---
_id: '1540'
abstract:
- lang: eng
text: 'Plant sexual reproduction involves highly structured and specialized organs:
stamens (male) and gynoecia (female, containing ovules). These organs synchronously
develop within protective flower buds, until anthesis, via tightly coordinated
mechanisms that are essential for effective fertilization and production of viable
seeds. The phytohormone auxin is one of the key endogenous signalling molecules
controlling initiation and development of these, and other, plant organs. In particular,
its uneven distribution, resulting from tightly controlled production, metabolism
and directional transport, is an important morphogenic factor. In this review
we discuss how developmentally controlled and localized auxin biosynthesis and
transport contribute to the coordinated development of plants'' reproductive organs,
and their fertilized derivatives (embryos) via the regulation of auxin levels
and distribution within and around them. Current understanding of the links between
de novo local auxin biosynthesis, auxin transport and/or signalling is presented
to highlight the importance of the non-cell autonomous action of auxin production
on development and morphogenesis of reproductive organs and embryos. An overview
of transcription factor families, which spatiotemporally define local auxin production
by controlling key auxin biosynthetic enzymes, is also presented.'
acknowledgement: 'The work was supported by grants from: the Employment of Best Young
Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037)
to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and
the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and
the EU (FP7/2007–2013 People Programme), to HSR.'
article_processing_charge: No
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Lucie
full_name: Crhák Khaitová, Lucie
last_name: Crhák Khaitová
- first_name: Souad
full_name: Mroue, Souad
last_name: Mroue
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized
auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis.
Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256
apa: Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance
of localized auxin production for morphogenesis of reproductive organs and embryos
in Arabidopsis. Journal of Experimental Botany. Oxford University Press.
https://doi.org/10.1093/jxb/erv256
chicago: Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The
Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs
and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University
Press, 2015. https://doi.org/10.1093/jxb/erv256.
ieee: H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of
localized auxin production for morphogenesis of reproductive organs and embryos
in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford
University Press, pp. 5029–5042, 2015.
ista: Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized
auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis.
Journal of Experimental Botany. 66(16), 5029–5042.
mla: Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis
of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental
Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.
short: H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental
Botany 66 (2015) 5029–5042.
date_created: 2018-12-11T11:52:36Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2025-09-23T13:51:25Z
day: '05'
department:
- _id: EvBe
doi: 10.1093/jxb/erv256
external_id:
isi:
- '000359688300015'
intvolume: ' 66'
isi: 1
issue: '16'
language:
- iso: eng
month: '05'
oa_version: None
page: 5029 - 5042
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5631'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The importance of localized auxin production for morphogenesis of reproductive
organs and embryos in Arabidopsis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 66
year: '2015'
...
---
_id: '1541'
abstract:
- lang: eng
text: We present XSpeed a parallel state-space exploration algorithm for continuous
systems with linear dynamics and nondeterministic inputs. The motivation of having
parallel algorithms is to exploit the computational power of multi-core processors
to speed-up performance. The parallelization is achieved on two fronts. First,
we propose a parallel implementation of the support function algorithm by sampling
functions in parallel. Second, we propose a parallel state-space exploration by
slicing the time horizon and computing the reachable states in the time slices
in parallel. The second method can be however applied only to a class of linear
systems with invertible dynamics and fixed input. A GP-GPU implementation is also
presented following a lazy evaluation strategy on support functions. The parallel
algorithms are implemented in the tool XSpeed. We evaluated the performance on
two benchmarks including an 28 dimension Helicopter model. Comparison with the
sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread
Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up
of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario),
the state of the art tool for reachability analysis of linear hybrid systems.
Experiments illustrate that our parallel algorithm with time slicing not only
speeds-up performance but also improves precision.
acknowledgement: This work was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants
S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
author:
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Amit
full_name: Gurung, Amit
last_name: Gurung
- first_name: Binayak
full_name: Das, Binayak
last_name: Das
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating
reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1'
apa: 'Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R.
(2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented
at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1'
chicago: 'Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov,
and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.”
Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1.'
ieee: 'R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed:
Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer,
pp. 3–18, 2015.'
ista: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating
reachability analysis on multi-core processors. 9434, 3–18.'
mla: 'Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core
Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.'
short: R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015)
3–18.
conference:
end_date: 2015-11-19
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2015-11-17
date_created: 2018-12-11T11:52:37Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2025-04-15T06:26:02Z
day: '28'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_1
ec_funded: 1
intvolume: ' 9434'
language:
- iso: eng
month: '11'
oa_version: None
page: 3 - 18
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Springer
publist_id: '5630'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'XSpeed: Accelerating reachability analysis on multi-core processors'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal
of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
corr_author: '1'
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2025-09-23T14:55:02Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
external_id:
isi:
- '000362056300005'
file:
- access_level: open_access
checksum: 33b60ecfea60764756a9ee9df5eb65ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:53Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5244'
file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf
file_size: 595307
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 383'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: ' Journal of Theoretical Biology'
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a unifying framework for evolutionary processes
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 383
year: '2015'
...
---
_id: '1543'
abstract:
- lang: eng
text: A plethora of diverse programmed cell death (PCD) processes has been described
in living organisms. In animals and plants, different forms of PCD play crucial
roles in development, immunity, and responses to the environment. While the molecular
control of some animal PCD forms such as apoptosis is known in great detail, we
still know comparatively little about the regulation of the diverse types of plant
PCD. In part, this deficiency in molecular understanding is caused by the lack
of reliable reporters to detect PCD processes. Here, we addressed this issue by
using a combination of bioinformatics approaches to identify commonly regulated
genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana).
Our results indicate that the transcriptional signatures of developmentally controlled
cell death are largely distinct from the ones associated with environmentally
induced cell death. Moreover, different cases of developmental PCD share a set
of cell death-associated genes. Most of these genes are evolutionary conserved
within the green plant lineage, arguing for an evolutionary conserved core machinery
of developmental PCD. Based on this information, we established an array of specific
promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators
represent a powerful resource that can be used in addition to established morphological
and biochemical methods to detect and analyze PCD processes in vivo and in planta.
article_processing_charge: No
author:
- first_name: Yadira
full_name: Olvera Carrillo, Yadira
last_name: Olvera Carrillo
- first_name: Michiel
full_name: Van Bel, Michiel
last_name: Van Bel
- first_name: Tom
full_name: Van Hautegem, Tom
last_name: Van Hautegem
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Marlies
full_name: Huysmans, Marlies
last_name: Huysmans
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Matthias
full_name: Van Durme, Matthias
last_name: Van Durme
- first_name: Pierre
full_name: Buscaill, Pierre
last_name: Buscaill
- first_name: Susana
full_name: Rivas, Susana
last_name: Rivas
- first_name: Núria
full_name: Coll, Núria
last_name: Coll
- first_name: Frederik
full_name: Coppens, Frederik
last_name: Coppens
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
citation:
ama: Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed
cell death indicator genes discriminates developmentally and environmentally induced
programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699.
doi:10.1104/pp.15.00769
apa: Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans,
M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death
indicator genes discriminates developmentally and environmentally induced programmed
cell death in plants. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1104/pp.15.00769
chicago: Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych,
Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core
of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally
Induced Programmed Cell Death in Plants.” Plant Physiology. American Society
of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769.
ieee: Y. Olvera Carrillo et al., “A conserved core of programmed cell death
indicator genes discriminates developmentally and environmentally induced programmed
cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society
of Plant Biologists, pp. 2684–2699, 2015.
ista: Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková
M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015.
A conserved core of programmed cell death indicator genes discriminates developmentally
and environmentally induced programmed cell death in plants. Plant Physiology.
169(4), 2684–2699.
mla: Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death
Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed
Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society
of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.
short: Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans,
M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere,
M. Nowack, Plant Physiology 169 (2015) 2684–2699.
date_created: 2018-12-11T11:52:38Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2025-09-22T14:28:43Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.15.00769
external_id:
isi:
- '000368472700025'
intvolume: ' 169'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 2684 - 2699
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5628'
scopus_import: '1'
status: public
title: A conserved core of programmed cell death indicator genes discriminates developmentally
and environmentally induced programmed cell death in plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 169
year: '2015'
...
---
_id: '1544'
abstract:
- lang: eng
text: 'Cell division in prokaryotes and eukaryotes is commonly initiated by the
well-controlled binding of proteins to the cytoplasmic side of the cell membrane.
However, a precise characterization of the spatiotemporal dynamics of membrane-bound
proteins is often difficult to achieve in vivo. Here, we present protocols for
the use of supported lipid bilayers to rebuild the cytokinetic machineries of
cells with greatly different dimensions: the bacterium Escherichia coli and eggs
of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence
microscopy, these experimental setups allow for precise quantitative analyses
of membrane-bound proteins. The protocols described to obtain glass-supported
membranes from bacterial and vertebrate lipids can be used as starting points
for other reconstitution experiments. We believe that similar biochemical assays
will be instrumental to study the biochemistry and biophysics underlying a variety
of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.'
article_processing_charge: No
author:
- first_name: Phuong
full_name: Nguyen, Phuong
last_name: Nguyen
- first_name: Christine
full_name: Field, Christine
last_name: Field
- first_name: Aaron
full_name: Groen, Aaron
last_name: Groen
- first_name: Timothy
full_name: Mitchison, Timothy
last_name: Mitchison
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007'
apa: Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using
supported bilayers to study the spatiotemporal organization of membrane-bound
proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241).
Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007
chicago: Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin
Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound
Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic
Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007.
ieee: P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported
bilayers to study the spatiotemporal organization of membrane-bound proteins,”
in Building a Cell from its Components Parts, vol. 128, Academic Press,
2015, pp. 223–241.
ista: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from its Components Parts. vol. 128, 223–241.'
mla: Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal
Organization of Membrane-Bound Proteins.” Building a Cell from Its Components
Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.
short: P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell
from Its Components Parts, Academic Press, 2015, pp. 223–241.
corr_author: '1'
date_created: 2018-12-11T11:52:38Z
date_published: 2015-04-08T00:00:00Z
date_updated: 2025-09-29T11:03:06Z
day: '08'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2015.01.007
external_id:
isi:
- '000370490800013'
pmid:
- '25997350'
intvolume: ' 128'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/
month: '04'
oa: 1
oa_version: Submitted Version
page: 223 - 241
pmid: 1
publication: Building a Cell from its Components Parts
publication_status: published
publisher: Academic Press
publist_id: '5627'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using supported bilayers to study the spatiotemporal organization of membrane-bound
proteins
type: book_chapter
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 128
year: '2015'
...
---
_id: '10748'
abstract:
- lang: eng
text: The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based
superconducting rings is valuable for characterizing the basic properties of the
superconductor, and may also provide important insight into the superconducting
paring symmetry. We report the fabrications of micron-sized rings and disks from
thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid
states in rings we developed a custom-tailored version of magnetic force microscopy
(MFM). This technique has a number of qualitative advantages for working with
mesoscopic superconducting samples in comparison to the conventional MFM and other
imaging techniques. We observed metastable fluxoid states in rings of different
sizes. Thermally activated fluxoid dynamics of these states was studied and modeled.
In addition, we found different regimes of interaction between Fe(Se, Te) ring
and MFM tip which are explained. Possibilities of the existence of exotic vortex
states and proposals for experiments to test the symmetry of the superconducting
order parameter in iron based superconductors are analyzed.
alternative_title:
- Bulletin of the American Physical Society
article_number: G16.00009
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Can
full_name: Zhang, Can
last_name: Zhang
- first_name: Tyler
full_name: Naibert, Tyler
last_name: Naibert
- first_name: James
full_name: Eckstein, James
last_name: Eckstein
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: 'Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te)
micron-sized rings by magnetic force microscopy. In: APS March Meeting 2015.
Vol 60. American Physical Society; 2015.'
apa: 'Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., & Budakian, R. (2015).
Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In APS
March Meeting 2015 (Vol. 60). San Antonio, TX, United States: American Physical
Society.'
chicago: Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi
Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.”
In APS March Meeting 2015, Vol. 60. American Physical Society, 2015.
ieee: H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of
Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in APS March
Meeting 2015, San Antonio, TX, United States, 2015, vol. 60, no. 1.
ista: 'Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe
(Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015.
APS: American Physical Society, Bulletin of the American Physical Society, vol.
60, G16.00009.'
mla: Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic
Force Microscopy.” APS March Meeting 2015, vol. 60, no. 1, G16.00009, American
Physical Society, 2015.
short: H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March
Meeting 2015, American Physical Society, 2015.
conference:
end_date: 2015-03-06
location: San Antonio, TX, United States
name: 'APS: American Physical Society'
start_date: 2015-03-02
date_created: 2022-02-08T10:17:09Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2022-02-08T10:42:53Z
day: '01'
extern: '1'
intvolume: ' 60'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR15/Event/238442
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2015
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 60
year: '2015'
...
---
_id: '10794'
abstract:
- lang: eng
text: Mathematical models are of fundamental importance in the understanding of
complex population dynamics. For instance, they can be used to predict the population
evolution starting from different initial conditions or to test how a system responds
to external perturbations. For this analysis to be meaningful in real applications,
however, it is of paramount importance to choose an appropriate model structure
and to infer the model parameters from measured data. While many parameter inference
methods are available for models based on deterministic ordinary differential
equations, the same does not hold for more detailed individual-based models. Here
we consider, in particular, stochastic models in which the time evolution of the
species abundances is described by a continuous-time Markov chain. These models
are governed by a master equation that is typically difficult to solve. Consequently,
traditional inference methods that rely on iterative evaluation of parameter likelihoods
are computationally intractable. The aim of this paper is to present recent advances
in parameter inference for continuous-time Markov chain models, based on a moment
closure approximation of the parameter likelihood, and to investigate how these
results can help in understanding, and ultimately controlling, complex systems
in ecology. Specifically, we illustrate through an agricultural pest case study
how parameters of a stochastic individual-based model can be identified from measured
data and how the resulting model can be used to solve an optimal control problem
in a stochastic setting. In particular, we show how the matter of determining
the optimal combination of two different pest control methods can be formulated
as a chance constrained optimization problem where the control action is modeled
as a state reset, leading to a hybrid system formulation.
acknowledgement: "The authors would like to acknowledge contributions from Baptiste
Mottet who performed preliminary analysis regarding parameter inference for the
considered case study in a student project (Mottet, 2014/2015).\r\nThe research
leading to these results has received funding from the People Programme (Marie Curie
Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement No. [291734] and from SystemsX under the project SignalX."
article_number: '42'
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: 'Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in
Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042'
apa: 'Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic
individual-based models of ecological systems: a pest control simulation study.
Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042'
chicago: 'Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference
for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation
Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.'
ieee: 'F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study,” Frontiers in
Environmental Science, vol. 3. Frontiers, 2015.'
ista: 'Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in Environmental
Science. 3, 42.'
mla: 'Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based
Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in
Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.'
short: F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
corr_author: '1'
date_created: 2022-02-25T11:42:25Z
date_published: 2015-06-10T00:00:00Z
date_updated: 2025-04-15T06:50:01Z
day: '10'
ddc:
- '000'
- '570'
department:
- _id: ToHe
- _id: GaTk
doi: 10.3389/fenvs.2015.00042
ec_funded: 1
file:
- access_level: open_access
checksum: 26c222487564e1be02a11d688d6f769d
content_type: application/pdf
creator: dernst
date_created: 2022-02-25T11:55:26Z
date_updated: 2022-02-25T11:55:26Z
file_id: '10795'
file_name: 2015_FrontiersEnvironmScience_Parise.pdf
file_size: 1371201
relation: main_file
success: 1
file_date_updated: 2022-02-25T11:55:26Z
has_accepted_license: '1'
intvolume: ' 3'
keyword:
- General Environmental Science
language:
- iso: eng
month: '06'
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: Frontiers in Environmental Science
publication_identifier:
issn:
- 2296-665X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bayesian inference for stochastic individual-based models of ecological systems:
a pest control simulation study'
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: '2015'
...
---
OA_place: publisher
OA_type: green
_id: '10796'
abstract:
- lang: eng
text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player
(player 1 vs player 2) zero-sum games on finite-state graphs where every transition
is assigned a reward between 0 and 1, and the payoff function is the long-run
average of the rewards. The value is the maximal expected payoff that player 1
can guarantee against all strategies of player 2. We consider the computation
of the set of states with value 1 under finite-memory strategies for player 1,
and our main results for the problem are as follows: (1) we present a polynomial-time
algorithm; (2) we show that whenever there is a finite-memory strategy, there
is a stationary strategy that does not need memory at all; and (3) we present
an optimal bound (which is double exponential) on the patience of stationary strategies
(where patience of a distribution is the inverse of the smallest positive probability
and represents a complexity measure of a stationary strategy).'
acknowledgement: "The research was partly supported by FWF Grant No P 23499-N23, FWF
NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award."
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies
for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029.
doi:10.1137/1.9781611973730.69'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029).
San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings
of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29.
SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.
ieee: K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory
strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States,
2015, vol. 2015, no. 1, pp. 1018–1029.
ista: 'Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms
vol. 2015, 1018–1029.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of
the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015,
no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.
conference:
end_date: 2015-01-06
location: San Diego, CA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2015-01-04
corr_author: '1'
date_created: 2022-02-25T12:18:43Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2025-06-26T06:54:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973730.69
ec_funded: 1
external_id:
arxiv:
- '1409.6690'
intvolume: ' 2015'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1409.6690
month: '01'
oa: 1
oa_version: Preprint
page: 1018-1029
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete
Algorithms
publication_identifier:
isbn:
- 978-161197374-7
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: The value 1 problem under finite-memory strategies for concurrent mean-payoff
games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1106'
abstract:
- lang: eng
text: Circumferential skin creases Kunze type (CSC-KT) is a specific congenital
entity with an unknown genetic cause. The disease phenotype comprises characteristic
circumferential skin creases accompanied by intellectual disability, a cleft palate,
short stature, and dysmorphic features. Here, we report that mutations in either
MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a
member of the microtubule end-binding family of proteins that bind to the guanosine
triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin
isotype that is expressed abundantly in the developing brain. Functional analyses
of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer
folding and assembly pathway that leads to a compromised yield of native heterodimers.
The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we
show that the mutations result in enhanced MAPRE2 binding to microtubules, implying
an increased dwell time at microtubule plus ends. Further, in vivo analysis of
MAPRE2 mutations in a zebrafish model of craniofacial development shows that the
variants most likely perturb the patterning of branchial arches, either through
excessive activity (under a recessive paradigm) or through haploinsufficiency
(dominant de novo paradigm). Taken together, our data add CSC-KT to the growing
list of tubulinopathies and highlight how multiple inheritance paradigms can affect
dosage-sensitive biological systems so as to result in the same clinical defect.
article_processing_charge: No
author:
- first_name: Mala
full_name: Isrie, Mala
last_name: Isrie
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Guoling
full_name: Tian, Guoling
last_name: Tian
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Francesca
full_name: Cristofoli, Francesca
last_name: Cristofoli
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Zachari A
full_name: Kupchinsky, Zachari A
last_name: Kupchinsky
- first_name: Alejandro
full_name: Sifrim, Alejandro
last_name: Sifrim
- first_name: Celia
full_name: Rodriguez Rodriguez, Celia
last_name: Rodriguez Rodriguez
- first_name: Elena P
full_name: Dapena, Elena P
last_name: Dapena
- first_name: Kurston
full_name: Doonanco, Kurston
last_name: Doonanco
- first_name: Norma
full_name: Leonard, Norma
last_name: Leonard
- first_name: Faten
full_name: Tinsa, Faten
last_name: Tinsa
- first_name: Stéphanie
full_name: Moortgat, Stéphanie
last_name: Moortgat
- first_name: Hakan
full_name: Ulucan, Hakan
last_name: Ulucan
- first_name: Erkan
full_name: Koparir, Erkan
last_name: Koparir
- first_name: Ender
full_name: Karaca, Ender
last_name: Karaca
- first_name: Nicholas
full_name: Katsanis, Nicholas
last_name: Katsanis
- first_name: Valeria
full_name: Marton, Valeria
last_name: Marton
- first_name: Joris R
full_name: Vermeesch, Joris R
last_name: Vermeesch
- first_name: Erica E
full_name: Davis, Erica E
last_name: Davis
- first_name: Nicholas J
full_name: Cowan, Nicholas J
last_name: Cowan
- first_name: David
full_name: Keays, David
last_name: Keays
- first_name: Hilde
full_name: Van Esch, Hilde
last_name: Van Esch
citation:
ama: Isrie M, Breuss M, Tian G, et al. Mutations in either TUBB or MAPRE2 cause
circumferential skin creases Kunze type. The American Journal of Human Genetics.
2015;97(6):790-800. doi:10.1016/j.ajhg.2015.10.014
apa: Isrie, M., Breuss, M., Tian, G., Hansen, A. H., Cristofoli, F., Morandell,
J., … Van Esch, H. (2015). Mutations in either TUBB or MAPRE2 cause circumferential
skin creases Kunze type. The American Journal of Human Genetics. Cell Press.
https://doi.org/10.1016/j.ajhg.2015.10.014
chicago: Isrie, Mala, Martin Breuss, Guoling Tian, Andi H Hansen, Francesca Cristofoli,
Jasmin Morandell, Zachari A Kupchinsky, et al. “Mutations in Either TUBB or MAPRE2
Cause Circumferential Skin Creases Kunze Type.” The American Journal of Human
Genetics. Cell Press, 2015. https://doi.org/10.1016/j.ajhg.2015.10.014.
ieee: M. Isrie et al., “Mutations in either TUBB or MAPRE2 cause circumferential
skin creases Kunze type,” The American Journal of Human Genetics, vol.
97, no. 6. Cell Press, pp. 790–800, 2015.
ista: Isrie M, Breuss M, Tian G, Hansen AH, Cristofoli F, Morandell J, Kupchinsky
ZA, Sifrim A, Rodriguez Rodriguez C, Dapena EP, Doonanco K, Leonard N, Tinsa F,
Moortgat S, Ulucan H, Koparir E, Karaca E, Katsanis N, Marton V, Vermeesch JR,
Davis EE, Cowan NJ, Keays D, Van Esch H. 2015. Mutations in either TUBB or MAPRE2
cause circumferential skin creases Kunze type. The American Journal of Human Genetics.
97(6), 790–800.
mla: Isrie, Mala, et al. “Mutations in Either TUBB or MAPRE2 Cause Circumferential
Skin Creases Kunze Type.” The American Journal of Human Genetics, vol.
97, no. 6, Cell Press, 2015, pp. 790–800, doi:10.1016/j.ajhg.2015.10.014.
short: M. Isrie, M. Breuss, G. Tian, A.H. Hansen, F. Cristofoli, J. Morandell, Z.A.
Kupchinsky, A. Sifrim, C. Rodriguez Rodriguez, E.P. Dapena, K. Doonanco, N. Leonard,
F. Tinsa, S. Moortgat, H. Ulucan, E. Koparir, E. Karaca, N. Katsanis, V. Marton,
J.R. Vermeesch, E.E. Davis, N.J. Cowan, D. Keays, H. Van Esch, The American Journal
of Human Genetics 97 (2015) 790–800.
date_created: 2018-12-11T11:50:11Z
date_published: 2015-12-03T00:00:00Z
date_updated: 2025-09-23T09:38:06Z
day: '03'
doi: 10.1016/j.ajhg.2015.10.014
extern: '1'
external_id:
isi:
- '000368437900002'
intvolume: ' 97'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 790 - 800
publication: The American Journal of Human Genetics
publication_status: published
publisher: Cell Press
publist_id: '6264'
quality_controlled: '1'
status: public
title: Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze
type
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 97
year: '2015'
...
---
_id: '11073'
abstract:
- lang: eng
text: Human cancer cells bear complex chromosome rearrangements that can be potential
drivers of cancer development. However, the molecular mechanisms underlying these
rearrangements have been unclear. Zhang et al. use a new technique combining live-cell
imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated
to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent
cell cycle.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- 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: Hatch EM, Hetzer M. Linking micronuclei to chromosome fragmentation. Cell.
2015;161(7):1502-1504. doi:10.1016/j.cell.2015.06.005
apa: Hatch, E. M., & Hetzer, M. (2015). Linking micronuclei to chromosome fragmentation.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2015.06.005
chicago: Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome
Fragmentation.” Cell. Elsevier, 2015. https://doi.org/10.1016/j.cell.2015.06.005.
ieee: E. M. Hatch and M. Hetzer, “Linking micronuclei to chromosome fragmentation,”
Cell, vol. 161, no. 7. Elsevier, pp. 1502–1504, 2015.
ista: Hatch EM, Hetzer M. 2015. Linking micronuclei to chromosome fragmentation.
Cell. 161(7), 1502–1504.
mla: Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome Fragmentation.”
Cell, vol. 161, no. 7, Elsevier, 2015, pp. 1502–04, doi:10.1016/j.cell.2015.06.005.
short: E.M. Hatch, M. Hetzer, Cell 161 (2015) 1502–1504.
date_created: 2022-04-07T07:48:49Z
date_published: 2015-06-18T00:00:00Z
date_updated: 2024-10-14T11:22:03Z
day: '18'
doi: 10.1016/j.cell.2015.06.005
extern: '1'
external_id:
pmid:
- '26091034'
intvolume: ' 161'
issue: '7'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2015.06.005
month: '06'
oa: 1
oa_version: Published Version
page: 1502-1504
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Linking micronuclei to chromosome fragmentation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 161
year: '2015'
...
---
_id: '11074'
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- 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: Hatch EM, Hetzer M. Chromothripsis. Current Biology. 2015;25(10):PR397-R399.
doi:10.1016/j.cub.2015.02.033
apa: Hatch, E. M., & Hetzer, M. (2015). Chromothripsis. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2015.02.033
chicago: Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology.
Elsevier, 2015. https://doi.org/10.1016/j.cub.2015.02.033.
ieee: E. M. Hatch and M. Hetzer, “Chromothripsis,” Current Biology, vol.
25, no. 10. Elsevier, pp. PR397-R399, 2015.
ista: Hatch EM, Hetzer M. 2015. Chromothripsis. Current Biology. 25(10), PR397-R399.
mla: Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology,
vol. 25, no. 10, Elsevier, 2015, pp. PR397-R399, doi:10.1016/j.cub.2015.02.033.
short: E.M. Hatch, M. Hetzer, Current Biology 25 (2015) PR397-R399.
date_created: 2022-04-07T07:49:00Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2024-10-14T11:22:15Z
day: '18'
doi: 10.1016/j.cub.2015.02.033
extern: '1'
external_id:
pmid:
- '25989073'
intvolume: ' 25'
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2015.02.033
month: '05'
oa: 1
oa_version: Published Version
page: PR397-R399
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromothripsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '11075'
abstract:
- lang: eng
text: Previously, we identified the nucleoporin gp210/Nup210 as a critical regulator
of muscle and neuronal differentiation, but how this nucleoporin exerts its function
and whether it modulates nuclear pore complex (NPC) activity remain unknown. Here,
we show that gp210/Nup210 mediates muscle cell differentiation in vitro via its
conserved N-terminal domain that extends into the perinuclear space. Removal of
the C-terminal domain, which partially mislocalizes gp210/Nup210 away from NPCs,
efficiently rescues the differentiation defect caused by the knockdown of endogenous
gp210/Nup210. Unexpectedly, a gp210/Nup210 mutant lacking the NPC-targeting transmembrane
and C-terminal domains is sufficient for C2C12 myoblast differentiation. We demonstrate
that the endoplasmic reticulum (ER) stress-specific caspase cascade is exacerbated
during Nup210 depletion and that blocking ER stress-mediated apoptosis rescues
differentiation of Nup210-deficient cells. Our results suggest that the role of
gp210/Nup210 in cell differentiation is mediated by its large luminal domain,
which can act independently of NPC association and appears to play a pivotal role
in the maintenance of nuclear envelope/ER homeostasis.
article_processing_charge: No
article_type: original
author:
- first_name: J. Sebastian
full_name: Gomez-Cavazos, J. Sebastian
last_name: Gomez-Cavazos
- 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: Gomez-Cavazos JS, Hetzer M. The nucleoporin gp210/Nup210 controls muscle differentiation
by regulating nuclear envelope/ER homeostasis. Journal of Cell Biology.
2015;208(6):671-681. doi:10.1083/jcb.201410047
apa: Gomez-Cavazos, J. S., & Hetzer, M. (2015). The nucleoporin gp210/Nup210
controls muscle differentiation by regulating nuclear envelope/ER homeostasis.
Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201410047
chicago: Gomez-Cavazos, J. Sebastian, and Martin Hetzer. “The Nucleoporin Gp210/Nup210
Controls Muscle Differentiation by Regulating Nuclear Envelope/ER Homeostasis.”
Journal of Cell Biology. Rockefeller University Press, 2015. https://doi.org/10.1083/jcb.201410047.
ieee: J. S. Gomez-Cavazos and M. Hetzer, “The nucleoporin gp210/Nup210 controls
muscle differentiation by regulating nuclear envelope/ER homeostasis,” Journal
of Cell Biology, vol. 208, no. 6. Rockefeller University Press, pp. 671–681,
2015.
ista: Gomez-Cavazos JS, Hetzer M. 2015. The nucleoporin gp210/Nup210 controls muscle
differentiation by regulating nuclear envelope/ER homeostasis. Journal of Cell
Biology. 208(6), 671–681.
mla: Gomez-Cavazos, J. Sebastian, and Martin Hetzer. “The Nucleoporin Gp210/Nup210
Controls Muscle Differentiation by Regulating Nuclear Envelope/ER Homeostasis.”
Journal of Cell Biology, vol. 208, no. 6, Rockefeller University Press,
2015, pp. 671–81, doi:10.1083/jcb.201410047.
short: J.S. Gomez-Cavazos, M. Hetzer, Journal of Cell Biology 208 (2015) 671–681.
date_created: 2022-04-07T07:49:10Z
date_published: 2015-03-16T00:00:00Z
date_updated: 2024-10-14T11:22:26Z
day: '16'
doi: 10.1083/jcb.201410047
extern: '1'
external_id:
pmid:
- '25778917'
intvolume: ' 208'
issue: '6'
keyword:
- Cell Biology
language:
- iso: eng
month: '03'
oa_version: Published Version
page: 671-681
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The nucleoporin gp210/Nup210 controls muscle differentiation by regulating
nuclear envelope/ER homeostasis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 208
year: '2015'
...
---
_id: '11076'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different
proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE)
and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this
vital role, NPC components influence genome functions in a transport-independent
manner. Nups play an evolutionarily conserved role in gene expression regulation
that, in metazoans, extends into the nuclear interior. Additionally, in proliferative
cells, Nups play a crucial role in genome integrity maintenance and mitotic progression.
Here we discuss genome-related functions of Nups and their impact on essential
DNA metabolism processes such as transcription, chromosome duplication, and segregation.
article_processing_charge: No
article_type: original
author:
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- 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: Ibarra A, Hetzer M. Nuclear pore proteins and the control of genome functions.
Genes & Development. 2015;29(4):337-349. doi:10.1101/gad.256495.114
apa: Ibarra, A., & Hetzer, M. (2015). Nuclear pore proteins and the control
of genome functions. Genes & Development. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/gad.256495.114
chicago: Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control
of Genome Functions.” Genes & Development. Cold Spring Harbor Laboratory,
2015. https://doi.org/10.1101/gad.256495.114.
ieee: A. Ibarra and M. Hetzer, “Nuclear pore proteins and the control of genome
functions,” Genes & Development, vol. 29, no. 4. Cold Spring Harbor
Laboratory, pp. 337–349, 2015.
ista: Ibarra A, Hetzer M. 2015. Nuclear pore proteins and the control of genome
functions. Genes & Development. 29(4), 337–349.
mla: Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control
of Genome Functions.” Genes & Development, vol. 29, no. 4, Cold Spring
Harbor Laboratory, 2015, pp. 337–49, doi:10.1101/gad.256495.114.
short: A. Ibarra, M. Hetzer, Genes & Development 29 (2015) 337–349.
date_created: 2022-04-07T07:49:21Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2024-10-14T11:22:36Z
day: '01'
doi: 10.1101/gad.256495.114
extern: '1'
external_id:
pmid:
- '25691464'
intvolume: ' 29'
issue: '4'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.256495.114
month: '02'
oa: 1
oa_version: Published Version
page: 337-349
pmid: 1
publication: Genes & Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear pore proteins and the control of genome functions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2015'
...
---
_id: '11077'
abstract:
- lang: eng
text: Nucleoporins (Nups) are a family of proteins best known as the constituent
building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that
mediate nuclear transport across the nuclear envelope. Recent evidence suggests
that several Nups have additional roles in controlling the activation and silencing
of developmental genes; however, the mechanistic details of these functions remain
poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem
cells (mESCs) causes the derepression of developmental genes and induction of
early differentiation. This loss of stem cell identity is not associated with
defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds
around the transcriptional start site (TSS) of developmental genes and mediates
the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its
target loci. Our results demonstrate a chromatin-associated role of Nup153 in
maintaining stem cell pluripotency by functioning in mammalian epigenetic gene
silencing.
article_processing_charge: No
article_type: original
author:
- first_name: Filipe V.
full_name: Jacinto, Filipe V.
last_name: Jacinto
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- 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: Jacinto FV, Benner C, Hetzer M. The nucleoporin Nup153 regulates embryonic
stem cell pluripotency through gene silencing. Genes & Development.
2015;29(12):1224-1238. doi:10.1101/gad.260919.115
apa: Jacinto, F. V., Benner, C., & Hetzer, M. (2015). The nucleoporin Nup153
regulates embryonic stem cell pluripotency through gene silencing. Genes &
Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.260919.115
chicago: Jacinto, Filipe V., Chris Benner, and Martin Hetzer. “The Nucleoporin Nup153
Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” Genes &
Development. Cold Spring Harbor Laboratory, 2015. https://doi.org/10.1101/gad.260919.115.
ieee: F. V. Jacinto, C. Benner, and M. Hetzer, “The nucleoporin Nup153 regulates
embryonic stem cell pluripotency through gene silencing,” Genes & Development,
vol. 29, no. 12. Cold Spring Harbor Laboratory, pp. 1224–1238, 2015.
ista: Jacinto FV, Benner C, Hetzer M. 2015. The nucleoporin Nup153 regulates embryonic
stem cell pluripotency through gene silencing. Genes & Development. 29(12),
1224–1238.
mla: Jacinto, Filipe V., et al. “The Nucleoporin Nup153 Regulates Embryonic Stem
Cell Pluripotency through Gene Silencing.” Genes & Development, vol.
29, no. 12, Cold Spring Harbor Laboratory, 2015, pp. 1224–38, doi:10.1101/gad.260919.115.
short: F.V. Jacinto, C. Benner, M. Hetzer, Genes & Development 29 (2015) 1224–1238.
date_created: 2022-04-07T07:49:31Z
date_published: 2015-06-16T00:00:00Z
date_updated: 2024-10-14T11:22:47Z
day: '16'
doi: 10.1101/gad.260919.115
extern: '1'
external_id:
pmid:
- '26080816'
intvolume: ' 29'
issue: '12'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.260919.115
month: '06'
oa: 1
oa_version: Published Version
page: 1224-1238
pmid: 1
publication: Genes & Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene
silencing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2015'
...
---
_id: '11078'
abstract:
- lang: eng
text: Aging is associated with the decline of protein, cell, and organ function.
Here, we use an integrated approach to characterize gene expression, bulk translation,
and cell biology in the brains and livers of young and old rats. We identify 468
differences in protein abundance between young and old animals. The majority are
a consequence of altered translation output, that is, the combined effect of changes
in transcript abundance and translation efficiency. In addition, we identify 130
proteins whose overall abundance remains unchanged but whose sub-cellular localization,
phosphorylation state, or splice-form varies. While some protein-level differences
appear to be a generic property of the rats’ chronological age, the majority are
specific to one organ. These may be a consequence of the organ’s physiology or
the chronological age of the cells within the tissue. Taken together, our study
provides an initial view of the proteome at the molecular, sub-cellular, and organ
level in young and old rats.
article_processing_charge: No
article_type: original
author:
- first_name: Alessandro
full_name: Ori, Alessandro
last_name: Ori
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Michael S.
full_name: Harris, Michael S.
last_name: Harris
- first_name: Thomas
full_name: Bock, Thomas
last_name: Bock
- first_name: Murat
full_name: Iskar, Murat
last_name: Iskar
- first_name: Peer
full_name: Bork, Peer
last_name: Bork
- first_name: Nicholas T.
full_name: Ingolia, Nicholas T.
last_name: Ingolia
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Martin
full_name: Beck, Martin
last_name: Beck
citation:
ama: Ori A, Toyama BH, Harris MS, et al. Integrated transcriptome and proteome analyses
reveal organ-specific proteome deterioration in old rats. Cell Systems.
2015;1(3):P224-237. doi:10.1016/j.cels.2015.08.012
apa: Ori, A., Toyama, B. H., Harris, M. S., Bock, T., Iskar, M., Bork, P., … Beck,
M. (2015). Integrated transcriptome and proteome analyses reveal organ-specific
proteome deterioration in old rats. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2015.08.012
chicago: Ori, Alessandro, Brandon H. Toyama, Michael S. Harris, Thomas Bock, Murat
Iskar, Peer Bork, Nicholas T. Ingolia, Martin Hetzer, and Martin Beck. “Integrated
Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration
in Old Rats.” Cell Systems. Elsevier, 2015. https://doi.org/10.1016/j.cels.2015.08.012.
ieee: A. Ori et al., “Integrated transcriptome and proteome analyses reveal
organ-specific proteome deterioration in old rats,” Cell Systems, vol.
1, no. 3. Elsevier, pp. P224-237, 2015.
ista: Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer M,
Beck M. 2015. Integrated transcriptome and proteome analyses reveal organ-specific
proteome deterioration in old rats. Cell Systems. 1(3), P224-237.
mla: Ori, Alessandro, et al. “Integrated Transcriptome and Proteome Analyses Reveal
Organ-Specific Proteome Deterioration in Old Rats.” Cell Systems, vol.
1, no. 3, Elsevier, 2015, pp. P224-237, doi:10.1016/j.cels.2015.08.012.
short: A. Ori, B.H. Toyama, M.S. Harris, T. Bock, M. Iskar, P. Bork, N.T. Ingolia,
M. Hetzer, M. Beck, Cell Systems 1 (2015) P224-237.
date_created: 2022-04-07T07:49:39Z
date_published: 2015-09-23T00:00:00Z
date_updated: 2024-10-14T11:23:01Z
day: '23'
doi: 10.1016/j.cels.2015.08.012
extern: '1'
external_id:
pmid:
- '27135913'
intvolume: ' 1'
issue: '3'
keyword:
- Cell Biology
- Histology
- Pathology and Forensic Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cels.2015.08.012
month: '09'
oa: 1
oa_version: Published Version
page: P224-237
pmid: 1
publication: Cell Systems
publication_identifier:
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Integrated transcriptome and proteome analyses reveal organ-specific proteome
deterioration in old rats
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '11079'
abstract:
- lang: eng
text: Aging is a major risk factor for many human diseases, and in vitro generation
of human neurons is an attractive approach for modeling aging-related brain disorders.
However, modeling aging in differentiated human neurons has proved challenging.
We generated neurons from human donors across a broad range of ages, either by
iPSC-based reprogramming and differentiation or by direct conversion into induced
neurons (iNs). While iPSCs and derived neurons did not retain aging-associated
gene signatures, iNs displayed age-specific transcriptional profiles and revealed
age-associated decreases in the nuclear transport receptor RanBP17. We detected
an age-dependent loss of nucleocytoplasmic compartmentalization (NCC) in donor
fibroblasts and corresponding iNs and found that reduced RanBP17 impaired NCC
in young cells, while iPSC rejuvenation restored NCC in aged cells. These results
show that iNs retain important aging-related signatures, thus allowing modeling
of the aging process in vitro, and they identify impaired NCC as an important
factor in human aging.
article_processing_charge: No
article_type: original
author:
- first_name: Jerome
full_name: Mertens, Jerome
last_name: Mertens
- first_name: Apuã C.M.
full_name: Paquola, Apuã C.M.
last_name: Paquola
- first_name: Manching
full_name: Ku, Manching
last_name: Ku
- first_name: Emily
full_name: Hatch, Emily
last_name: Hatch
- first_name: Lena
full_name: Böhnke, Lena
last_name: Böhnke
- first_name: Shauheen
full_name: Ladjevardi, Shauheen
last_name: Ladjevardi
- first_name: Sean
full_name: McGrath, Sean
last_name: McGrath
- first_name: Benjamin
full_name: Campbell, Benjamin
last_name: Campbell
- first_name: Hyungjun
full_name: Lee, Hyungjun
last_name: Lee
- first_name: Joseph R.
full_name: Herdy, Joseph R.
last_name: Herdy
- first_name: J. Tiago
full_name: Gonçalves, J. Tiago
last_name: Gonçalves
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
- first_name: Yongsung
full_name: Kim, Yongsung
last_name: Kim
- first_name: Jürgen
full_name: Winkler, Jürgen
last_name: Winkler
- first_name: Jun
full_name: Yao, Jun
last_name: Yao
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
citation:
ama: Mertens J, Paquola ACM, Ku M, et al. Directly reprogrammed human neurons retain
aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic
defects. Cell Stem Cell. 2015;17(6):705-718. doi:10.1016/j.stem.2015.09.001
apa: Mertens, J., Paquola, A. C. M., Ku, M., Hatch, E., Böhnke, L., Ladjevardi,
S., … Gage, F. H. (2015). Directly reprogrammed human neurons retain aging-associated
transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell
Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2015.09.001
chicago: Mertens, Jerome, Apuã C.M. Paquola, Manching Ku, Emily Hatch, Lena Böhnke,
Shauheen Ladjevardi, Sean McGrath, et al. “Directly Reprogrammed Human Neurons
Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic
Defects.” Cell Stem Cell. Elsevier, 2015. https://doi.org/10.1016/j.stem.2015.09.001.
ieee: J. Mertens et al., “Directly reprogrammed human neurons retain aging-associated
transcriptomic signatures and reveal age-related nucleocytoplasmic defects,” Cell
Stem Cell, vol. 17, no. 6. Elsevier, pp. 705–718, 2015.
ista: Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S,
Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer
M, Gage FH. 2015. Directly reprogrammed human neurons retain aging-associated
transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell
Stem Cell. 17(6), 705–718.
mla: Mertens, Jerome, et al. “Directly Reprogrammed Human Neurons Retain Aging-Associated
Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects.” Cell
Stem Cell, vol. 17, no. 6, Elsevier, 2015, pp. 705–18, doi:10.1016/j.stem.2015.09.001.
short: J. Mertens, A.C.M. Paquola, M. Ku, E. Hatch, L. Böhnke, S. Ladjevardi, S.
McGrath, B. Campbell, H. Lee, J.R. Herdy, J.T. Gonçalves, T. Toda, Y. Kim, J.
Winkler, J. Yao, M. Hetzer, F.H. Gage, Cell Stem Cell 17 (2015) 705–718.
date_created: 2022-04-07T07:49:51Z
date_published: 2015-12-03T00:00:00Z
date_updated: 2022-07-18T08:44:21Z
day: '03'
doi: 10.1016/j.stem.2015.09.001
extern: '1'
external_id:
pmid:
- '26456686'
intvolume: ' 17'
issue: '6'
keyword:
- Cell Biology
- Genetics
- Molecular Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.stem.2015.09.001
month: '12'
oa: 1
oa_version: Published Version
page: 705-718
pmid: 1
publication: Cell Stem Cell
publication_identifier:
issn:
- 1934-5909
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directly reprogrammed human neurons retain aging-associated transcriptomic
signatures and reveal age-related nucleocytoplasmic defects
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 17
year: '2015'
...
---
_id: '2085'
abstract:
- lang: eng
text: 'We study the spectrum of a large system of N identical bosons interacting
via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov''s
theory predicts that the spectrum of the N-particle Hamiltonian can be approximated
by that of an effective quadratic Hamiltonian acting on Fock space, which describes
the fluctuations around a condensed state. Recently, Bogoliubov''s theory has
been justified rigorously in the case that the low-energy eigenvectors of the
N-particle Hamiltonian display complete condensation in the unique minimizer of
the corresponding Hartree functional. In this paper, we shall justify Bogoliubov''s
theory for the high-energy part of the spectrum of the N-particle Hamiltonian
corresponding to (non-linear) excited states of the Hartree functional. Moreover,
we shall extend the existing results on the excitation spectrum to the case of
non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the
latter covers the case of rotating Bose gases, when the rotation speed is large
enough to break the symmetry and to produce multiple quantized vortices in the
Hartree minimizer. '
article_processing_charge: No
arxiv: 1
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field
regime. Archive for Rational Mechanics and Analysis. 2015;215(2):381-417.
doi:10.1007/s00205-014-0781-6
apa: Nam, P., & Seiringer, R. (2015). Collective excitations of Bose gases in
the mean-field regime. Archive for Rational Mechanics and Analysis. Springer.
https://doi.org/10.1007/s00205-014-0781-6
chicago: Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases
in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis.
Springer, 2015. https://doi.org/10.1007/s00205-014-0781-6.
ieee: P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field
regime,” Archive for Rational Mechanics and Analysis, vol. 215, no. 2.
Springer, pp. 381–417, 2015.
ista: Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field
regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.
mla: Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the
Mean-Field Regime.” Archive for Rational Mechanics and Analysis, vol. 215,
no. 2, Springer, 2015, pp. 381–417, doi:10.1007/s00205-014-0781-6.
short: P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015)
381–417.
corr_author: '1'
date_created: 2018-12-11T11:55:37Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2025-09-23T08:17:14Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00205-014-0781-6
external_id:
arxiv:
- '1402.1153'
isi:
- '000347150400002'
intvolume: ' 215'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.1153
month: '02'
oa: 1
oa_version: Preprint
page: 381 - 417
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '4951'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Collective excitations of Bose gases in the mean-field regime
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 215
year: '2015'
...
---
OA_type: closed access
_id: '21103'
abstract:
- lang: eng
text: The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at
a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which
the direction of progression of the backbone changes at the two thymine residues.
Intra-strand stacking interactions (including an interaction between the endocylic
O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion
interactions stabilize the double-folded structure of the single strand. Two such
double-folded strands come together in the crystal to form a dimer. Inter-strand
Watson–Crick hydrogen bonds form four base pairs. This portion of the decamer
structure is similar to that observed in other previously reported oligonucleotide
structures and has been dubbed a `bi-loop'. Both the double-folded single-strand
structure, as well as the dimeric bi-loop structure, serve as starting points
to construct models for triplet-repeat DNA sequences, which have been implicated
in many human diseases.
article_processing_charge: No
article_type: original
author:
- first_name: Arunachalam
full_name: Thirugnanasambandam, Arunachalam
last_name: Thirugnanasambandam
- first_name: Selvam
full_name: Karthik, Selvam
last_name: Karthik
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Namasivayam
full_name: Gautham, Namasivayam
last_name: Gautham
citation:
ama: 'Thirugnanasambandam A, Karthik S, Mandal PK, Gautham N. The novel double-folded
structure of d(GCATGCATGC): A possible model for triplet-repeat sequences. Acta
Crystallographica Section D Structural Biology. 2015;71(10):2119-2126. doi:10.1107/s1399004715013930'
apa: 'Thirugnanasambandam, A., Karthik, S., Mandal, P. K., & Gautham, N. (2015).
The novel double-folded structure of d(GCATGCATGC): A possible model for triplet-repeat
sequences. Acta Crystallographica Section D Structural Biology. International
Union of Crystallography. https://doi.org/10.1107/s1399004715013930'
chicago: 'Thirugnanasambandam, Arunachalam, Selvam Karthik, Pradeep K Mandal, and
Namasivayam Gautham. “The Novel Double-Folded Structure of d(GCATGCATGC): A Possible
Model for Triplet-Repeat Sequences.” Acta Crystallographica Section D Structural
Biology. International Union of Crystallography, 2015. https://doi.org/10.1107/s1399004715013930.'
ieee: 'A. Thirugnanasambandam, S. Karthik, P. K. Mandal, and N. Gautham, “The novel
double-folded structure of d(GCATGCATGC): A possible model for triplet-repeat
sequences,” Acta Crystallographica Section D Structural Biology, vol. 71,
no. 10. International Union of Crystallography, pp. 2119–2126, 2015.'
ista: 'Thirugnanasambandam A, Karthik S, Mandal PK, Gautham N. 2015. The novel double-folded
structure of d(GCATGCATGC): A possible model for triplet-repeat sequences. Acta
Crystallographica Section D Structural Biology. 71(10), 2119–2126.'
mla: 'Thirugnanasambandam, Arunachalam, et al. “The Novel Double-Folded Structure
of d(GCATGCATGC): A Possible Model for Triplet-Repeat Sequences.” Acta Crystallographica
Section D Structural Biology, vol. 71, no. 10, International Union of Crystallography,
2015, pp. 2119–26, doi:10.1107/s1399004715013930.'
short: A. Thirugnanasambandam, S. Karthik, P.K. Mandal, N. Gautham, Acta Crystallographica
Section D Structural Biology 71 (2015) 2119–2126.
date_created: 2026-01-29T21:56:58Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2026-02-23T09:09:14Z
day: '01'
doi: 10.1107/s1399004715013930
extern: '1'
has_accepted_license: '1'
intvolume: ' 71'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 2119-2126
publication: Acta Crystallographica Section D Structural Biology
publication_identifier:
issn:
- 1399-0047
publication_status: published
publisher: International Union of Crystallography
quality_controlled: '1'
status: public
title: 'The novel double-folded structure of d(GCATGCATGC): A possible model for triplet-repeat
sequences'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2015'
...
---
_id: '2166'
abstract:
- lang: eng
text: 'We consider the spectral statistics of large random band matrices on mesoscopic
energy scales. We show that the correlation function of the local eigenvalue density
exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta
statistics. This law had been predicted in the physics literature by Altshuler
and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it
describes the correlations of the eigenvalue density in general metallic sampleswith
weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas
for band matrices. In two dimensions, where the leading term vanishes owing to
an algebraic cancellation, we identify the first non-vanishing term and show that
it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev
Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion
(Ann. H. Poincaré. arXiv:1309.5107, 2014). '
article_processing_charge: No
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
citation:
ama: 'Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices
I: the unimodular case. Communications in Mathematical Physics. 2015;333(3):1365-1416.
doi:10.1007/s00220-014-2119-5'
apa: 'Erdös, L., & Knowles, A. (2015). The Altshuler-Shklovskii formulas for
random band matrices I: the unimodular case. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-014-2119-5'
chicago: 'Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for
Random Band Matrices I: The Unimodular Case.” Communications in Mathematical
Physics. Springer, 2015. https://doi.org/10.1007/s00220-014-2119-5.'
ieee: 'L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band
matrices I: the unimodular case,” Communications in Mathematical Physics,
vol. 333, no. 3. Springer, pp. 1365–1416, 2015.'
ista: 'Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band
matrices I: the unimodular case. Communications in Mathematical Physics. 333(3),
1365–1416.'
mla: 'Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random
Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics,
vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:10.1007/s00220-014-2119-5.'
short: L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.
date_created: 2018-12-11T11:56:05Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2025-09-23T13:39:37Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00220-014-2119-5
external_id:
arxiv:
- '1309.5106'
isi:
- '000348303100008'
intvolume: ' 333'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1309.5106
month: '02'
oa: 1
oa_version: Preprint
page: 1365 - 1416
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4818'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Altshuler-Shklovskii formulas for random band matrices I: the unimodular
case'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 333
year: '2015'
...
---
_id: '2271'
abstract:
- lang: eng
text: "A class of valued constraint satisfaction problems (VCSPs) is characterised
by a valued constraint language, a fixed set of cost functions on a finite domain.
Finite-valued constraint languages contain functions that take on rational costs
and general-valued constraint languages contain functions that take on rational
or infinite costs. An instance of the problem is specified by a sum of functions
from the language with the goal to minimise the sum. This framework includes and
generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint
satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation
of valued constraint languages whose instances can be solved exactly by the basic
linear programming relaxation (BLP). For a general-valued constraint language
Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional
polymorphism of every arity. For a finite-valued constraint language Γ, BLP is
a decision procedure if and only if Γ admits a symmetric fractional polymorphism
of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism
of arity 2.\r\nUsing these results, we obtain tractability of several novel and
previously widely-open classes of VCSPs, including problems over valued constraint
languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also
known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly)
tree-submodular on arbitrary trees. "
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Johan
full_name: Thapper, Johan
last_name: Thapper
- first_name: Stanislav
full_name: Živný, Stanislav
last_name: Živný
citation:
ama: Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued
CSPs. SIAM Journal on Computing. 2015;44(1):1-36. doi:10.1137/130945648
apa: Kolmogorov, V., Thapper, J., & Živný, S. (2015). The power of linear programming
for general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/130945648
chicago: Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of
Linear Programming for General-Valued CSPs.” SIAM Journal on Computing.
SIAM, 2015. https://doi.org/10.1137/130945648.
ieee: V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming
for general-valued CSPs,” SIAM Journal on Computing, vol. 44, no. 1. SIAM,
pp. 1–36, 2015.
ista: Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for
general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36.
mla: Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued
CSPs.” SIAM Journal on Computing, vol. 44, no. 1, SIAM, 2015, pp. 1–36,
doi:10.1137/130945648.
short: V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015)
1–36.
date_created: 2018-12-11T11:56:41Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2025-09-23T14:14:57Z
day: '01'
department:
- _id: VlKo
doi: 10.1137/130945648
external_id:
arxiv:
- '1311.4219'
isi:
- '000353967100001'
intvolume: ' 44'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1311.4219
month: '02'
oa: 1
oa_version: Preprint
page: 1 - 36
publication: SIAM Journal on Computing
publication_status: published
publisher: SIAM
publist_id: '4673'
quality_controlled: '1'
related_material:
record:
- id: '2518'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The power of linear programming for general-valued CSPs
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 44
year: '2015'
...