-sized particles is also discussed. Finally, several
perspectives on further developments in the field are offered.
article_number: '1905866'
article_processing_charge: No
article_type: original
author:
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Bian T, Chu Z, Klajn R. The many ways to assemble nanoparticles using light.
Advanced Materials. 2019;32(20). doi:10.1002/adma.201905866
apa: Bian, T., Chu, Z., & Klajn, R. (2019). The many ways to assemble nanoparticles
using light. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201905866
chicago: Bian, Tong, Zonglin Chu, and Rafal Klajn. “The Many Ways to Assemble Nanoparticles
Using Light.” Advanced Materials. Wiley, 2019. https://doi.org/10.1002/adma.201905866.
ieee: T. Bian, Z. Chu, and R. Klajn, “The many ways to assemble nanoparticles using
light,” Advanced Materials, vol. 32, no. 20. Wiley, 2019.
ista: Bian T, Chu Z, Klajn R. 2019. The many ways to assemble nanoparticles using
light. Advanced Materials. 32(20), 1905866.
mla: Bian, Tong, et al. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced
Materials, vol. 32, no. 20, 1905866, Wiley, 2019, doi:10.1002/adma.201905866.
short: T. Bian, Z. Chu, R. Klajn, Advanced Materials 32 (2019).
date_created: 2023-08-01T09:37:26Z
date_published: 2019-11-19T00:00:00Z
date_updated: 2023-08-07T10:23:41Z
day: '19'
doi: 10.1002/adma.201905866
extern: '1'
external_id:
pmid:
- '31709655'
intvolume: ' 32'
issue: '20'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- General Materials Science
language:
- iso: eng
month: '11'
oa_version: None
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The many ways to assemble nanoparticles using light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '13373'
abstract:
- lang: eng
text: The reversible photoisomerization of azobenzene has been utilized to construct
a plethora of systems in which optical, electronic, catalytic, and other properties
can be controlled by light. However, owing to azobenzene’s hydrophobic nature,
most of these examples have been realized only in organic solvents, and systems
operating in water are relatively scarce. Here, we show that by coadsorbing the
inherently hydrophobic azobenzenes with water-solubilizing ligands on the same
nanoparticulate platforms, it is possible to render them essentially water-soluble.
To this end, we developed a modified nanoparticle functionalization procedure
allowing us to precisely fine-tune the amount of azobenzene on the functionalized
nanoparticles. Molecular dynamics simulations helped us to identify two distinct
supramolecular architectures (depending on the length of the background ligand)
on these nanoparticles, which can explain their excellent aqueous solubilities.
Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible
photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer
approach allowed us to systematically investigate how the background ligand affects
the switching properties of azobenzene. We found that the nature of the background
ligand has a profound effect on the kinetics of azobenzene switching. For example,
a hydroxy-terminated background ligand is capable of accelerating the back-isomerization
reaction by more than 6000-fold. These results pave the way toward the development
of novel light-responsive nanomaterials operating in aqueous media and, in the
long run, in biological environments.
article_processing_charge: No
article_type: original
author:
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Yanxiao
full_name: Han, Yanxiao
last_name: Han
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Soumen
full_name: De, Soumen
last_name: De
- 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: Chu Z, Han Y, Bian T, De S, Král P, Klajn R. Supramolecular control of azobenzene
switching on nanoparticles. Journal of the American Chemical Society. 2019;141(5):1949-1960.
doi:10.1021/jacs.8b09638
apa: Chu, Z., Han, Y., Bian, T., De, S., Král, P., & Klajn, R. (2019). Supramolecular
control of azobenzene switching on nanoparticles. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09638
chicago: Chu, Zonglin, Yanxiao Han, Tong Bian, Soumen De, Petr Král, and Rafal Klajn.
“Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal
of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09638.
ieee: Z. Chu, Y. Han, T. Bian, S. De, P. Král, and R. Klajn, “Supramolecular control
of azobenzene switching on nanoparticles,” Journal of the American Chemical
Society, vol. 141, no. 5. American Chemical Society, pp. 1949–1960, 2019.
ista: Chu Z, Han Y, Bian T, De S, Král P, Klajn R. 2019. Supramolecular control
of azobenzene switching on nanoparticles. Journal of the American Chemical Society.
141(5), 1949–1960.
mla: Chu, Zonglin, et al. “Supramolecular Control of Azobenzene Switching on Nanoparticles.”
Journal of the American Chemical Society, vol. 141, no. 5, American Chemical
Society, 2019, pp. 1949–60, doi:10.1021/jacs.8b09638.
short: Z. Chu, Y. Han, T. Bian, S. De, P. Král, R. Klajn, Journal of the American
Chemical Society 141 (2019) 1949–1960.
date_created: 2023-08-01T09:39:19Z
date_published: 2019-02-06T00:00:00Z
date_updated: 2023-08-07T10:51:12Z
day: '06'
doi: 10.1021/jacs.8b09638
extern: '1'
external_id:
pmid:
- '30595017'
intvolume: ' 141'
issue: '5'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '02'
oa_version: Published Version
page: 1949-1960
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Supramolecular control of azobenzene switching on nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2019'
...
---
_id: '13372'
abstract:
- lang: eng
text: 'The capacity to respond or adapt to environmental changes is an intrinsic
property of living systems that comprise highly-connected subcomponents communicating
through chemical networks. The development of responsive synthetic systems is
a relatively new research area that covers different disciplines, among which
nanochemistry brings conceptually new demonstrations. Especially attractive are
ligand-protected gold nanoparticles, which have been extensively used over the
last decade as building blocks in constructing superlattices or dynamic aggregates,
under the effect of an applied stimulus. To reflect the importance of surface
chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles,
we provide here an overview of various available stimuli, as tools for synthetic
chemists to exploit. Along with this task, the review starts with the use of chemical
stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses
on physical stimuli: temperature, magnetic and electric fields, as well as light.
To reflect on the increasing complexity of current architectures, we discuss systems
that are responsive to more than one stimulus, to finally encourage further research
by proposing future challenges.'
article_processing_charge: No
article_type: original
author:
- first_name: Marek
full_name: Grzelczak, Marek
last_name: Grzelczak
- first_name: Luis M.
full_name: Liz-Marzán, Luis M.
last_name: Liz-Marzán
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles.
Chemical Society Reviews. 2019;48(5):1342-1361. doi:10.1039/c8cs00787j
apa: Grzelczak, M., Liz-Marzán, L. M., & Klajn, R. (2019). Stimuli-responsive
self-assembly of nanoparticles. Chemical Society Reviews. Royal Society
of Chemistry. https://doi.org/10.1039/c8cs00787j
chicago: Grzelczak, Marek, Luis M. Liz-Marzán, and Rafal Klajn. “Stimuli-Responsive
Self-Assembly of Nanoparticles.” Chemical Society Reviews. Royal Society
of Chemistry, 2019. https://doi.org/10.1039/c8cs00787j.
ieee: M. Grzelczak, L. M. Liz-Marzán, and R. Klajn, “Stimuli-responsive self-assembly
of nanoparticles,” Chemical Society Reviews, vol. 48, no. 5. Royal Society
of Chemistry, pp. 1342–1361, 2019.
ista: Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly
of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361.
mla: Grzelczak, Marek, et al. “Stimuli-Responsive Self-Assembly of Nanoparticles.”
Chemical Society Reviews, vol. 48, no. 5, Royal Society of Chemistry, 2019,
pp. 1342–61, doi:10.1039/c8cs00787j.
short: M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019)
1342–1361.
date_created: 2023-08-01T09:38:52Z
date_published: 2019-01-28T00:00:00Z
date_updated: 2023-08-07T10:48:31Z
day: '28'
doi: 10.1039/c8cs00787j
extern: '1'
external_id:
pmid:
- '30688963'
intvolume: ' 48'
issue: '5'
keyword:
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C8CS00787J
month: '01'
oa: 1
oa_version: Published Version
page: 1342-1361
pmid: 1
publication: Chemical Society Reviews
publication_identifier:
eissn:
- 1460-4744
issn:
- 0306-0012
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stimuli-responsive self-assembly of nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2019'
...
---
_id: '13369'
abstract:
- lang: eng
text: Arylazopyrazoles represent a new family of molecular photoswitches characterized
by a near-quantitative conversion between two states and long thermal half-lives
of the metastable state. Here, we investigated the behavior of a model arylazopyrazole
in the presence of a self-assembled cage based on Pd–imidazole coordination. Owing
to its high water solubility, the cage can solubilize the E isomer of arylazopyrazole,
which, by itself, is not soluble in water. NMR spectroscopy and X-ray crystallography
have independently demonstrated that each cage can encapsulate two molecules of
E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the
release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole
inclusion complex. DFT calculations suggest that this process involves a dramatic
change in the conformation of the cage. Back-isomerization was induced with green
light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization
reaction also proceeded in the dark, with a rate significantly higher than in
the absence of the cage.
article_processing_charge: No
article_type: original
author:
- first_name: Anton I
full_name: Hanopolskyi, Anton I
last_name: Hanopolskyi
- first_name: Soumen
full_name: De, Soumen
last_name: De
- first_name: Michał J
full_name: Białek, Michał J
last_name: Białek
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Moran
full_name: Feller, Moran
last_name: Feller
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Hanopolskyi AI, De S, Białek MJ, et al. Reversible switching of arylazopyrazole
within a metal–organic cage. Beilstein Journal of Organic Chemistry. 2019;15:2398-2407.
doi:10.3762/bjoc.15.232
apa: Hanopolskyi, A. I., De, S., Białek, M. J., Diskin-Posner, Y., Avram, L., Feller,
M., & Klajn, R. (2019). Reversible switching of arylazopyrazole within a metal–organic
cage. Beilstein Journal of Organic Chemistry. Beilstein Institut. https://doi.org/10.3762/bjoc.15.232
chicago: Hanopolskyi, Anton I, Soumen De, Michał J Białek, Yael Diskin-Posner, Liat
Avram, Moran Feller, and Rafal Klajn. “Reversible Switching of Arylazopyrazole
within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry. Beilstein
Institut, 2019. https://doi.org/10.3762/bjoc.15.232.
ieee: A. I. Hanopolskyi et al., “Reversible switching of arylazopyrazole
within a metal–organic cage,” Beilstein Journal of Organic Chemistry, vol.
15. Beilstein Institut, pp. 2398–2407, 2019.
ista: Hanopolskyi AI, De S, Białek MJ, Diskin-Posner Y, Avram L, Feller M, Klajn
R. 2019. Reversible switching of arylazopyrazole within a metal–organic cage.
Beilstein Journal of Organic Chemistry. 15, 2398–2407.
mla: Hanopolskyi, Anton I., et al. “Reversible Switching of Arylazopyrazole within
a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry, vol. 15,
Beilstein Institut, 2019, pp. 2398–407, doi:10.3762/bjoc.15.232.
short: A.I. Hanopolskyi, S. De, M.J. Białek, Y. Diskin-Posner, L. Avram, M. Feller,
R. Klajn, Beilstein Journal of Organic Chemistry 15 (2019) 2398–2407.
date_created: 2023-08-01T09:38:06Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-08-07T10:34:56Z
day: '10'
doi: 10.3762/bjoc.15.232
extern: '1'
external_id:
pmid:
- '31666874'
intvolume: ' 15'
keyword:
- Organic Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3762/bjoc.15.232
month: '10'
oa: 1
oa_version: Published Version
page: 2398-2407
pmid: 1
publication: Beilstein Journal of Organic Chemistry
publication_identifier:
eissn:
- 1860-5397
publication_status: published
publisher: Beilstein Institut
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible switching of arylazopyrazole within a metal–organic cage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...
---
_id: '13370'
abstract:
- lang: eng
text: Efficient isomerization of photochromic molecules often requires conformational
freedom and is typically not available under solvent-free conditions. Here, we
report a general methodology allowing for reversible switching of such molecules
on the surfaces of solid materials. Our method is based on dispersing photochromic
compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated
as transparent, highly porous, micrometer-thick layers on various substrates.
We found that azobenzene switching within the PNNs proceeded unusually fast compared
with the same molecules in liquid solvents. Efficient isomerization of another
photochromic system, spiropyran, from a colorless to a colored form was used to
create reversible images in PNN-coated glass. The coloration reaction could be
induced with sunlight and is of interest for developing “smart” windows.
article_processing_charge: No
article_type: original
author:
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Chu Z, Klajn R. Polysilsesquioxane nanowire networks as an “Artificial Solvent”
for reversible operation of photochromic molecules. Nano Letters. 2019;19(10):7106-7111.
doi:10.1021/acs.nanolett.9b02642
apa: Chu, Z., & Klajn, R. (2019). Polysilsesquioxane nanowire networks as an
“Artificial Solvent” for reversible operation of photochromic molecules. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b02642
chicago: Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as
an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano
Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b02642.
ieee: Z. Chu and R. Klajn, “Polysilsesquioxane nanowire networks as an ‘Artificial
Solvent’ for reversible operation of photochromic molecules,” Nano Letters,
vol. 19, no. 10. American Chemical Society, pp. 7106–7111, 2019.
ista: Chu Z, Klajn R. 2019. Polysilsesquioxane nanowire networks as an “Artificial
Solvent” for reversible operation of photochromic molecules. Nano Letters. 19(10),
7106–7111.
mla: Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an
‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano
Letters, vol. 19, no. 10, American Chemical Society, 2019, pp. 7106–11, doi:10.1021/acs.nanolett.9b02642.
short: Z. Chu, R. Klajn, Nano Letters 19 (2019) 7106–7111.
date_created: 2023-08-01T09:38:23Z
date_published: 2019-09-20T00:00:00Z
date_updated: 2023-08-07T10:39:34Z
day: '20'
doi: 10.1021/acs.nanolett.9b02642
extern: '1'
external_id:
pmid:
- '31539469'
intvolume: ' 19'
issue: '10'
keyword:
- Mechanical Engineering
- Condensed Matter Physics
- General Materials Science
- General Chemistry
- Bioengineering
language:
- iso: eng
month: '09'
oa_version: None
page: 7106-7111
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible
operation of photochromic molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2019'
...
---
_id: '13371'
abstract:
- lang: eng
text: Diamondoid nanoporous crystals represent a synthetically challenging class
of materials that typically have been obtained from tetrahedral building blocks.
In this issue of Chem, Stoddart and coworkers demonstrate that it is possible
to generate diamondoid frameworks from a hexacationic building block lacking a
tetrahedral symmetry. These results highlight the great potential of self-assembly
for rapidly transforming small molecules into structurally complex functional
materials.
article_processing_charge: No
article_type: original
author:
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Białek MJ, Klajn R. Diamond grows up. Chem. 2019;5(9):2283-2285. doi:10.1016/j.chempr.2019.08.012
apa: Białek, M. J., & Klajn, R. (2019). Diamond grows up. Chem. Elsevier.
https://doi.org/10.1016/j.chempr.2019.08.012
chicago: Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem. Elsevier,
2019. https://doi.org/10.1016/j.chempr.2019.08.012.
ieee: M. J. Białek and R. Klajn, “Diamond grows up,” Chem, vol. 5, no. 9.
Elsevier, pp. 2283–2285, 2019.
ista: Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285.
mla: Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem, vol. 5,
no. 9, Elsevier, 2019, pp. 2283–85, doi:10.1016/j.chempr.2019.08.012.
short: M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.
date_created: 2023-08-01T09:38:38Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-07T10:46:50Z
day: '12'
doi: 10.1016/j.chempr.2019.08.012
extern: '1'
intvolume: ' 5'
issue: '9'
keyword:
- Materials Chemistry
- Biochemistry (medical)
- General Chemical Engineering
- Environmental Chemistry
- Biochemistry
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chempr.2019.08.012
month: '09'
oa: 1
oa_version: Published Version
page: 2283-2285
publication: Chem
publication_identifier:
eissn:
- 2451-9294
issn:
- 2451-9308
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diamond grows up
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2019'
...
---
_id: '6884'
abstract:
- lang: eng
text: 'In two-player games on graphs, the players move a token through a graph to
produce a finite or infinite path, which determines the qualitative winner or
quantitative payoff of the game. We study bidding games in which the players bid
for the right to move the token. Several bidding rules were studied previously.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the "bank" rather than the
other player. Taxman bidding spans the spectrum between Richman and poorman bidding.
They are parameterized by a constant tau in [0,1]: portion tau of the winning
bid is paid to the other player, and portion 1-tau to the bank. While finite-duration
(reachability) taxman games have been studied before, we present, for the first
time, results on infinite-duration taxman games. It was previously shown that
both Richman and poorman infinite-duration games with qualitative objectives reduce
to reachability games, and we show a similar result here. Our most interesting
results concern quantitative taxman games, namely mean-payoff games, where poorman
and Richman bidding differ significantly. A central quantity in these games is
the ratio between the two players'' initial budgets. While in poorman mean-payoff
games, the optimal payoff of a player depends on the initial ratio, in Richman
bidding, the payoff depends only on the structure of the game. In both games the
optimal payoffs can be found using (different) probabilistic connections with
random-turn games in which in each turn, instead of bidding, a coin is tossed
to determine which player moves. While the value with Richman bidding equals the
value of a random-turn game with an un-biased coin, with poorman bidding, the
bias in the coin is the initial ratio of the budgets. We give a complete classification
of mean-payoff taxman games that is based on a probabilistic connection: the value
of a taxman bidding game with parameter tau and initial ratio r, equals the value
of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau).
Thus, we show that Richman bidding is the exception; namely, for every tau <1,
the value of the game depends on the initial ratio. Our proof technique simplifies
and unifies the previous proof techniques for both Richman and poorman bidding. '
alternative_title:
- LIPIcs
article_number: '11'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
citation:
ama: 'Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol
138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11'
apa: 'Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in
graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical
Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11'
chicago: Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in
Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.
https://doi.org/10.4230/LIPICS.MFCS.2019.11.
ieee: 'G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,”
presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer
Science, Aachen, Germany, 2019, vol. 138.'
ista: 'Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games.
MFCS: nternational Symposium on Mathematical Foundations of Computer Science,
LIPIcs, vol. 138, 11.'
mla: Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11.
short: G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019.
conference:
end_date: 2019-08-30
location: Aachen, Germany
name: 'MFCS: nternational Symposium on Mathematical Foundations of Computer Science'
start_date: 2019-08-26
date_created: 2019-09-18T08:04:26Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-07T14:08:34Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPICS.MFCS.2019.11
ec_funded: 1
external_id:
arxiv:
- '1905.03835'
file:
- access_level: open_access
checksum: 6346e116a4f4ed1414174d96d2c4fbd7
content_type: application/pdf
creator: kschuh
date_created: 2019-09-27T11:45:15Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6913'
file_name: 2019_LIPIcs_Avni.pdf
file_size: 554457
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 138'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '9239'
relation: later_version
status: public
scopus_import: 1
status: public
title: Bidding mechanisms in graph games
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: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2019'
...
---
_id: '13471'
abstract:
- lang: eng
text: We perform an extensive numerical study of the evolution of massive binary
systems to predict the peculiar velocities that stars obtain when their companion
collapses and disrupts the system. Our aim is to (i) identify which predictions
are robust against model uncertainties and assess their implications, (ii) investigate
which physical processes leave a clear imprint and may therefore be constrained
observationally, and (iii) provide a suite of publicly available model predictions
to allow for the use of kinematic constraints from the Gaia mission. We find that
22+26−8% of all massive binary systems merge prior to the first core-collapse
in the system. Of the remainder, 86+11−9% become unbound because of the core-collapse.
Remarkably, this rarely produces runaway stars (observationally defined as stars
with velocities above 30 km s−1). These are outnumbered by more than an order
of magnitude by slower unbound companions, or “walkaway stars”. This is a robust
outcome of our simulations and is due to the reversal of the mass ratio prior
to the explosion and widening of the orbit, as we show analytically and numerically.
For stars more massive than 15 M⊙, we estimate that 10+5−8% are walkaways and
only 0.5+1.0−0.4% are runaways, nearly all of which have accreted mass from their
companion. Our findings are consistent with earlier studies; however, the low
runaway fraction we find is in tension with observed fractions of about 10%. Thus,
astrometric data on presently single massive stars can potentially constrain the
physics of massive binary evolution. Finally, we show that the high end of the
mass distributions of runaway stars is very sensitive to the assumed black hole
natal kicks, and we propose this as a potentially stringent test for the explosion
mechanism. We also discuss companions remaining bound that can evolve into X-ray
and gravitational wave sources.
article_number: A66
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Renzo, M.
last_name: Renzo
- first_name: E.
full_name: Zapartas, E.
last_name: Zapartas
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: S.
full_name: Justham, S.
last_name: Justham
- first_name: R. J.
full_name: Farmer, R. J.
last_name: Farmer
- first_name: R. G.
full_name: Izzard, R. G.
last_name: Izzard
- first_name: S.
full_name: Toonen, S.
last_name: Toonen
- first_name: H.
full_name: Sana, H.
last_name: Sana
citation:
ama: Renzo M, Zapartas E, de Mink SE, et al. Massive runaway and walkaway stars.
Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201833297
apa: Renzo, M., Zapartas, E., de Mink, S. E., Götberg, Y. L. L., Justham, S., Farmer,
R. J., … Sana, H. (2019). Massive runaway and walkaway stars. Astronomy &
Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833297
chicago: Renzo, M., E. Zapartas, S. E. de Mink, Ylva Louise Linsdotter Götberg,
S. Justham, R. J. Farmer, R. G. Izzard, S. Toonen, and H. Sana. “Massive Runaway
and Walkaway Stars.” Astronomy & Astrophysics. EDP Sciences, 2019.
https://doi.org/10.1051/0004-6361/201833297.
ieee: M. Renzo et al., “Massive runaway and walkaway stars,” Astronomy
& Astrophysics, vol. 624. EDP Sciences, 2019.
ista: Renzo M, Zapartas E, de Mink SE, Götberg YLL, Justham S, Farmer RJ, Izzard
RG, Toonen S, Sana H. 2019. Massive runaway and walkaway stars. Astronomy &
Astrophysics. 624, A66.
mla: Renzo, M., et al. “Massive Runaway and Walkaway Stars.” Astronomy &
Astrophysics, vol. 624, A66, EDP Sciences, 2019, doi:10.1051/0004-6361/201833297.
short: M. Renzo, E. Zapartas, S.E. de Mink, Y.L.L. Götberg, S. Justham, R.J. Farmer,
R.G. Izzard, S. Toonen, H. Sana, Astronomy & Astrophysics 624 (2019).
date_created: 2023-08-03T10:14:18Z
date_published: 2019-04-11T00:00:00Z
date_updated: 2023-08-09T12:26:08Z
day: '11'
doi: 10.1051/0004-6361/201833297
extern: '1'
external_id:
arxiv:
- '1804.09164'
intvolume: ' 624'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201833297
month: '04'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Massive runaway and walkaway stars
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 624
year: '2019'
...
---
_id: '13470'
abstract:
- lang: eng
text: "Context. Massive Wolf–Rayet (WR) stars dominate the radiative and mechanical
energy budget of galaxies and probe a critical phase in the evolution of massive
stars prior to core collapse. It is not known whether core He-burning WR stars
(classical WR; cWR) form predominantly through wind stripping (w-WR) or binary
stripping (b-WR). Whereas spectroscopy of WR binaries has so-far largely been
avoided because of its complexity, our study focuses on the 44 WR binaries and
binary candidates of the Large Magellanic Cloud (LMC; metallicity Z ≈ 0.5 Z⊙),
which were identified on the basis of radial velocity variations, composite spectra,
or high X-ray luminosities.\r\n\r\nAims. Relying on a diverse spectroscopic database,
we aim to derive the physical and orbital parameters of our targets, confronting
evolution models of evolved massive stars at subsolar metallicity and constraining
the impact of binary interaction in forming these stars.\r\n\r\nMethods. Spectroscopy
was performed using the Potsdam Wolf–Rayet (PoWR) code and cross-correlation techniques.
Disentanglement was performed using the code Spectangular or the shift-and-add
algorithm. Evolutionary status was interpreted using the Binary Population and
Spectral Synthesis (BPASS) code, exploring binary interaction and chemically homogeneous
evolution.\r\n\r\nResults. Among our sample, 28/44 objects show composite spectra
and are analyzed as such. An additional five targets show periodically moving
WR primaries but no detected companions (SB1); two (BAT99 99 and 112) are potential
WR + compact-object candidates owing to their high X-ray luminosities. We cannot
confirm the binary nature of the remaining 11 candidates. About two-thirds of
the WN components in binaries are identified as cWR, and one-third as hydrogen-burning
WR stars. We establish metallicity-dependent mass-loss recipes, which broadly
agree with those recently derived for single WN stars, and in which so-called
WN3/O3 stars are clear outliers. We estimate that 45 ± 30% of the cWR stars
in our sample have interacted with a companion via mass transfer. However, only
≈12 ± 7% of the cWR stars in our sample naively appear to have formed purely
owing to stripping via a companion (12% b-WR). Assuming that apparently single
WR stars truly formed as single stars, this comprises ≈4% of the whole LMC WN
population, which is about ten times less than expected. No obvious differences
in the properties of single and binary WN stars, whose luminosities extend down
to log L ≈ 5.2 [L⊙], are apparent. With the exception of a few systems (BAT99
19, 49, and 103), the equatorial rotational velocities of the OB-type companions
are moderate (veq ≲ 250 km s−1) and challenge standard formalisms of angular-momentum
accretion. For most objects, chemically homogeneous evolution can be rejected
for the secondary, but not for the WR progenitor.\r\n\r\nConclusions. No obvious
dichotomy in the locations of apparently single and binary WN stars on the Hertzsprung-Russell
diagram is apparent. According to commonly used stellar evolution models (BPASS,
Geneva), most apparently single WN stars could not have formed as single stars,
implying that they were stripped by an undetected companion. Otherwise, it must
follow that pre-WR mass-loss/mixing (e.g., during the red supergiant phase) are
strongly underestimated in standard stellar evolution models."
article_number: A151
article_processing_charge: No
article_type: original
author:
- first_name: T.
full_name: Shenar, T.
last_name: Shenar
- first_name: D. P.
full_name: Sablowski, D. P.
last_name: Sablowski
- first_name: R.
full_name: Hainich, R.
last_name: Hainich
- first_name: H.
full_name: Todt, H.
last_name: Todt
- first_name: A. F. J.
full_name: Moffat, A. F. J.
last_name: Moffat
- first_name: L. M.
full_name: Oskinova, L. M.
last_name: Oskinova
- first_name: V.
full_name: Ramachandran, V.
last_name: Ramachandran
- first_name: H.
full_name: Sana, H.
last_name: Sana
- first_name: A. A. C.
full_name: Sander, A. A. C.
last_name: Sander
- first_name: O.
full_name: Schnurr, O.
last_name: Schnurr
- first_name: N.
full_name: St-Louis, N.
last_name: St-Louis
- first_name: D.
full_name: Vanbeveren, D.
last_name: Vanbeveren
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: W.-R.
full_name: Hamann, W.-R.
last_name: Hamann
citation:
ama: Shenar T, Sablowski DP, Hainich R, et al. The Wolf–Rayet binaries of the nitrogen
sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 2019;627.
doi:10.1051/0004-6361/201935684
apa: Shenar, T., Sablowski, D. P., Hainich, R., Todt, H., Moffat, A. F. J., Oskinova,
L. M., … Hamann, W.-R. (2019). The Wolf–Rayet binaries of the nitrogen sequence
in the Large Magellanic Cloud. Astronomy & Astrophysics. EDP Sciences.
https://doi.org/10.1051/0004-6361/201935684
chicago: Shenar, T., D. P. Sablowski, R. Hainich, H. Todt, A. F. J. Moffat, L. M.
Oskinova, V. Ramachandran, et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence
in the Large Magellanic Cloud.” Astronomy & Astrophysics. EDP Sciences,
2019. https://doi.org/10.1051/0004-6361/201935684.
ieee: T. Shenar et al., “The Wolf–Rayet binaries of the nitrogen sequence
in the Large Magellanic Cloud,” Astronomy & Astrophysics, vol. 627.
EDP Sciences, 2019.
ista: Shenar T, Sablowski DP, Hainich R, Todt H, Moffat AFJ, Oskinova LM, Ramachandran
V, Sana H, Sander AAC, Schnurr O, St-Louis N, Vanbeveren D, Götberg YLL, Hamann
W-R. 2019. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic
Cloud. Astronomy & Astrophysics. 627, A151.
mla: Shenar, T., et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the
Large Magellanic Cloud.” Astronomy & Astrophysics, vol. 627, A151,
EDP Sciences, 2019, doi:10.1051/0004-6361/201935684.
short: T. Shenar, D.P. Sablowski, R. Hainich, H. Todt, A.F.J. Moffat, L.M. Oskinova,
V. Ramachandran, H. Sana, A.A.C. Sander, O. Schnurr, N. St-Louis, D. Vanbeveren,
Y.L.L. Götberg, W.-R. Hamann, Astronomy & Astrophysics 627 (2019).
date_created: 2023-08-03T10:14:09Z
date_published: 2019-07-16T00:00:00Z
date_updated: 2023-08-09T12:29:58Z
day: '16'
doi: 10.1051/0004-6361/201935684
extern: '1'
intvolume: ' 627'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201935684
month: '07'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1051/0004-6361/201935684e
scopus_import: '1'
status: public
title: The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 627
year: '2019'
...
---
_id: '13472'
abstract:
- lang: eng
text: Massive stars in binaries can give rise to extreme phenomena such as X-ray
binaries and gravitational wave sources after one or both stars end their lives
as core-collapse supernovae. Stars in close orbit around a stellar or compact
companion are expected to explode as “stripped-envelope supernovae”, showing no
(Type Ib/c) or little (Type IIb) signs of hydrogen in the spectra, because hydrogen-rich
progenitors are too large to fit. The physical processes responsible for the stripping
process and the fate of the companion are still very poorly understood. Aiming
to find new clues, we investigate Cas A, which is a very young (∼340 yr) and near
(∼3.4 kpc) remnant of a core-collapse supernova. Cas A has been subject to several
searches for possible companions, all unsuccessfully. We present new measurements
of the proper motions and photometry of stars in the vicinity based on deep HST
ACS/WFC and WFC3-IR data. We identify stellar sources that are close enough in
projection but using their proper motions we show that none are compatible with
being at the location of center at the time of explosion, in agreement with earlier
findings. Our photometric measurements allow us to place much deeper (order-of-magnitude)
upper limits on the brightness of possible undetected companions. We systematically
compare them with model predictions for a wide variety of scenarios. We can confidently
rule out the presence of any stellar companion of any reasonable mass and age
(main sequence, pre main sequence or stripped) ruling out what many considered
to be likely evolutionary scenarios for Type IIb supernova (SN IIb). More exotic
scenarios that predict the presence of a compact companion (white dwarf, neutron
star or black hole) are still possible as well as scenarios where the progenitor
of Cas A was single at the moment of explosion (either because it was truly single,
or resulted from a binary that was disrupted, or from a binary merger). The presence
of a compact companion would imply that Cas A is of interest to study exotic outcomes
of binary evolution. The single-at-death solution would still require fine-tuning
of the process that removed most of the envelope through a mass-loss mechanism
yet to be identified. We discuss how future constraints from Gaia and even deeper
photometric studies may help to place further constraints.
article_number: A34
article_processing_charge: No
article_type: original
author:
- first_name: Wolfgang E.
full_name: Kerzendorf, Wolfgang E.
last_name: Kerzendorf
- first_name: Tuan
full_name: Do, Tuan
last_name: Do
- first_name: Selma E.
full_name: de Mink, Selma E.
last_name: de Mink
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: Dan
full_name: Milisavljevic, Dan
last_name: Milisavljevic
- first_name: Emmanouil
full_name: Zapartas, Emmanouil
last_name: Zapartas
- first_name: Mathieu
full_name: Renzo, Mathieu
last_name: Renzo
- first_name: Stephen
full_name: Justham, Stephen
last_name: Justham
- first_name: Philipp
full_name: Podsiadlowski, Philipp
last_name: Podsiadlowski
- first_name: Robert A.
full_name: Fesen, Robert A.
last_name: Fesen
citation:
ama: Kerzendorf WE, Do T, de Mink SE, et al. No surviving non-compact stellar companion
to Cassiopeia A. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201732206
apa: Kerzendorf, W. E., Do, T., de Mink, S. E., Götberg, Y. L. L., Milisavljevic,
D., Zapartas, E., … Fesen, R. A. (2019). No surviving non-compact stellar companion
to Cassiopeia A. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732206
chicago: Kerzendorf, Wolfgang E., Tuan Do, Selma E. de Mink, Ylva Louise Linsdotter
Götberg, Dan Milisavljevic, Emmanouil Zapartas, Mathieu Renzo, Stephen Justham,
Philipp Podsiadlowski, and Robert A. Fesen. “No Surviving Non-Compact Stellar
Companion to Cassiopeia A.” Astronomy & Astrophysics. EDP Sciences,
2019. https://doi.org/10.1051/0004-6361/201732206.
ieee: W. E. Kerzendorf et al., “No surviving non-compact stellar companion
to Cassiopeia A,” Astronomy & Astrophysics, vol. 623. EDP Sciences,
2019.
ista: Kerzendorf WE, Do T, de Mink SE, Götberg YLL, Milisavljevic D, Zapartas E,
Renzo M, Justham S, Podsiadlowski P, Fesen RA. 2019. No surviving non-compact
stellar companion to Cassiopeia A. Astronomy & Astrophysics. 623, A34.
mla: Kerzendorf, Wolfgang E., et al. “No Surviving Non-Compact Stellar Companion
to Cassiopeia A.” Astronomy & Astrophysics, vol. 623, A34, EDP Sciences,
2019, doi:10.1051/0004-6361/201732206.
short: W.E. Kerzendorf, T. Do, S.E. de Mink, Y.L.L. Götberg, D. Milisavljevic, E.
Zapartas, M. Renzo, S. Justham, P. Podsiadlowski, R.A. Fesen, Astronomy &
Astrophysics 623 (2019).
date_created: 2023-08-03T10:14:27Z
date_published: 2019-03-27T00:00:00Z
date_updated: 2023-08-09T12:28:17Z
day: '27'
doi: 10.1051/0004-6361/201732206
extern: '1'
external_id:
arxiv:
- '1711.00055'
intvolume: ' 623'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201732206
month: '03'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: No surviving non-compact stellar companion to Cassiopeia A
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 623
year: '2019'
...
---
_id: '13468'
abstract:
- lang: eng
text: Hydrogen-rich supernovae, known as Type II (SNe II), are the most common class
of explosions observed following the collapse of the core of massive stars. We
used analytical estimates and population synthesis simulations to assess the fraction
of SNe II progenitors that are expected to have exchanged mass with a companion
prior to explosion. We estimate that 1/3 to 1/2 of SN II progenitors have a history
of mass exchange with a binary companion before exploding. The dominant binary
channels leading to SN II progenitors involve the merger of binary stars. Mergers
are expected to produce a diversity of SN II progenitor characteristics, depending
on the evolutionary timing and properties of the merger. Alternatively, SN II
progenitors from interacting binaries may have accreted mass from their companion,
and subsequently been ejected from the binary system after their companion exploded.
We show that the overall fraction of SN II progenitors that are predicted to have
experienced binary interaction is robust against the main physical uncertainties
in our models. However, the relative importance of different binary evolutionary
channels is affected by changing physical assumptions. We further discuss ways
in which binarity might contribute to the observed diversity of SNe II by considering
potential observational signatures arising from each binary channel. For supernovae
which have a substantial H-rich envelope at explosion (i.e., excluding Type IIb
SNe), a surviving non-compact companion would typically indicate that the supernova
progenitor star was in a wide, non-interacting binary. We argue that a significant
fraction of even Type II-P SNe are expected to have gained mass from a companion
prior to explosion.
article_number: A5
article_processing_charge: No
article_type: original
author:
- first_name: Emmanouil
full_name: Zapartas, Emmanouil
last_name: Zapartas
- first_name: Selma E.
full_name: de Mink, Selma E.
last_name: de Mink
- first_name: Stephen
full_name: Justham, Stephen
last_name: Justham
- first_name: Nathan
full_name: Smith, Nathan
last_name: Smith
- first_name: Alex
full_name: de Koter, Alex
last_name: de Koter
- first_name: Mathieu
full_name: Renzo, Mathieu
last_name: Renzo
- first_name: Iair
full_name: Arcavi, Iair
last_name: Arcavi
- first_name: Rob
full_name: Farmer, Rob
last_name: Farmer
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: Silvia
full_name: Toonen, Silvia
last_name: Toonen
citation:
ama: 'Zapartas E, de Mink SE, Justham S, et al. The diverse lives of progenitors
of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy
& Astrophysics. 2019;631. doi:10.1051/0004-6361/201935854'
apa: 'Zapartas, E., de Mink, S. E., Justham, S., Smith, N., de Koter, A., Renzo,
M., … Toonen, S. (2019). The diverse lives of progenitors of hydrogen-rich core-collapse
supernovae: The role of binary interaction. Astronomy & Astrophysics.
EDP Sciences. https://doi.org/10.1051/0004-6361/201935854'
chicago: 'Zapartas, Emmanouil, Selma E. de Mink, Stephen Justham, Nathan Smith,
Alex de Koter, Mathieu Renzo, Iair Arcavi, Rob Farmer, Ylva Louise Linsdotter
Götberg, and Silvia Toonen. “The Diverse Lives of Progenitors of Hydrogen-Rich
Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy &
Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935854.'
ieee: 'E. Zapartas et al., “The diverse lives of progenitors of hydrogen-rich
core-collapse supernovae: The role of binary interaction,” Astronomy &
Astrophysics, vol. 631. EDP Sciences, 2019.'
ista: 'Zapartas E, de Mink SE, Justham S, Smith N, de Koter A, Renzo M, Arcavi I,
Farmer R, Götberg YLL, Toonen S. 2019. The diverse lives of progenitors of hydrogen-rich
core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics.
631, A5.'
mla: 'Zapartas, Emmanouil, et al. “The Diverse Lives of Progenitors of Hydrogen-Rich
Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy &
Astrophysics, vol. 631, A5, EDP Sciences, 2019, doi:10.1051/0004-6361/201935854.'
short: E. Zapartas, S.E. de Mink, S. Justham, N. Smith, A. de Koter, M. Renzo, I.
Arcavi, R. Farmer, Y.L.L. Götberg, S. Toonen, Astronomy & Astrophysics 631
(2019).
date_created: 2023-08-03T10:13:52Z
date_published: 2019-11-20T00:00:00Z
date_updated: 2023-08-09T12:36:09Z
day: '20'
doi: 10.1051/0004-6361/201935854
extern: '1'
external_id:
arxiv:
- '1907.06687'
intvolume: ' 631'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201935854
month: '11'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The diverse lives of progenitors of hydrogen-rich core-collapse supernovae:
The role of binary interaction'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 631
year: '2019'
...
---
_id: '13469'
abstract:
- lang: eng
text: Stars stripped of their envelopes from interaction with a binary companion
emit a significant fraction of their radiation as ionizing photons. They are potentially
important stellar sources of ionizing radiation, however, they are still often
neglected in spectral synthesis simulations or simulations of stellar feedback.
In anticipating the large datasets of galaxy spectra from the upcoming James Webb
Space Telescope, we modeled the radiative contribution from stripped stars by
using detailed evolutionary and spectral models. We estimated their impact on
the integrated spectra and specifically on the emission rates of H I-, He I-,
and He II-ionizing photons from stellar populations. We find that stripped stars
have the largest impact on the ionizing spectrum of a population in which star
formation halted several Myr ago. In such stellar populations, stripped stars
dominate the emission of ionizing photons, mimicking a younger stellar population
in which massive stars are still present. Our models also suggest that stripped
stars have harder ionizing spectra than massive stars. The additional ionizing
radiation, with which stripped stars contribute affects observable properties
that are related to the emission of ionizing photons from stellar populations.
In co-eval stellar populations, the ionizing radiation from stripped stars increases
the ionization parameter and the production efficiency of hydrogen ionizing photons.
They also cause high values for these parameters for about ten times longer than
what is predicted for massive stars. The effect on properties related to non-ionizing
wavelengths is less pronounced, such as on the ultraviolet continuum slope or
stellar contribution to emission lines. However, the hard ionizing radiation from
stripped stars likely introduces a characteristic ionization structure of the
nebula, which leads to the emission of highly ionized elements such as O2+ and
C3+. We, therefore, expect that the presence of stripped stars affects the location
in the BPT diagram and the diagnostic ratio of O III to O II nebular emission
lines. Our models are publicly available through CDS database and on the STARBURST99
website.
article_number: A134
article_processing_charge: No
article_type: original
author:
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: J. H.
full_name: Groh, J. H.
last_name: Groh
- first_name: C.
full_name: Leitherer, C.
last_name: Leitherer
- first_name: C.
full_name: Norman, C.
last_name: Norman
citation:
ama: Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. The impact of stars
stripped in binaries on the integrated spectra of stellar populations. Astronomy
& Astrophysics. 2019;629. doi:10.1051/0004-6361/201834525
apa: Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Leitherer, C., & Norman,
C. (2019). The impact of stars stripped in binaries on the integrated spectra
of stellar populations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834525
chicago: Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, C. Leitherer,
and C. Norman. “The Impact of Stars Stripped in Binaries on the Integrated Spectra
of Stellar Populations.” Astronomy & Astrophysics. EDP Sciences, 2019.
https://doi.org/10.1051/0004-6361/201834525.
ieee: Y. L. L. Götberg, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman,
“The impact of stars stripped in binaries on the integrated spectra of stellar
populations,” Astronomy & Astrophysics, vol. 629. EDP Sciences, 2019.
ista: Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. 2019. The impact
of stars stripped in binaries on the integrated spectra of stellar populations.
Astronomy & Astrophysics. 629, A134.
mla: Götberg, Ylva Louise Linsdotter, et al. “The Impact of Stars Stripped in Binaries
on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics,
vol. 629, A134, EDP Sciences, 2019, doi:10.1051/0004-6361/201834525.
short: Y.L.L. Götberg, S.E. de Mink, J.H. Groh, C. Leitherer, C. Norman, Astronomy
& Astrophysics 629 (2019).
date_created: 2023-08-03T10:14:00Z
date_published: 2019-09-17T00:00:00Z
date_updated: 2023-08-09T12:34:11Z
day: '17'
doi: 10.1051/0004-6361/201834525
extern: '1'
external_id:
arxiv:
- '1908.06102'
intvolume: ' 629'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/201834525
month: '09'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The impact of stars stripped in binaries on the integrated spectra of stellar
populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 629
year: '2019'
...
---
_id: '9726'
abstract:
- lang: eng
text: A detailed description of the two stochastic models, table of parameters,
supplementary data for Figures 4 and 5, parameter dependence of the results, and
an analysis on motors with different force–velocity functions (PDF)
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Reinhard
full_name: Lipowsky, Reinhard
last_name: Lipowsky
citation:
ama: Ucar MC, Lipowsky R. Supplementary information - Collective force generation
by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001
apa: Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective
force generation by molecular motors is determined by strain-induced unbinding.
American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective
Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.”
American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.
ieee: M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force
generation by molecular motors is determined by strain-induced unbinding.” American
Chemical Society , 2019.
ista: Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation
by molecular motors is determined by strain-induced unbinding, American Chemical
Society , 10.1021/acs.nanolett.9b04445.s001.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective
Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.
American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.
short: M.C. Ucar, R. Lipowsky, (2019).
date_created: 2021-07-27T09:51:46Z
date_published: 2019-12-19T00:00:00Z
date_updated: 2023-08-17T14:07:52Z
day: '19'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445.s001
month: '12'
oa_version: Published Version
publisher: 'American Chemical Society '
related_material:
record:
- id: '7166'
relation: used_in_publication
status: public
status: public
title: Supplementary information - Collective force generation by molecular motors
is determined by strain-induced unbinding
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '14001'
abstract:
- lang: eng
text: Chiral molecules interact and react differently with other chiral objects,
depending on their handedness. Therefore, it is essential to understand and ultimately
control the evolution of molecular chirality during chemical reactions. Although
highly sophisticated techniques for the controlled synthesis of chiral molecules
have been developed, the observation of chirality on the natural femtosecond time
scale of a chemical reaction has so far remained out of reach in the gas phase.
Here, we demonstrate a general experimental technique, based on high-harmonic
generation in tailored laser fields, and apply it to probe the time evolution
of molecular chirality during the photodissociation of 2-iodobutane. These measurements
show a change in sign and a pronounced increase in the magnitude of the chiral
response over the first 100 fs, followed by its decay within less than 500 fs,
revealing the photodissociation to achiral products. The observed time evolution
is explained in terms of the variation of the electric and magnetic transition-dipole
moments between the lowest electronic states of the cation as a function of the
reaction coordinate. These results open the path to investigations of the chirality
of molecular-reaction pathways, light-induced chirality in chemical processes,
and the control of molecular chirality through tailored laser pulses.
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Daniel
full_name: Zindel, Daniel
last_name: Zindel
- first_name: Vít
full_name: Svoboda, Vít
last_name: Svoboda
- first_name: Elias
full_name: Bommeli, Elias
last_name: Bommeli
- first_name: Manuel
full_name: Ochsner, Manuel
last_name: Ochsner
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during
a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929.
doi:10.1073/pnas.1907189116
apa: Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar,
A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical
reaction. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116
chicago: Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli,
Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality
during a Chemical Reaction.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116.
ieee: D. R. Baykusheva et al., “Real-time probing of chirality during a chemical
reaction,” Proceedings of the National Academy of Sciences, vol. 116, no.
48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.
ista: Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner
HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings
of the National Academy of Sciences. 116(48), 23923–23929.
mla: Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during
a Chemical Reaction.” Proceedings of the National Academy of Sciences,
vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29,
doi:10.1073/pnas.1907189116.
short: D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar,
H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.
date_created: 2023-08-09T13:10:36Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2023-08-22T07:40:05Z
day: '13'
doi: 10.1073/pnas.1907189116
extern: '1'
external_id:
arxiv:
- '1906.10818'
pmid:
- '31723044'
intvolume: ' 116'
issue: '48'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1907189116
month: '11'
oa: 1
oa_version: Published Version
page: 23923-23929
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Real-time probing of chirality during a chemical reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '14002'
abstract:
- lang: eng
text: The advancement of attosecond chronoscopy has made it possible to reveal ultrashort
time dynamics of photoionization [1]. Ionization delay measurements in atomic
targets provide a wealth of information about the timing of the photoelectric
effect [2], resonances, electron correlations and transport. The extension of
this approach to molecules, however, presents great challenges. In addition to
the difficulty of identifying correct ionization channels, it is hard to disentangle
the role of the anisotropic molecular landscape from the delays inherent to the
excitation process itself. Here, we present the measurements of ionization delays
from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond
streaking spectroscopy, which enables to disentangle the contribution to the delay
from the functional ethyl group, being responsible for the characteristic chemical
reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes
the molecule around the energy of the giant resonance and the released electron
is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field,
which yields a streaking spectrogram (see figure). Comparative phase analysis
of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting
overall photoemission delays for ethyl iodide. The data is recorded for multiple
photon energies around the iodine 4d resonance and compared to classical Wigner
propagation [3] and quantum scattering [4] calculations. Here the outgoing electron,
produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby
hardly influenced by the molecular potential during the birth process, acquires
the necessary information about the influence of the functional ethyl group during
its propagation. We find significant delay contributions that can distinguish
between different functional groups, providing a sensitive probe of the local
molecular environment [5]. This would stimulate to perform further angle resolved
measurements in molecules to probe the potential landscape in three dimension.
article_number: '8871819'
article_processing_charge: No
author:
- first_name: Shubhadeep
full_name: Biswas, Shubhadeep
last_name: Biswas
- first_name: I.
full_name: Liontos, I.
last_name: Liontos
- first_name: A. M.
full_name: Kamal, A. M.
last_name: Kamal
- first_name: N. G.
full_name: Kling, N. G.
last_name: Kling
- first_name: A. F.
full_name: Alharbi, A. F.
last_name: Alharbi
- first_name: M.
full_name: Alharbi, M.
last_name: Alharbi
- first_name: A. M.
full_name: Azzeer, A. M.
last_name: Azzeer
- first_name: H. J.
full_name: Worner, H. J.
last_name: Worner
- first_name: A. S.
full_name: Landsman, A. S.
last_name: Landsman
- first_name: M. F.
full_name: Kling, M. F.
last_name: Kling
- first_name: B.
full_name: Forg, B.
last_name: Forg
- first_name: J.
full_name: Schotz, J.
last_name: Schotz
- first_name: W.
full_name: Schweinberger, W.
last_name: Schweinberger
- first_name: L.
full_name: Ortmann, L.
last_name: Ortmann
- first_name: T.
full_name: Zimmermann, T.
last_name: Zimmermann
- first_name: L.-W.
full_name: Pi, L.-W.
last_name: Pi
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H. A.
full_name: Masood, H. A.
last_name: Masood
citation:
ama: 'Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission
delays. In: 2019 Conference on Lasers and Electro-Optics Europe & European
Quantum Electronics Conference. Institute of Electrical and Electronics Engineers;
2019. doi:10.1109/cleoe-eqec.2019.8871819'
apa: 'Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi,
M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays.
In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference. Munich, Germany: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/cleoe-eqec.2019.8871819'
chicago: Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi,
M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission
Delays.” In 2019 Conference on Lasers and Electro-Optics Europe & European
Quantum Electronics Conference. Institute of Electrical and Electronics Engineers,
2019. https://doi.org/10.1109/cleoe-eqec.2019.8871819.
ieee: S. Biswas et al., “Probing molecular influence on photoemission delays,”
in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference, Munich, Germany, 2019.
ista: 'Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM,
Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L,
Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence
on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe &
European Quantum Electronics Conference. CLEO: European Conference on Lasers and
Electro-Optics, 8871819.'
mla: Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.”
2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference, 8871819, Institute of Electrical and Electronics Engineers,
2019, doi:10.1109/cleoe-eqec.2019.8871819.
short: S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi,
A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger,
L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference
on Lasers and Electro-Optics Europe & European Quantum Electronics Conference,
Institute of Electrical and Electronics Engineers, 2019.
conference:
end_date: 2019-06-27
location: Munich, Germany
name: 'CLEO: European Conference on Lasers and Electro-Optics'
start_date: 2019-06-23
date_created: 2023-08-09T13:10:49Z
date_published: 2019-10-17T00:00:00Z
date_updated: 2023-08-22T09:32:56Z
day: '17'
doi: 10.1109/cleoe-eqec.2019.8871819
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
publication: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference
publication_identifier:
eisbn:
- '9781728104690'
isbn:
- '9781728104706'
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing molecular influence on photoemission delays
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6671'
abstract:
- lang: eng
text: 'In this paper we discuss three results. The first two concern general sets
of positive reach: we first characterize the reach of a closed set by means of
a bound on the metric distortion between the distance measured in the ambient
Euclidean space and the shortest path distance measured in the set. Secondly,
we prove that the intersection of a ball with radius less than the reach with
the set is geodesically convex, meaning that the shortest path between any two
points in the intersection lies itself in the intersection. For our third result
we focus on manifolds with positive reach and give a bound on the angle between
tangent spaces at two different points in terms of the reach and the distance
between the two points.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jean-Daniel
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic
convexity and the variation of tangent spaces. Journal of Applied and Computational
Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8
apa: Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric
distortion, geodesic convexity and the variation of tangent spaces. Journal
of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8
chicago: Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The
Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.”
Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8.
ieee: J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion,
geodesic convexity and the variation of tangent spaces,” Journal of Applied
and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.
ista: Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion,
geodesic convexity and the variation of tangent spaces. Journal of Applied and
Computational Topology. 3(1–2), 29–58.
mla: Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity
and the Variation of Tangent Spaces.” Journal of Applied and Computational
Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.
short: J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational
Topology 3 (2019) 29–58.
date_created: 2019-07-24T08:37:29Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-22T12:37:47Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s41468-019-00029-8
ec_funded: 1
file:
- access_level: open_access
checksum: a5b244db9f751221409cf09c97ee0935
content_type: application/pdf
creator: dernst
date_created: 2019-07-31T08:09:56Z
date_updated: 2020-07-14T12:47:36Z
file_id: '6741'
file_name: 2019_JournAppliedComputTopol_Boissonnat.pdf
file_size: 2215157
relation: main_file
file_date_updated: 2020-07-14T12:47:36Z
has_accepted_license: '1'
intvolume: ' 3'
issue: 1-2
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 29–58
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The reach, metric distortion, geodesic convexity and the variation of tangent
spaces
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: 3
year: '2019'
...
---
_id: '301'
abstract:
- lang: eng
text: A representation formula for solutions of stochastic partial differential
equations with Dirichlet boundary conditions is proved. The scope of our setting
is wide enough to cover the general situation when the backward characteristics
that appear in the usual formulation are not even defined in the Itô sense.
article_processing_charge: No
article_type: original
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: István
full_name: Gyöngy, István
last_name: Gyöngy
citation:
ama: Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems.
Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003
apa: Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic
Dirichlet problems. Stochastic Processes and Their Applications. Elsevier.
https://doi.org/10.1016/j.spa.2018.04.003
chicago: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic
Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier,
2019. https://doi.org/10.1016/j.spa.2018.04.003.
ieee: M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet
problems,” Stochastic Processes and their Applications, vol. 129, no. 3.
Elsevier, pp. 995–1012, 2019.
ista: Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet
problems. Stochastic Processes and their Applications. 129(3), 995–1012.
mla: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet
Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3,
Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.
short: M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129
(2019) 995–1012.
date_created: 2018-12-11T11:45:42Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:20:49Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.spa.2018.04.003
external_id:
arxiv:
- '1611.04177'
isi:
- '000458945300012'
intvolume: ' 129'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.04177
month: '03'
oa: 1
oa_version: Preprint
page: 995-1012
publication: Stochastic Processes and their Applications
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Feynman–Kac formula for stochastic Dirichlet problems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 129
year: '2019'
...
---
_id: '80'
abstract:
- lang: eng
text: 'We consider an interacting, dilute Bose gas trapped in a harmonic potential
at a positive temperature. The system is analyzed in a combination of a thermodynamic
and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature
T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering
length is so small that the interaction energy per particle around the center
of the trap is of the same order of magnitude as the spectral gap in the trap.
We prove that the difference between the canonical free energy of the interacting
gas and the one of the noninteracting system can be obtained by minimizing the
GP energy functional. We also prove Bose–Einstein condensation in the following
sense: The one-particle density matrix of any approximate minimizer of the canonical
free energy functional is to leading order given by that of the noninteracting
gas but with the free condensate wavefunction replaced by the GP minimizer.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute,
trapped gas at positive temperature. Communications in Mathematical Physics.
2019;368(2):723-776. doi:10.1007/s00220-018-3239-0
apa: Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation
in a dilute, trapped gas at positive temperature. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0
chicago: Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein
Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications
in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0.
ieee: A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in
a dilute, trapped gas at positive temperature,” Communications in Mathematical
Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019.
ista: Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a
dilute, trapped gas at positive temperature. Communications in Mathematical Physics.
368(2), 723–776.
mla: Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped
Gas at Positive Temperature.” Communications in Mathematical Physics, vol.
368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0.
short: A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics
368 (2019) 723–776.
date_created: 2018-12-11T11:44:31Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-24T14:27:51Z
day: '01'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00220-018-3239-0
ec_funded: 1
external_id:
isi:
- '000467796800007'
file:
- access_level: open_access
checksum: c7e9880b43ac726712c1365e9f2f73a6
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:34:06Z
date_updated: 2020-07-14T12:48:07Z
file_id: '5688'
file_name: 2018_CommunMathPhys_Deuchert.pdf
file_size: 893902
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
intvolume: ' 368'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 723-776
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '7974'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bose–Einstein condensation in a dilute, trapped gas at positive temperature
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 368
year: '2019'
...
---
_id: '5911'
abstract:
- lang: eng
text: Empirical data suggest that inversions in many species contain genes important
for intraspecific divergence and speciation, yet mechanisms of evolution remain
unclear. While genes inside an inversion are tightly linked, inversions are not
static but evolve separately from the rest of the genome by new mutations, recombination
within arrangements, and gene flux between arrangements. Inversion polymorphisms
are maintained by different processes, for example, divergent or balancing selection,
or a mix of multiple processes. Moreover, the relative roles of selection, drift,
mutation, and recombination will change over the lifetime of an inversion and
within its area of distribution. We believe inversions are central to the evolution
of many species, but we need many more data and new models to understand the complex
mechanisms involved.
article_processing_charge: No
article_type: original
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends
in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005
apa: Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving
inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005
chicago: Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving
Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005.
ieee: R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,”
Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248,
2019.
ista: Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions.
Trends in Ecology and Evolution. 34(3), 239–248.
mla: Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution,
vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005.
short: R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and
Evolution 34 (2019) 239–248.
date_created: 2019-02-03T22:59:15Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:29:48Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tree.2018.12.005
ec_funded: 1
external_id:
isi:
- '000459899000013'
file:
- access_level: open_access
checksum: ef24572d6ebcc1452c067e05410cc4a2
content_type: application/pdf
creator: cziletti
date_created: 2020-01-09T10:55:58Z
date_updated: 2020-07-14T12:47:13Z
file_id: '7245'
file_name: 2019_Trends_Evolution_Faria.pdf
file_size: 1946795
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 239-248
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Trends in Ecology and Evolution
publication_identifier:
issn:
- '01695347'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolving inversions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2019'
...
---
_id: '439'
abstract:
- lang: eng
text: "We count points over a finite field on wild character varieties,of Riemann
surfaces for singularities with regular semisimple leading term. The new feature
in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras.
Our result leads to the conjecture that the mixed Hodge polynomials of these character
varieties agree with previously conjectured perverse Hodge polynomials of certain
twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P =
W conjecture for a suitable wild Hitchin system."
article_processing_charge: No
article_type: original
author:
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Martin
full_name: Mereb, Martin
id: 43D735EE-F248-11E8-B48F-1D18A9856A87
last_name: Mereb
- first_name: Michael
full_name: Wong, Michael
last_name: Wong
citation:
ama: Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character
varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052.
doi:10.4171/JEMS/896
apa: Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation
theory of wild character varieties. Journal of the European Mathematical Society.
European Mathematical Society. https://doi.org/10.4171/JEMS/896
chicago: Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation
Theory of Wild Character Varieties.” Journal of the European Mathematical Society.
European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.
ieee: T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of
wild character varieties,” Journal of the European Mathematical Society,
vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.
ista: Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild
character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.
mla: Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character
Varieties.” Journal of the European Mathematical Society, vol. 21, no.
10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896.
short: T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society
21 (2019) 2995–3052.
date_created: 2018-12-11T11:46:29Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-24T14:24:49Z
day: '01'
department:
- _id: TaHa
doi: 10.4171/JEMS/896
ec_funded: 1
external_id:
arxiv:
- '1604.03382'
isi:
- '000480413600002'
intvolume: ' 21'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.03382
month: '10'
oa: 1
oa_version: Preprint
page: 2995-3052
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Journal of the European Mathematical Society
publication_identifier:
eissn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society
publist_id: '7384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arithmetic and representation theory of wild character varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2019'
...
---
_id: '105'
abstract:
- lang: eng
text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar
hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease:
615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2
at 1p13.3. 4. OMIM# of the Gene(s): 102771.'
acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing
as part of health care”), a Coordination Action under FP7 (Grant Agreement Number
261469) and the European Society of Human Genetics. We acknowledge the participation
of the patients and their families in these studies, as well as the generous financial
support of the Lefroy and Handbury families. APLM was supported by an Australian
Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364).
RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.'
article_processing_charge: No
article_type: original
author:
- first_name: Ashley
full_name: Marsh, Ashley
last_name: Marsh
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Paul
full_name: Lockhart, Paul
last_name: Lockhart
- first_name: Richard
full_name: Leventer, Richard
last_name: Leventer
citation:
ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia
type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166.
doi:10.1038/s41431-018-0231-2
apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for
pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal
of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2
chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC
for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European
Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2.
ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar
hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics,
vol. 27. Springer Nature, pp. 161–166, 2019.
ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar
hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics.
27, 161–166.
mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic
Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature,
2019, pp. 161–66, doi:10.1038/s41431-018-0231-2.
short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human
Genetics 27 (2019) 161–166.
date_created: 2018-12-11T11:44:39Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:28:24Z
day: '01'
department:
- _id: GaNo
doi: 10.1038/s41431-018-0231-2
external_id:
isi:
- '000454111500019'
pmid:
- '30089829'
intvolume: ' 27'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41431-018-0231-2
month: '01'
oa: 1
oa_version: Published Version
page: 161-166
pmid: 1
publication: European Journal of Human Genetics
publication_status: published
publisher: Springer Nature
publist_id: '7949'
quality_controlled: '1'
scopus_import: '1'
status: public
title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2019'
...
---
_id: '65'
abstract:
- lang: eng
text: We provide an entropy formulation for porous medium-type equations with a
stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction
is obtained in the class of entropy solutions. Our scope allows for porous medium
operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity
with exponent 1/2.
article_processing_charge: No
article_type: original
author:
- first_name: Konstantinos
full_name: Dareiotis, Konstantinos
last_name: Dareiotis
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Benjamin
full_name: Gess, Benjamin
last_name: Gess
citation:
ama: Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media
equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012
apa: Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for
stochastic porous media equations. Journal of Differential Equations. Elsevier.
https://doi.org/10.1016/j.jde.2018.09.012
chicago: Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions
for Stochastic Porous Media Equations.” Journal of Differential Equations.
Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.
ieee: K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic
porous media equations,” Journal of Differential Equations, vol. 266, no.
6. Elsevier, pp. 3732–3763, 2019.
ista: Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous
media equations. Journal of Differential Equations. 266(6), 3732–3763.
mla: Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media
Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier,
2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012.
short: K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266
(2019) 3732–3763.
date_created: 2018-12-11T11:44:26Z
date_published: 2019-03-05T00:00:00Z
date_updated: 2023-08-24T14:30:16Z
day: '5'
department:
- _id: JaMa
doi: 10.1016/j.jde.2018.09.012
external_id:
arxiv:
- '1803.06953'
isi:
- '000456332500026'
intvolume: ' 266'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1803.06953
month: '03'
oa: 1
oa_version: Preprint
page: 3732-3763
publication: Journal of Differential Equations
publication_status: published
publisher: Elsevier
publist_id: '7989'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Entropy solutions for stochastic porous media equations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 266
year: '2019'
...
---
_id: '5907'
abstract:
- lang: eng
text: Microalgae of the genus Chlorella vulgaris are candidates for the production
of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed
as protein and vitamin rich food additive. Its potential as a novel expression
system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides
(N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic
N-glycans with up to nine mannoses were the structures found in culture collection
strains as well as several commercial products. These glycans co-eluted with plant
N-glycans in the highly shape selective porous graphitic carbon chromatography.
Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural
type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as
substrate for GlcNAc-transferase I and a trace of an endogenous structure with
terminal GlcNAc was seen. The unusual more linear Man5 structure recently found
on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces
only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated
with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This
modification has so far been neither found on plant nor vertebrate N-glycans.
It’s possible immunogenicity raises concerns as to the use of C. vulgaris for
production of pharmaceutical glycoproteins.
article_number: '331'
article_processing_charge: No
author:
- first_name: Réka
full_name: Mócsai, Réka
last_name: Mócsai
- first_name: Rudolf
full_name: Figl, Rudolf
last_name: Figl
- first_name: Clemens
full_name: Troschl, Clemens
last_name: Troschl
- first_name: Richard
full_name: Strasser, Richard
last_name: Strasser
- first_name: Elisabeth
full_name: Svehla, Elisabeth
last_name: Svehla
- first_name: Markus
full_name: Windwarder, Markus
last_name: Windwarder
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Friedrich
full_name: Altmann, Friedrich
last_name: Altmann
citation:
ama: Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris
are of the oligomannosidic type but highly methylated. Scientific Reports.
2019;9(1). doi:10.1038/s41598-018-36884-1
apa: Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M.,
… Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the
oligomannosidic type but highly methylated. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/s41598-018-36884-1
chicago: Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth
Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of
the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.”
Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1.
ieee: R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are
of the oligomannosidic type but highly methylated,” Scientific Reports,
vol. 9, no. 1. Nature Publishing Group, 2019.
ista: Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A,
Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic
type but highly methylated. Scientific Reports. 9(1), 331.
mla: Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of
the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol.
9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.
short: R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A.
Thader, F. Altmann, Scientific Reports 9 (2019).
date_created: 2019-02-03T22:59:13Z
date_published: 2019-01-23T00:00:00Z
date_updated: 2023-08-24T14:33:16Z
day: '23'
ddc:
- '580'
department:
- _id: FlSc
doi: 10.1038/s41598-018-36884-1
external_id:
isi:
- '000456392400012'
file:
- access_level: open_access
checksum: 4129c7d7663d1f8a1edf8c4232372f66
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T13:10:02Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5923'
file_name: 2019_ScientificReports_Mocsai.pdf
file_size: 2124292
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type
but highly methylated
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '5908'
abstract:
- lang: eng
text: The interorganelle communication mediated by membrane contact sites (MCSs)
is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular
exchange of information between organelles and allow them to coordinate responses
to changing cellular environments. In plants, the importance of MCS components
in the responses to environmental stress has been widely established, but the
molecular mechanisms regulating interorganelle connectivity during stress still
remain opaque. In this report, we use the model plant Arabidopsis thaliana to
show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM)
connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched
ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton
in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the
accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as
a molecular signal associated with the ER–PM connectivity changes. Our study highlights
the functional conservation of EPCS components and PM phosphoinositides as modulators
of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal
regulation of ER–PM connectivity in plants.
article_processing_charge: No
article_type: original
author:
- first_name: Eunkyoung
full_name: Lee, Eunkyoung
last_name: Lee
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jessica
full_name: Pérez-Sancho, Jessica
last_name: Pérez-Sancho
- first_name: Francisco
full_name: Benitez-Fuente, Francisco
last_name: Benitez-Fuente
- first_name: Matthew
full_name: Strelau, Matthew
last_name: Strelau
- first_name: Alberto P.
full_name: Macho, Alberto P.
last_name: Macho
- first_name: Miguel A.
full_name: Botella, Miguel A.
last_name: Botella
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Abel
full_name: Rosado, Abel
last_name: Rosado
citation:
ama: Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity
via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings
of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429.
doi:10.1073/pnas.1818099116
apa: Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho,
A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated
SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1818099116
chicago: Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente,
Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado.
“Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1
Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2019. https://doi.org/10.1073/pnas.1818099116.
ieee: E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated
SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 4. National Academy
of Sciences, pp. 1420–1429, 2019.
ista: Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP,
Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity
via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings
of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.
mla: Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated
SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 4, National Academy
of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116.
short: E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P.
Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy
of Sciences of the United States of America 116 (2019) 1420–1429.
date_created: 2019-02-03T22:59:14Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-08-24T14:31:09Z
day: '22'
department:
- _id: JiFr
doi: 10.1073/pnas.1818099116
external_id:
isi:
- '000456336100050'
pmid:
- '30610176'
intvolume: ' 116'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1818099116
month: '01'
oa: 1
oa_version: Published Version
page: 1420-1429
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1
contact site expansion in Arabidopsis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 116
year: '2019'
...
---
_id: '5680'
abstract:
- lang: eng
text: Pollinators display a remarkable diversity of foraging strategies with flowering
plants, from primarily mutualistic interactions to cheating through nectar robbery.
Despite numerous studies on the effect of nectar robbing on components of plant
fitness, its contribution to reproductive isolation is unclear. We experimentally
tested the impact of different pollinator strategies in a natural hybrid zone
between two subspecies of Antirrhinum majus with alternate flower colour guides.
On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus
(magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral
visitors at different time points during the flowering season. Using long-run
camera surveys, we quantify the impact of nectar robbing on the number of flowers
visited per inflorescence and the flower probing time. We further experimentally
tested the effect of nectar robbing on female reproductive success by manipulating
the intensity of robbing. While robbing increased over time the number of legitimate
visitors tended to decrease concomitantly. We found that the number of flowers
pollinated on a focal inflorescence decreased with the number of prior robbing
events. However, in the manipulative experiment, fruit set and fruit volume did
not vary significantly between low robbing and control treatments. Our findings
challenge the idea that robbers have a negative impact on plant fitness through
female function. This study also adds to our understanding of the components of
pollinator-mediated reproductive isolation and the maintenance of Antirrhinum
hybrid zones.
article_processing_charge: No
author:
- first_name: Christophe
full_name: Andalo, Christophe
last_name: Andalo
- first_name: Monique
full_name: Burrus, Monique
last_name: Burrus
- first_name: Sandrine
full_name: Paute, Sandrine
last_name: Paute
- first_name: Christine
full_name: Lauzeral, Christine
last_name: Lauzeral
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate
pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum
majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142
apa: Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence
of legitimate pollinators and nectar robbers and the consequences for fruit set
in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis.
https://doi.org/10.1080/23818107.2018.1545142
chicago: Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral,
and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and
the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany
Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.
ieee: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of
legitimate pollinators and nectar robbers and the consequences for fruit set in
an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor
and Francis, pp. 80–92, 2019.
ista: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate
pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum
majus hybrid zone. Botany Letters. 166(1), 80–92.
mla: Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar
Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.”
Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142.
short: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166
(2019) 80–92.
date_created: 2018-12-16T22:59:20Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:34:12Z
day: '01'
department:
- _id: NiBa
doi: 10.1080/23818107.2018.1545142
external_id:
isi:
- '000463802800009'
intvolume: ' 166'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 80-92
publication: Botany Letters
publication_identifier:
eissn:
- '23818115'
issn:
- '23818107'
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Prevalence of legitimate pollinators and nectar robbers and the consequences
for fruit set in an Antirrhinum majus hybrid zone
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 166
year: '2019'
...
---
_id: '5790'
abstract:
- lang: eng
text: The partial representation extension problem is a recently introduced generalization
of the recognition problem. A circle graph is an intersection graph of chords
of a circle. We study the partial representation extension problem for circle
graphs, where the input consists of a graph G and a partial representation R′
giving some predrawn chords that represent an induced subgraph of G. The question
is whether one can extend R′ to a representation R of the entire graph G, that
is, whether one can draw the remaining chords into a partially predrawn representation
to obtain a representation of G. Our main result is an O(n3) time algorithm for
partial representation extension of circle graphs, where n is the number of vertices.
To show this, we describe the structure of all representations of a circle graph
using split decomposition. This can be of independent interest.
article_processing_charge: No
article_type: original
author:
- first_name: Steven
full_name: Chaplick, Steven
last_name: Chaplick
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Pavel
full_name: Klavík, Pavel
last_name: Klavík
citation:
ama: Chaplick S, Fulek R, Klavík P. Extending partial representations of circle
graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436
apa: Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations
of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436
chicago: Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial
Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019.
https://doi.org/10.1002/jgt.22436.
ieee: S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of
circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394,
2019.
ista: Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of
circle graphs. Journal of Graph Theory. 91(4), 365–394.
mla: Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.”
Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.
short: S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.
date_created: 2018-12-30T22:59:15Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-24T14:30:43Z
day: '01'
department:
- _id: UlWa
doi: 10.1002/jgt.22436
ec_funded: 1
external_id:
arxiv:
- '1309.2399'
isi:
- '000485392800004'
intvolume: ' 91'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.2399
month: '08'
oa: 1
oa_version: Preprint
page: 365-394
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Graph Theory
publication_identifier:
issn:
- '03649024'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending partial representations of circle graphs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 91
year: '2019'
...
---
_id: '405'
abstract:
- lang: eng
text: We investigate the quantum Jensen divergences from the viewpoint of joint
convexity. It turns out that the set of the functions which generate jointly convex
quantum Jensen divergences on positive matrices coincides with the Matrix Entropy
Class which has been introduced by Chen and Tropp quite recently.
acknowledgement: The author was supported by the ISTFELLOW program of the Institute
of Science and Technology Austria (project code IC1027FELL01) and partially supported
by the Hungarian National Research, Development and Innovation Office – NKFIH (grant
no. K124152)
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and
Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002
apa: Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear
Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002
chicago: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear
Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002.
ieee: D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra
and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.
ista: Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra
and Its Applications. 576, 67–78.
mla: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra
and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.
short: D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.
date_created: 2018-12-11T11:46:17Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-24T14:31:47Z
day: '01'
department:
- _id: LaEr
doi: 10.1016/j.laa.2018.03.002
ec_funded: 1
external_id:
arxiv:
- '1712.05324'
isi:
- '000470955300005'
intvolume: ' 576'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.05324
month: '09'
oa: 1
oa_version: Preprint
page: 67-78
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Linear Algebra and Its Applications
publication_status: published
publisher: Elsevier
publist_id: '7424'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Jointly convex quantum Jensen divergences
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 576
year: '2019'
...
---
_id: '175'
abstract:
- lang: eng
text: An upper bound sieve for rational points on suitable varieties isdeveloped,
together with applications tocounting rational points in thin sets,to local solubility
in families, and to the notion of “friable” rational pointswith respect to divisors.
In the special case of quadrics, sharper estimates areobtained by developing a
version of the Selberg sieve for rational points.
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Daniel
full_name: Loughran, Daniel
last_name: Loughran
citation:
ama: Browning TD, Loughran D. Sieving rational points on varieties. Transactions
of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514
apa: Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/7514
chicago: Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.”
Transactions of the American Mathematical Society. American Mathematical
Society, 2019. https://doi.org/10.1090/tran/7514.
ieee: T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions
of the American Mathematical Society, vol. 371, no. 8. American Mathematical
Society, pp. 5757–5785, 2019.
ista: Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions
of the American Mathematical Society. 371(8), 5757–5785.
mla: Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.”
Transactions of the American Mathematical Society, vol. 371, no. 8, American
Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514.
short: T.D. Browning, D. Loughran, Transactions of the American Mathematical Society
371 (2019) 5757–5785.
date_created: 2018-12-11T11:45:01Z
date_published: 2019-04-15T00:00:00Z
date_updated: 2023-08-24T14:34:56Z
day: '15'
department:
- _id: TiBr
doi: 10.1090/tran/7514
external_id:
arxiv:
- '1705.01999'
isi:
- '000464034200019'
intvolume: ' 371'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.01999
month: '04'
oa: 1
oa_version: Preprint
page: 5757-5785
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- '10886850'
issn:
- '00029947'
publication_status: published
publisher: American Mathematical Society
publist_id: '7746'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sieving rational points on varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 371
year: '2019'
...
---
_id: '319'
abstract:
- lang: eng
text: We study spaces of modelled distributions with singular behaviour near the
boundary of a domain that, in the context of the theory of regularity structures,
allow one to give robust solution theories for singular stochastic PDEs with boundary
conditions. The calculus of modelled distributions established in Hairer (Invent
Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended
to this setting. We formulate and solve fixed point problems in these spaces with
a class of kernels that is sufficiently large to cover in particular the Dirichlet
and Neumann heat kernels. These results are then used to provide solution theories
for the KPZ equation with Dirichlet and Neumann boundary conditions and for the
2D generalised parabolic Anderson model with Dirichlet boundary conditions. In
the case of the KPZ equation with Neumann boundary conditions, we show that, depending
on the class of mollifiers one considers, a “boundary renormalisation” takes place.
In other words, there are situations in which a certain boundary condition is
applied to an approximation to the KPZ equation, but the limiting process is the
Hopf–Cole solution to the KPZ equation with a different boundary condition.
acknowledgement: "MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n"
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Martin
full_name: Hairer, Martin
last_name: Hairer
citation:
ama: Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability
Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1
apa: Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries.
Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1
chicago: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.”
Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1.
ieee: M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability
Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.
ista: Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability
Theory and Related Fields. 173(3–4), 697–758.
mla: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.”
Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019,
pp. 697–758, doi:10.1007/s00440-018-0841-1.
short: M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019)
697–758.
date_created: 2018-12-11T11:45:48Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-24T14:38:32Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00440-018-0841-1
external_id:
isi:
- '000463613800001'
file:
- access_level: open_access
checksum: 288d16ef7291242f485a9660979486e3
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:25:24Z
date_updated: 2020-07-14T12:46:03Z
file_id: '5722'
file_name: 2018_ProbTheory_Gerencser.pdf
file_size: 893182
relation: main_file
file_date_updated: 2020-07-14T12:46:03Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: 3-4
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 697–758
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- '14322064'
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '7546'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Singular SPDEs in domains with boundaries
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 173
year: '2019'
...
---
_id: '429'
abstract:
- lang: eng
text: We consider real symmetric or complex hermitian random matrices with correlated
entries. We prove local laws for the resolvent and universality of the local eigenvalue
statistics in the bulk of the spectrum. The correlations have fast decay but are
otherwise of general form. The key novelty is the detailed stability analysis
of the corresponding matrix valued Dyson equation whose solution is the deterministic
limit of the resolvent.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria).\r\n"
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random
matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373.
doi:10.1007/s00440-018-0835-z
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix
Dyson equation and random matrices with correlations. Probability Theory and
Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the
Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory
and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation
and random matrices with correlations,” Probability Theory and Related Fields,
vol. 173, no. 1–2. Springer, pp. 293–373, 2019.
ista: Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation
and random matrices with correlations. Probability Theory and Related Fields.
173(1–2), 293–373.
mla: Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random
Matrices with Correlations.” Probability Theory and Related Fields, vol.
173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
173 (2019) 293–373.
date_created: 2018-12-11T11:46:25Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-08-24T14:39:00Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00440-018-0835-z
ec_funded: 1
external_id:
isi:
- '000459396500007'
file:
- access_level: open_access
checksum: f9354fa5c71f9edd17132588f0dc7d01
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:12:08Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5720'
file_name: 2018_ProbTheory_Ajanki.pdf
file_size: 1201840
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: 1-2
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 293–373
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- '14322064'
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '7394'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stability of the matrix Dyson equation and random matrices with correlations
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 173
year: '2019'
...
---
_id: '5947'
abstract:
- lang: eng
text: Graph algorithms applied in many applications, including social networks,
communication networks, VLSI design, graphics, and several others, require dynamic
modifications - addition and removal of vertices and/or edges - in the graph.
This paper presents a novel concurrent non-blocking algorithm to implement a dynamic
unbounded directed graph in a shared-memory machine. The addition and removal
operations of vertices and edges are lock-free. For a finite sized graph, the
lookup operations are wait-free. Most significant component of the presented algorithm
is the reachability query in a concurrent graph. The reachability queries in our
algorithm are obstruction-free and thus impose minimal additional synchronization
cost over other operations. We prove that each of the data structure operations
are linearizable. We extensively evaluate a sample C/C++ implementation of the
algorithm through a number of micro-benchmarks. The experimental results show
that the proposed algorithm scales well with the number of threads and on an average
provides 5 to 7x performance improvement over a concurrent graph implementation
using coarse-grained locking.
article_processing_charge: No
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Sathya
full_name: Peri, Sathya
last_name: Peri
- first_name: Muktikanta
full_name: Sa, Muktikanta
last_name: Sa
- first_name: Nandini
full_name: Singhal, Nandini
last_name: Singhal
citation:
ama: 'Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking
unbounded graph with linearizable reachability queries. In: ACM International
Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617'
apa: 'Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical
concurrent non-blocking unbounded graph with linearizable reachability queries.
In ACM International Conference Proceeding Series (pp. 168–177). Bangalore,
India: ACM. https://doi.org/10.1145/3288599.3288617'
chicago: Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple
and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability
Queries.” In ACM International Conference Proceeding Series, 168–77. ACM,
2019. https://doi.org/10.1145/3288599.3288617.
ieee: B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent
non-blocking unbounded graph with linearizable reachability queries,” in ACM
International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177.
ista: 'Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent
non-blocking unbounded graph with linearizable reachability queries. ACM International
Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking,
168–177.'
mla: Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded
Graph with Linearizable Reachability Queries.” ACM International Conference
Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617.
short: B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference
Proceeding Series, ACM, 2019, pp. 168–177.
conference:
end_date: 2019-01-07
location: Bangalore, India
name: 'ICDCN: Conference on Distributed Computing and Networking'
start_date: 2019-01-04
date_created: 2019-02-10T22:59:17Z
date_published: 2019-01-04T00:00:00Z
date_updated: 2023-08-24T14:41:53Z
day: '04'
department:
- _id: DaAl
doi: 10.1145/3288599.3288617
external_id:
arxiv:
- '1809.00896'
isi:
- '000484491600019'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.00896
month: '01'
oa: 1
oa_version: Preprint
page: 168-177
publication: ACM International Conference Proceeding Series
publication_identifier:
isbn:
- '978-1-4503-6094-4 '
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: A simple and practical concurrent non-blocking unbounded graph with linearizable
reachability queries
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '5857'
abstract:
- lang: eng
text: 'A thrackle is a graph drawn in the plane so that every pair of its edges
meet exactly once: either at a common end vertex or in a proper crossing. We prove
that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are
defined similarly, except that every pair of edges that do not share a vertex
are allowed to cross an odd number of times. It is also shown that the maximum
number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1),
and that this bound is best possible for infinitely many values of n.'
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: János
full_name: Pach, János
last_name: Pach
citation:
ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics.
2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025'
apa: 'Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete
Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025'
chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.”
Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.'
ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied
Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.'
ista: 'Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied
Mathematics. 259(4), 266–231.'
mla: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete
Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.'
short: R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.
date_created: 2019-01-20T22:59:17Z
date_published: 2019-04-30T00:00:00Z
date_updated: 2023-08-24T14:39:33Z
day: '30'
department:
- _id: UlWa
doi: 10.1016/j.dam.2018.12.025
external_id:
arxiv:
- '1708.08037'
isi:
- '000466061100020'
intvolume: ' 259'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08037
month: '04'
oa: 1
oa_version: Preprint
page: 266-231
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '433'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Thrackles: An improved upper bound'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 259
year: '2019'
...
---
_id: '5944'
abstract:
- lang: eng
text: Understanding the thermodynamics of the duplication process is a fundamental
step towards a comprehensive physical theory of biological systems. However, the
immense complexity of real cells obscures the fundamental tensions between energy
gradients and entropic contributions that underlie duplication. The study of synthetic,
feasible systems reproducing part of the key ingredients of living entities but
overcoming major sources of biological complexity is of great relevance to deepen
the comprehension of the fundamental thermodynamic processes underlying life and
its prevalence. In this paper an abstract—yet realistic—synthetic system made
of small synthetic protocell aggregates is studied in detail. A fundamental relation
between free energy and entropic gradients is derived for a general, non-equilibrium
scenario, setting the thermodynamic conditions for the occurrence and prevalence
of duplication phenomena. This relation sets explicitly how the energy gradients
invested in creating and maintaining structural—and eventually, functional—elements
of the system must always compensate the entropic gradients, whose contributions
come from changes in the translational, configurational, and macrostate entropies,
as well as from dissipation due to irreversible transitions. Work/energy relations
are also derived, defining lower bounds on the energy required for the duplication
event to take place. A specific example including real ternary emulsions is provided
in order to grasp the orders of magnitude involved in the problem. It is found
that the minimal work invested over the system to trigger a duplication event
is around ~ 10−13J , which results, in the case of duplication of all the vesicles
contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without
aiming to describe a truly biological process of duplication, this theoretical
contribution seeks to explicitly define and identify the key actors that participate
in it.
article_number: '9'
article_processing_charge: No
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
citation:
ama: Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell
systems. Life. 2019;9(1). doi:10.3390/life9010009
apa: Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic
protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009
chicago: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in
Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009.
ieee: B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic
protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.
ista: Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic
protocell systems. Life. 9(1), 9.
mla: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic
Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.
short: B. Corominas-Murtra, Life 9 (2019).
date_created: 2019-02-10T22:59:15Z
date_published: 2019-01-15T00:00:00Z
date_updated: 2023-08-24T14:43:41Z
day: '15'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.3390/life9010009
external_id:
isi:
- '000464125500001'
file:
- access_level: open_access
checksum: 7d2322cd96ace41959909b66702d5cf4
content_type: application/pdf
creator: dernst
date_created: 2019-02-11T10:45:27Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5951'
file_name: 2019_Life_Corominas.pdf
file_size: 963454
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Life
publication_identifier:
eissn:
- '20751729'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermodynamics of duplication thresholds in synthetic protocell systems
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6029'
abstract:
- lang: eng
text: Protein micropatterning has become an important tool for many biomedical applications
as well as in academic research. Current techniques that allow to reduce the feature
size of patterns below 1 μm are, however, often costly and require sophisticated
equipment. We present here a straightforward and convenient method to generate
highly condensed nanopatterns of proteins without the need for clean room facilities
or expensive equipment. Our approach is based on nanocontact printing and allows
for the fabrication of protein patterns with feature sizes of 80 nm and periodicities
down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane)
(X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle,
different proteins at various scales were printed and the pattern quality was
evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.
article_number: '655'
article_processing_charge: No
author:
- first_name: Marco
full_name: Lindner, Marco
last_name: Lindner
- first_name: Aliz
full_name: Tresztenyak, Aliz
last_name: Tresztenyak
- first_name: Gergö
full_name: Fülöp, Gergö
last_name: Fülöp
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- first_name: Adrian
full_name: Prinz, Adrian
last_name: Prinz
- first_name: Iris
full_name: Prinz, Iris
last_name: Prinz
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gerhard J.
full_name: Schütz, Gerhard J.
last_name: Schütz
- first_name: Eva
full_name: Sevcsik, Eva
last_name: Sevcsik
citation:
ama: Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing
approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6.
doi:10.3389/fchem.2018.00655
apa: Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., …
Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D
protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655
chicago: Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz,
Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple
Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in
Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655.
ieee: M. Lindner et al., “A fast and simple contact printing approach to
generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers
Media S.A., 2019.
ista: Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz
GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D
protein nanopatterns. Frontiers in Chemistry. 6, 655.
mla: Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate
2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers
Media S.A., 2019, doi:10.3389/fchem.2018.00655.
short: M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl,
G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).
date_created: 2019-02-17T22:59:24Z
date_published: 2019-01-24T00:00:00Z
date_updated: 2023-08-24T14:45:38Z
day: '24'
ddc:
- '540'
department:
- _id: JoDa
doi: 10.3389/fchem.2018.00655
external_id:
isi:
- '000456718000001'
file:
- access_level: open_access
checksum: 7841301d7c53b56ef873791b4b6f7b24
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T15:10:34Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6039'
file_name: 2019_frontiers_Lindner.pdf
file_size: 1766820
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Frontiers in Chemistry
publication_identifier:
eissn:
- '22962646'
publication_status: published
publisher: Frontiers Media S.A.
quality_controlled: '1'
scopus_import: '1'
status: public
title: A fast and simple contact printing approach to generate 2D protein nanopatterns
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2019'
...
---
_id: '6028'
abstract:
- lang: eng
text: We give a construction allowing us to build local renormalized solutions to
general quasilinear stochastic PDEs within the theory of regularity structures,
thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking,
our construction covers quasilinear variants of all classes of equations for which
the general construction of [3, 4, 7] applies, including in particular one‐dimensional
systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less
singular and more specific case, we furthermore show that the counterterms introduced
by the renormalization procedure are given by local functionals of the solution.
The main feature of our construction is that it allows exploitation of a number
of existing results developed for the semilinear case, so that the number of additional
arguments it requires is relatively small.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Martin
full_name: Hairer, Martin
last_name: Hairer
citation:
ama: Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications
on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816
apa: Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular
SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816
chicago: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear
Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley,
2019. https://doi.org/10.1002/cpa.21816.
ieee: M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,”
Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley,
pp. 1983–2005, 2019.
ista: Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs.
Communications on Pure and Applied Mathematics. 72(9), 1983–2005.
mla: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular
SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9,
Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.
short: M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72
(2019) 1983–2005.
date_created: 2019-02-17T22:59:24Z
date_published: 2019-02-08T00:00:00Z
date_updated: 2023-08-24T14:44:31Z
day: '08'
ddc:
- '500'
department:
- _id: JaMa
doi: 10.1002/cpa.21816
external_id:
isi:
- '000475465000003'
file:
- access_level: open_access
checksum: 09aec427eb48c0f96a1cce9ff53f013b
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:25:55Z
date_updated: 2020-07-14T12:47:17Z
file_id: '7237'
file_name: 2019_Wiley_Gerencser.pdf
file_size: 381350
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 72'
isi: 1
issue: '9'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1983-2005
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: A solution theory for quasilinear singular SPDEs
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 72
year: '2019'
...
---
_id: '5948'
abstract:
- lang: eng
text: We study the termination problem for nondeterministic probabilistic programs.
We consider the bounded termination problem that asks whether the supremum of
the expected termination time over all schedulers is bounded. First, we show that
ranking supermartingales (RSMs) are both sound and complete for proving bounded
termination over nondeterministic probabilistic programs. For nondeterministic
probabilistic programs a previous result claimed that RSMs are not complete for
bounded termination, whereas our result corrects the previous flaw and establishes
completeness with a rigorous proof. Second, we present the first sound approach
to establish lower bounds on expected termination time through RSMs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs.
In: International Conference on Verification, Model Checking, and Abstract
Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22'
apa: 'Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic
programs. In International Conference on Verification, Model Checking, and
Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer
Nature. https://doi.org/10.1007/978-3-030-11245-5_22'
chicago: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic
Probabilistic Programs.” In International Conference on Verification, Model
Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019.
https://doi.org/10.1007/978-3-030-11245-5_22.
ieee: H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,”
in International Conference on Verification, Model Checking, and Abstract Interpretation,
Cascais, Portugal, 2019, vol. 11388, pp. 468–490.
ista: 'Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs.
International Conference on Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388,
468–490.'
mla: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic
Programs.” International Conference on Verification, Model Checking, and Abstract
Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22.
short: H. Fu, K. Chatterjee, in:, International Conference on Verification, Model
Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.
conference:
end_date: 2019-01-15
location: Cascais, Portugal
name: 'VMCAI: Verification, Model Checking, and Abstract Interpretation'
start_date: 2019-01-13
date_created: 2019-02-10T22:59:17Z
date_published: 2019-01-11T00:00:00Z
date_updated: 2023-08-24T14:42:22Z
day: '11'
department:
- _id: KrCh
doi: 10.1007/978-3-030-11245-5_22
external_id:
arxiv:
- '1701.02944'
isi:
- '000931943000022'
intvolume: ' 11388'
isi: 1
language:
- iso: eng
main_file_link:
- url: https://arxiv.org/abs/1701.02944
month: '01'
oa_version: Preprint
page: 468-490
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Conference on Verification, Model Checking, and Abstract
Interpretation
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Termination of nondeterministic probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11388
year: '2019'
...
---
_id: '5945'
abstract:
- lang: eng
text: In developing organisms, spatially prescribed cell identities are thought
to be determined by the expression levels of multiple genes. Quantitative tests
of this idea, however, require a theoretical framework capable of exposing the
rules and precision of cell specification over developmental time. We use the
gap gene network in the early fly embryo as an example to show how expression
levels of the four gap genes can be jointly decoded into an optimal specification
of position with 1% accuracy. The decoder correctly predicts, with no free parameters,
the dynamics of pair-rule expression patterns at different developmental time
points and in various mutant backgrounds. Precise cellular identities are thus
available at the earliest stages of development, contrasting the prevailing view
of positional information being slowly refined across successive layers of the
patterning network. Our results suggest that developmental enhancers closely approximate
a mathematically optimal decoding strategy.
article_processing_charge: No
article_type: original
author:
- first_name: Mariela D.
full_name: Petkova, Mariela D.
last_name: Petkova
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Eric F.
full_name: Wieschaus, Eric F.
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of
cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15.
doi:10.1016/j.cell.2019.01.007
apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T.
(2019). Optimal decoding of cellular identities in a genetic network. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2019.01.007
chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus,
and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.”
Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.
ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal
decoding of cellular identities in a genetic network,” Cell, vol. 176,
no. 4. Cell Press, p. 844–855.e15, 2019.
ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding
of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.
mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic
Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019)
844–855.e15.
date_created: 2019-02-10T22:59:16Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:42:47Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.cell.2019.01.007
external_id:
isi:
- '000457969200015'
pmid:
- '30712870'
intvolume: ' 176'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.01.007
month: '02'
oa: 1
oa_version: Published Version
page: 844-855.e15
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Cell
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/
scopus_import: '1'
status: public
title: Optimal decoding of cellular identities in a genetic network
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 176
year: '2019'
...
---
_id: '5943'
abstract:
- lang: eng
text: The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow
velocity ratio is investigated experimentally for a velocity ratio range of R
∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral
analysis we characterize the Strouhal number and amplitude of the hairpin instability
as a function of R and ReD. We demonstrate that the dynamics of the hairpins is
well described by the Landau model, and, hence, that the instability occurs through
Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind
different bluff bodies. Using the Landau model, we determine the precise threshold
values of hairpin shedding. We also study the spatial dependence of this hydrodynamical
instability, which shows a global behaviour.
article_processing_charge: No
article_type: original
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: Konrad
full_name: Gumowski, Konrad
last_name: Gumowski
- first_name: José Eduardo
full_name: Wesfreid, José Eduardo
last_name: Wesfreid
citation:
ama: Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the
low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406.
doi:10.1017/jfm.2018.974
apa: Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet
in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2018.974
chicago: Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments
on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid
Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974.
ieee: L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow
in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863.
Cambridge University Press, pp. 386–406, 2019.
ista: Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow
in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.
mla: Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio
Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press,
2019, pp. 386–406, doi:10.1017/jfm.2018.974.
short: L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019)
386–406.
date_created: 2019-02-10T22:59:15Z
date_published: 2019-03-25T00:00:00Z
date_updated: 2023-08-24T14:43:13Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2018.974
ec_funded: 1
external_id:
arxiv:
- '1902.07931'
isi:
- '000526029100016'
intvolume: ' 863'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07931
month: '03'
oa: 1
oa_version: Preprint
page: 386-406
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experiments on a jet in a crossflow in the low-velocity-ratio regime
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 863
year: '2019'
...
---
_id: '6042'
abstract:
- lang: eng
text: Static program analyzers are increasingly effective in checking correctness
properties of programs and reporting any errors found, often in the form of error
traces. However, developers still spend a significant amount of time on debugging.
This involves processing long error traces in an effort to localize a bug to a
relatively small part of the program and to identify its cause. In this paper,
we present a technique for automated fault localization that, given a program
and an error trace, efficiently narrows down the cause of the error to a few statements.
These statements are then ranked in terms of their suspiciousness. Our technique
relies only on the semantics of the given program and does not require any test
cases or user guidance. In experiments on a set of C benchmarks, we show that
our technique is effective in quickly isolating the cause of error while out-performing
other state-of-the-art fault-localization techniques.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Maria
full_name: Christakis, Maria
last_name: Christakis
- first_name: Matthias
full_name: Heizmann, Matthias
last_name: Heizmann
- first_name: Muhammad Numair
full_name: Mansur, Muhammad Numair
last_name: Mansur
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Valentin
full_name: Wüstholz, Valentin
last_name: Wüstholz
citation:
ama: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault
localization and suspiciousness ranking. In: 25th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems . Vol
11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13'
apa: 'Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz,
V. (2019). Semantic fault localization and suspiciousness ranking. In 25th
International Conference on Tools and Algorithms for the Construction and Analysis
of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature.
https://doi.org/10.1007/978-3-030-17462-0_13'
chicago: Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian
Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness
Ranking.” In 25th International Conference on Tools and Algorithms for the
Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019.
https://doi.org/10.1007/978-3-030-17462-0_13.
ieee: M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic
fault localization and suspiciousness ranking,” in 25th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems , Prague,
Czech Republic, 2019, vol. 11427, pp. 226–243.
ista: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic
fault localization and suspiciousness ranking. 25th International Conference on
Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427,
226–243.'
mla: Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.”
25th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13.
short: M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:,
25th International Conference on Tools and Algorithms for the Construction and
Analysis of Systems , Springer Nature, 2019, pp. 226–243.
conference:
end_date: 2019-04-11
location: Prague, Czech Republic
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2019-04-06
date_created: 2019-02-18T16:44:06Z
date_published: 2019-04-04T00:00:00Z
date_updated: 2023-08-24T14:47:45Z
day: '04'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-17462-0_13
ec_funded: 1
external_id:
isi:
- '000681166500013'
file:
- access_level: open_access
checksum: 9998496f6fe202c0a19124b4209154c6
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T14:16:05Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6408'
file_name: 2019_LNCS_Christakis.pdf
file_size: 773083
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 11427'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 226-243
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: '25th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems '
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semantic fault localization and suspiciousness ranking
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: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11427
year: '2019'
...
---
_id: '6035'
abstract:
- lang: eng
text: 'We present JuliaReach, a toolbox for set-based reachability analysis of dynamical
systems. JuliaReach consists of two main packages: Reachability, containing implementations
of reachability algorithms for continuous and hybrid systems, and LazySets, a
standalone library that implements state-of-the-art algorithms for calculus with
convex sets. The library offers both concrete and lazy set representations, where
the latter stands for the ability to delay set computations until they are needed.
The choice of the programming language Julia and the accompanying documentation
of our toolbox allow researchers to easily translate set-based algorithms from
mathematics to software in a platform-independent way, while achieving runtime
performance that is comparable to statically compiled languages. Combining lazy
operations in high dimensions and explicit computations in low dimensions, JuliaReach
can be applied to solve complex, large-scale problems.'
article_processing_charge: No
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Kostiantyn
full_name: Potomkin, Kostiantyn
last_name: Potomkin
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox
for set-based reachability. In: Proceedings of the 22nd International Conference
on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804'
apa: 'Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019).
JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd
International Conference on Hybrid Systems: Computation and Control (Vol.
22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804'
chicago: 'Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin,
and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In
Proceedings of the 22nd International Conference on Hybrid Systems: Computation
and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.'
ieee: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach:
A toolbox for set-based reachability,” in Proceedings of the 22nd International
Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada,
2019, vol. 22, pp. 39–44.'
ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach:
A toolbox for set-based reachability. Proceedings of the 22nd International Conference
on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and
Control vol. 22, 39–44.'
mla: 'Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.”
Proceedings of the 22nd International Conference on Hybrid Systems: Computation
and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.'
short: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings
of the 22nd International Conference on Hybrid Systems: Computation and Control,
ACM, 2019, pp. 39–44.'
conference:
end_date: 2019-04-18
location: Montreal, QC, Canada
name: 'HSCC: Hybrid Systems Computation and Control'
start_date: 2019-04-16
date_created: 2019-02-18T14:43:28Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2023-08-24T14:47:21Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3302504.3311804
ec_funded: 1
external_id:
arxiv:
- '1901.10736'
isi:
- '000516713900005'
file:
- access_level: open_access
checksum: 28ed56439aea5991c3122d4730fd828f
content_type: application/pdf
creator: cschilli
date_created: 2019-03-05T09:27:18Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6067'
file_name: hscc19.pdf
file_size: 3784414
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
keyword:
- reachability analysis
- hybrid systems
- lazy computation
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 39-44
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'Proceedings of the 22nd International Conference on Hybrid Systems:
Computation and Control'
publication_identifier:
isbn:
- '9781450362825'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'JuliaReach: A toolbox for set-based reachability'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2019'
...
---
_id: '6052'
abstract:
- lang: eng
text: 'Expansion microscopy is a relatively new approach to super-resolution imaging
that uses expandable hydrogels to isotropically increase the physical distance
between fluorophores in biological samples such as cell cultures or tissue slices.
The classic gel recipe results in an expansion factor of ~4×, with a resolution
of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that
achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide
a step-by-step protocol for X10 expansion microscopy. A typical experiment consists
of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization,
(iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol
presented here includes recommendations for optimization, pitfalls and their solutions,
and detailed guidelines that should increase reproducibility. Although our protocol
focuses on X10 expansion microscopy, we detail which of these suggestions are
also applicable to classic fourfold expansion microscopy. We exemplify our protocol
using primary hippocampal neurons from rats, but our approach can be used with
other primary cells or cultured cell lines of interest. This protocol will enable
any researcher with basic experience in immunostainings and access to an epifluorescence
microscope to perform super-resolution microscopy with X10. The procedure takes
3 d and requires ~5 h of actively handling the sample for labeling and expansion,
and another ~3 h for imaging and analysis.'
article_processing_charge: No
article_type: original
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Silvio O
full_name: Rizzoli, Silvio O
last_name: Rizzoli
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization
in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3
apa: Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019).
A practical guide to optimization in X10 expansion microscopy. Nature Protocols.
Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3
chicago: Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann
G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature
Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.
ieee: S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical
guide to optimization in X10 expansion microscopy,” Nature Protocols, vol.
14, no. 3. Nature Publishing Group, pp. 832–863, 2019.
ista: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide
to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.
mla: Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion
Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group,
2019, pp. 832–863, doi:10.1038/s41596-018-0117-3.
short: S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols
14 (2019) 832–863.
date_created: 2019-02-24T22:59:20Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:48:33Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
- _id: Bio
doi: 10.1038/s41596-018-0117-3
ec_funded: 1
external_id:
isi:
- '000459890700008'
pmid:
- '30778205'
file:
- access_level: open_access
checksum: 7efb9951e7ddf3e3dcc2fb92b859c623
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: kschuh
date_created: 2021-06-29T14:41:46Z
date_updated: 2021-06-29T14:41:46Z
file_id: '9619'
file_name: 181031_Truckenbrodt_ExM_NatProtoc.docx
file_size: 84478958
relation: main_file
success: 1
file_date_updated: 2021-06-29T14:41:46Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 832–863
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: A practical guide to optimization in X10 expansion microscopy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2019'
...
---
_id: '6025'
abstract:
- lang: eng
text: Non-canonical Wnt signaling plays a central role for coordinated cell polarization
and directed migration in metazoan development. While spatiotemporally restricted
activation of non-canonical Wnt-signaling drives cell polarization in epithelial
tissues, it remains unclear whether such instructive activity is also critical
for directed mesenchymal cell migration. Here, we developed a light-activated
version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted
activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm
(prechordal plate, ppl) cell migration within the zebrafish gastrula. We found
that Fz7 signaling is required for ppl cell protrusion formation and migration
and that spatiotemporally restricted ectopic activation is capable of redirecting
their migration. Finally, we show that uniform activation of Fz7 signaling in
ppl cells fully rescues defective directed cell migration in fz7 mutant embryos.
Together, our findings reveal that in contrast to the situation in epithelial
cells, non-canonical Wnt signaling functions permissively rather than instructively
in directed mesenchymal cell migration during gastrulation.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_number: e42093
article_processing_charge: No
author:
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Alexandra Madelaine
full_name: Tichy, Alexandra Madelaine
last_name: Tichy
- first_name: Maurizio
full_name: Morri, Maurizio
id: 4863116E-F248-11E8-B48F-1D18A9856A87
last_name: Morri
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated
Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm
cell migration. eLife. 2019;8. doi:10.7554/eLife.42093
apa: Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg,
C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical
wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.42093
chicago: Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri,
Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals
a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.”
ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093.
ieee: D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg,
“Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling
in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications,
2019.
ista: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019.
Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling
in mesendoderm cell migration. eLife. 8, e42093.
mla: Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role
of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol.
8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093.
short: D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg,
ELife 8 (2019).
date_created: 2019-02-17T22:59:22Z
date_published: 2019-02-06T00:00:00Z
date_updated: 2023-08-24T14:46:01Z
day: '06'
ddc:
- '570'
department:
- _id: CaHe
- _id: HaJa
doi: 10.7554/eLife.42093
ec_funded: 1
external_id:
isi:
- '000458025300001'
file:
- access_level: open_access
checksum: 6cb4ca6d4aa96f6f187a5983aa3e660a
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T15:17:21Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6041'
file_name: 2019_elife_Capek.pdf
file_size: 5500707
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling
in mesendoderm cell migration
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6022'
abstract:
- lang: eng
text: The evolution of new species is made easier when traits under divergent ecological
selection are also mating cues. Such ecological mating cues are now considered
more common than previously thought, but we still know little about the genetic
changes underlying their evolution or more generally about the genetic basis for
assortative mating behaviors. Both tight physical linkage and the existence of
large-effect preference loci will strengthen genetic associations between behavioral
and ecological barriers, promoting the evolution of assortative mating. The warning
patterns of Heliconius melpomene and H. cydno are under disruptive selection due
to increased predation of nonmimetic hybrids and are used during mate recognition.
We carried out a genome-wide quantitative trait locus (QTL) analysis of preference
behaviors between these species and showed that divergent male preference has
a simple genetic basis. We identify three QTLs that together explain a large proportion
(approximately 60%) of the difference in preference behavior observed between
the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM)
from the major color pattern gene optix, and, individually, all three have a large
effect on the preference phenotype. Genomic divergence between H. cydno and H.
melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix
color pattern locus but not the other preference QTLs. The simple genetic architecture
we reveal will facilitate the evolution and maintenance of new species despite
ongoing gene flow by coupling behavioral and ecological aspects of reproductive
isolation.
article_number: e2005902
article_processing_charge: No
author:
- first_name: Richard M.
full_name: Merrill, Richard M.
last_name: Merrill
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Simon H.
full_name: Martin, Simon H.
last_name: Martin
- first_name: Maria C
full_name: Melo Hurtado, Maria C
id: 386D7308-F248-11E8-B48F-1D18A9856A87
last_name: Melo Hurtado
- first_name: Sarah
full_name: Barker, Sarah
last_name: Barker
- first_name: John
full_name: Davey, John
last_name: Davey
- first_name: W. Owen
full_name: Mcmillan, W. Owen
last_name: Mcmillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
citation:
ama: Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating
behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902
apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S.,
Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902
chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado,
Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection
of Assortative Mating Behavior.” PLoS Biology. Public Library of Science,
2019. https://doi.org/10.1371/journal.pbio.2005902.
ieee: R. M. Merrill et al., “Genetic dissection of assortative mating behavior,”
PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.
ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan
WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS
Biology. 17(2), e2005902.
mla: Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.”
PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019,
doi:10.1371/journal.pbio.2005902.
short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey,
W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).
date_created: 2019-02-17T22:59:21Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:46:23Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005902
external_id:
isi:
- '000460317100001'
file:
- access_level: open_access
checksum: 5f34001617ee729314ca520c049b1112
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T14:57:24Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6036'
file_name: 2019_PLOS_Merrill.pdf
file_size: 2005949
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9801'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic dissection of assortative mating behavior
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2019'
...
---
_id: '6023'
abstract:
- lang: eng
text: Multicellular development requires coordinated cell polarization relative
to body axes, and translation to oriented cell division 1–3 . In plants, it is
unknown how cell polarities are connected to organismal axes and translated to
division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal
and radial organismal axes to localize to polar cell edges. Localization does
not depend on tissue context, requires cell wall integrity and is defined by a
transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI
proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity
regulator. The DIX-like domain self-interacts and is required for edge localization
and for influencing division orientation, together with a second domain that defines
the polar membrane domain. Our work shows that SOSEKI proteins locally interpret
global polarity cues and can influence cell division orientation. Furthermore,
this work reveals that, despite fundamental differences, cell polarity mechanisms
in plants and animals converge on a similar protein domain.
article_processing_charge: No
author:
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Alja
full_name: Van Der Schuren, Alja
last_name: Van Der Schuren
- first_name: Maritza
full_name: Van Dop, Maritza
last_name: Van Dop
- first_name: Luc
full_name: Van Galen, Luc
last_name: Van Galen
- first_name: Shunsuke
full_name: Saiga, Shunsuke
last_name: Saiga
- first_name: Milad
full_name: Adibi, Milad
last_name: Adibi
- first_name: Barbara
full_name: Möller, Barbara
last_name: Möller
- first_name: Colette A.
full_name: Ten Hove, Colette A.
last_name: Ten Hove
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system
interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166.
doi:10.1038/s41477-019-0363-6
apa: Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi,
M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity
cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6
chicago: Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke
Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets
Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019.
https://doi.org/10.1038/s41477-019-0363-6.
ieee: S. Yoshida et al., “A SOSEKI-based coordinate system interprets global
polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature,
pp. 160–166, 2019.
ista: Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller
B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate
system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.
mla: Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global
Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature,
2019, pp. 160–66, doi:10.1038/s41477-019-0363-6.
short: S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi,
B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants
5 (2019) 160–166.
date_created: 2019-02-17T22:59:21Z
date_published: 2019-02-08T00:00:00Z
date_updated: 2023-08-24T14:46:47Z
day: '08'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1038/s41477-019-0363-6
ec_funded: 1
external_id:
isi:
- '000460479600014'
intvolume: ' 5'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/479113v1.abstract
month: '02'
oa: 1
oa_version: Submitted Version
page: 160-166
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Plants
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2019'
...
---
_id: '6053'
abstract:
- lang: eng
text: Recent technical developments in the fields of quantum electromechanics and
optomechanics have spawned nanoscale mechanical transducers with the sensitivity
to measure mechanical displacements at the femtometre scale and the ability to
convert electromagnetic signals at the single photon level. A key challenge in
this field is obtaining strong coupling between motion and electromagnetic fields
without adding additional decoherence. Here we present an electromechanical transducer
that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a
superconducting microwave circuit. The use of a phononic bandgap crystal enables
quantum-level transduction of hypersonic mechanical motion and concurrently eliminates
decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies
provide a natural pathway for integration with Josephson junction quantum circuits,
a leading quantum computing technology, and nanophotonic systems capable of optical
networking and distributing quantum information.
article_processing_charge: No
article_type: original
author:
- first_name: Mahmoud
full_name: Kalaee, Mahmoud
last_name: Kalaee
- first_name: Mohammad
full_name: Mirhosseini, Mohammad
last_name: Mirhosseini
- first_name: Paul B.
full_name: Dieterle, Paul B.
last_name: Dieterle
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
citation:
ama: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum
electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339.
doi:10.1038/s41565-019-0377-2
apa: Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., &
Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature
Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2
chicago: Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo,
Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic
Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2.
ieee: M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O.
Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology,
vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.
ista: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019.
Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4),
334–339.
mla: Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.”
Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339,
doi:10.1038/s41565-019-0377-2.
short: M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter,
Nature Nanotechnology 14 (2019) 334–339.
date_created: 2019-02-24T22:59:21Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-24T14:48:08Z
day: '01'
department:
- _id: JoFi
doi: 10.1038/s41565-019-0377-2
external_id:
isi:
- '000463195700014'
intvolume: ' 14'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://authors.library.caltech.edu/92123/
month: '04'
oa: 1
oa_version: Submitted Version
page: 334–339
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: Quantum electromechanics of a hypersonic crystal
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2019'
...
---
_id: '6050'
abstract:
- lang: eng
text: 'We answer a question of David Hilbert: given two circles it is not possible
in general to construct their centers using only a straightedge. On the other
hand, we give infinitely many families of pairs of circles for which such construction
is possible. '
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Roman
full_name: Fedorov, Roman
last_name: Fedorov
citation:
ama: Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of
the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240
apa: Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge.
Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240
chicago: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.”
Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240.
ieee: A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings
of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019.
ista: Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings
of the American Mathematical Society. 147, 91–102.
mla: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.”
Proceedings of the American Mathematical Society, vol. 147, AMS, 2019,
pp. 91–102, doi:10.1090/proc/14240.
short: A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society
147 (2019) 91–102.
date_created: 2019-02-24T22:59:19Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:48:59Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/14240
external_id:
arxiv:
- '1709.02562'
isi:
- '000450363900008'
intvolume: ' 147'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.02562
month: '01'
oa: 1
oa_version: Preprint
page: 91-102
publication: Proceedings of the American Mathematical Society
publication_status: published
publisher: AMS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two circles and only a straightedge
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 147
year: '2019'
...
---
_id: '9801'
article_processing_charge: No
author:
- first_name: Richard M.
full_name: Merrill, Richard M.
last_name: Merrill
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Simon H.
full_name: Martin, Simon H.
last_name: Martin
- first_name: Maria C
full_name: Melo Hurtado, Maria C
id: 386D7308-F248-11E8-B48F-1D18A9856A87
last_name: Melo Hurtado
- first_name: Sarah
full_name: Barker, Sarah
last_name: Barker
- first_name: John
full_name: Davey, John
last_name: Davey
- first_name: W. Owen
full_name: Mcmillan, W. Owen
last_name: Mcmillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
citation:
ama: Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006
apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S.,
Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science.
https://doi.org/10.1371/journal.pbio.2005902.s006
chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado,
Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral
Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006.
ieee: R. M. Merrill et al., “Raw behavioral data.” Public Library of Science,
2019.
ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan
WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006.
mla: Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science,
2019, doi:10.1371/journal.pbio.2005902.s006.
short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey,
W.O. Mcmillan, C.D. Jiggins, (2019).
date_created: 2021-08-06T11:34:56Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:46:23Z
day: '07'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005902.s006
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6022'
relation: used_in_publication
status: public
status: public
title: Raw behavioral data
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6095'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology.
2019;28(6):1375-1393. doi:10.1111/mec.14972
apa: Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid
zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972
chicago: Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology.
Wiley, 2019. https://doi.org/10.1111/mec.14972.
ieee: R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone
between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no.
6. Wiley, pp. 1375–1393, 2019.
ista: Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal
rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular
Ecology. 28(6), 1375–1393.
mla: Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between
Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley,
2019, pp. 1375–93, doi:10.1111/mec.14972.
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
Molecular Ecology 28 (2019) 1375–1393.
date_created: 2019-03-10T22:59:21Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:50:27Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.14972
external_id:
isi:
- '000465219200013'
file:
- access_level: open_access
checksum: f915885756057ec0ca5912a41f46a887
content_type: application/pdf
creator: dernst
date_created: 2019-03-11T16:12:54Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6097'
file_name: 2019_MolecularEcology_Faria.pdf
file_size: 1510715
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1375-1393
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9837'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 28
year: '2019'
...
---
_id: '6049'
abstract:
- lang: eng
text: 'In this article it is shown that large systems with many interacting units
endowing multiple phases display self-oscillations in the presence of linear feedback
between the control and order parameters, where an Andronov–Hopf bifurcation takes
over the phase transition. This is simply illustrated through the mean field Landau
theory whose feedback dynamics turn out to be described by the Van der Pol equation
and it is then validated for the fully connected Ising model following heat bath
dynamics. Despite its simplicity, this theory accounts potentially for a rich
range of phenomena: here it is applied to describe in a stylized way (i) excess
demand-price cycles due to strong herding in a simple agent-based market model;
(ii) congestion waves in queuing networks triggered by user feedback to delays
in overloaded conditions; and (iii) metabolic network oscillations resulting from
cell growth control in a bistable phenotypic landscape.'
article_number: '045002'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: 'De Martino D. Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical.
2019;52(4). doi:10.1088/1751-8121/aaf2dd'
apa: 'De Martino, D. (2019). Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical
and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd'
chicago: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.'
ieee: 'D. De Martino, “Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical,
vol. 52, no. 4. IOP Publishing, 2019.'
ista: 'De Martino D. 2019. Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical and
Theoretical. 52(4), 045002.'
mla: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.'
short: 'D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).'
date_created: 2019-02-24T22:59:19Z
date_published: 2019-01-07T00:00:00Z
date_updated: 2023-08-24T14:49:23Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1088/1751-8121/aaf2dd
ec_funded: 1
external_id:
isi:
- '000455379500001'
file:
- access_level: open_access
checksum: 1112304ad363a6d8afaeccece36473cf
content_type: application/pdf
creator: kschuh
date_created: 2019-04-19T12:18:57Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6344'
file_name: 2019_IOP_DeMartino.pdf
file_size: 1804557
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Feedback-induced self-oscillations in large interacting systems subjected to
phase transitions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2019'
...
---
_id: '6091'
abstract:
- lang: eng
text: Cortical networks are characterized by sparse connectivity, with synapses
found at only a subset of axo-dendritic contacts. Yet within these networks, neurons
can exhibit high connection probabilities, suggesting that cell-intrinsic factors,
not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a
factor that determines synapse density by mediating a cell-cell competition that
requires ephrin-B-EphB signaling. In a microisland culture system designed to
isolate cell-cell competition, we find that eB3 determines winning and losing
neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM)
genetic mouse model system in vivo the relative levels of eB3 control spine density
in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls
synapse density independently of action potential-driven activity. Our findings
illustrate a new class of competitive mechanism mediated by trans-synaptic organizing
proteins which control the number of synapses neurons receive relative to neighboring
neurons.
article_number: e41563
article_processing_charge: No
author:
- first_name: Nathan T.
full_name: Henderson, Nathan T.
last_name: Henderson
- first_name: Sylvain J.
full_name: Le Marchand, Sylvain J.
last_name: Le Marchand
- first_name: Martin
full_name: Hruska, Martin
last_name: Hruska
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Matthew B.
full_name: Dalva, Matthew B.
last_name: Dalva
citation:
ama: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3
controls excitatory synapse density through cell-cell competition for EphBs. eLife.
2019;8. doi:10.7554/eLife.41563
apa: Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L.,
& Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through
cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563
chicago: Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer,
Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density
through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/eLife.41563.
ieee: N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and
M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell
competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019.
Ephrin-B3 controls excitatory synapse density through cell-cell competition for
EphBs. eLife. 8, e41563.
mla: Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density
through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife
Sciences Publications, 2019, doi:10.7554/eLife.41563.
short: N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B.
Dalva, ELife 8 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-21T00:00:00Z
date_updated: 2023-08-24T14:50:50Z
day: '21'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/eLife.41563
external_id:
isi:
- '000459380600001'
pmid:
- '30789343'
file:
- access_level: open_access
checksum: 7b0800d003f14cd06b1802dea0c52941
content_type: application/pdf
creator: dernst
date_created: 2019-03-11T16:15:37Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6098'
file_name: 2019_eLife_Henderson.pdf
file_size: 7260753
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ephrin-B3 controls excitatory synapse density through cell-cell competition
for EphBs
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6046'
abstract:
- lang: eng
text: Sudden stress often triggers diverse, temporally structured gene expression
responses in microbes, but it is largely unknown how variable in time such responses
are and if genes respond in the same temporal order in every single cell. Here,
we quantified timing variability of individual promoters responding to sublethal
antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy.
We identified lower and upper bounds that put definite constraints on timing variability,
which varies strongly among promoters and conditions. Timing variability can be
interpreted using results from statistical kinetics, which enable us to estimate
the number of rate‐limiting molecular steps underlying different responses. We
found that just a few critical steps control some responses while others rely
on dozens of steps. To probe connections between different stress responses, we
then tracked the temporal order and response time correlations of promoter pairs
in individual cells. Our results support that, when bacteria are exposed to the
antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are
part of the same causal chain of molecular events. In contrast, under trimethoprim,
the acid stress response and the SOS response are part of different chains of
events running in parallel. Our approach reveals fundamental constraints on gene
expression timing and provides new insights into the molecular events that underlie
the timing of stress responses.
acknowledged_ssus:
- _id: Bio
article_number: e8470
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex
stress responses in individual bacteria. Molecular systems biology. 2019;15(2).
doi:10.15252/msb.20188470
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and
precision of complex stress responses in individual bacteria. Molecular Systems
Biology. Embo Press. https://doi.org/10.15252/msb.20188470
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order
and Precision of Complex Stress Responses in Individual Bacteria.” Molecular
Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision
of complex stress responses in individual bacteria,” Molecular systems biology,
vol. 15, no. 2. Embo Press, 2019.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of
complex stress responses in individual bacteria. Molecular systems biology. 15(2),
e8470.
mla: Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses
in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470,
Embo Press, 2019, doi:10.15252/msb.20188470.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
date_created: 2019-02-24T22:59:18Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2023-08-24T14:49:53Z
day: '14'
department:
- _id: GaTk
doi: 10.15252/msb.20188470
external_id:
isi:
- '000459628300003'
pmid:
- '30765425'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30765425
month: '02'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Molecular systems biology
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal order and precision of complex stress responses in individual bacteria
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...