---
_id: '10146'
abstract:
- lang: eng
text: The enzymes of the mitochondrial electron transport chain are key players
of cell metabolism. Despite being active when isolated, in vivo they associate
into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2
(refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in
mammals, but in contrast to CICIII2 and the respirasome, to date the only known
eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and
plants13, which have different organization. Here we present the first, to our
knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly
intermediates, in different conformations. We describe the assembly of CIII2CIV
from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion
of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while
its C terminus is integrated into CIV. Our structures (which include CICIII2 and
the respirasome) also confirm that SCAF1 is exclusively required for the assembly
of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2
is asymmetric due to the presence of only one copy of subunit 9, which straddles
both monomers and prevents the attachment of a second copy of SCAF1 to CIII2,
explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we
show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex
and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer
in the electron transport chain.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino
for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan
Krios data collection, performed at the IST Austria. The data processing was performed
at the IST high-performance computing cluster. This project has received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie grant agreement no. 754411.
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z
apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the
mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer
Nature. https://doi.org/10.1038/s41586-021-03927-z
chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the
Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer
Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z.
ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian
mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no.
7880. Springer Nature, pp. 364–367, 2021.
ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 598(7880), 364–367.
mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian
Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no.
7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.
short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.
date_created: 2021-10-17T22:01:17Z
date_published: 2021-10-14T00:00:00Z
date_updated: 2023-08-14T08:01:21Z
day: '14'
department:
- _id: LeSa
doi: 10.1038/s41586-021-03927-z
ec_funded: 1
external_id:
isi:
- '000704581600001'
pmid:
- '34616041'
intvolume: ' 598'
isi: 1
issue: '7880'
language:
- iso: eng
month: '10'
oa_version: None
page: 364-367
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/boosting-the-cells-power-house/
scopus_import: '1'
status: public
title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 598
year: '2021'
...
---
_id: '10148'
abstract:
- lang: eng
text: Tactile feedback of an object’s surface enables us to discern its material
properties and affordances. This understanding is used in digital fabrication
processes by creating objects with high-resolution surface variations to influence
a user’s tactile perception. As the design of such surface haptics commonly relies
on knowledge from real-life experiences, it is unclear how to adapt this information
for digital design methods. In this work, we investigate replicating the haptics
of real materials. Using an existing process for capturing an object’s microgeometry,
we digitize and reproduce the stable surface information of a set of 15 fabric
samples. In a psychophysical experiment, we evaluate the tactile qualities of
our set of original samples and their replicas. From our results, we see that
direct reproduction of surface variations is able to influence different psychophysical
dimensions of the tactile perception of surface textures. While the fabrication
process did not preserve all properties, our approach underlines that replication
of surface microgeometries benefits fabrication methods in terms of haptic perception
by covering a large range of tactile variations. Moreover, by changing the surface
structure of a single fabricated material, its material perception can be influenced.
We conclude by proposing strategies for capturing and reproducing digitized textures
to better resemble the perceived haptics of the originals.
acknowledgement: Our gratitude goes out to Kamila Mushkina, Akhmajon Makhsadov, Jordan
Espenshade, Bruno Fruchard, Roland Bennewitz, and Robert Drumm. This project has
received funding from the EU’s Horizon 2020 research and innovation programme, under
the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO).
article_processing_charge: No
author:
- first_name: Donald
full_name: Degraen, Donald
last_name: Degraen
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Antonio
full_name: Kruger, Antonio
last_name: Kruger
citation:
ama: 'Degraen D, Piovarci M, Bickel B, Kruger A. Capturing tactile properties of
real surfaces for haptic reproduction. In: 34th Annual ACM Symposium. Association
for Computing Machinery; 2021:954-971. doi:10.1145/3472749.3474798'
apa: 'Degraen, D., Piovarci, M., Bickel, B., & Kruger, A. (2021). Capturing
tactile properties of real surfaces for haptic reproduction. In 34th Annual
ACM Symposium (pp. 954–971). Virtual: Association for Computing Machinery.
https://doi.org/10.1145/3472749.3474798'
chicago: Degraen, Donald, Michael Piovarci, Bernd Bickel, and Antonio Kruger. “Capturing
Tactile Properties of Real Surfaces for Haptic Reproduction.” In 34th Annual
ACM Symposium, 954–71. Association for Computing Machinery, 2021. https://doi.org/10.1145/3472749.3474798.
ieee: D. Degraen, M. Piovarci, B. Bickel, and A. Kruger, “Capturing tactile properties
of real surfaces for haptic reproduction,” in 34th Annual ACM Symposium,
Virtual, 2021, pp. 954–971.
ista: 'Degraen D, Piovarci M, Bickel B, Kruger A. 2021. Capturing tactile properties
of real surfaces for haptic reproduction. 34th Annual ACM Symposium. UIST: User
Interface Software and Technology, 954–971.'
mla: Degraen, Donald, et al. “Capturing Tactile Properties of Real Surfaces for
Haptic Reproduction.” 34th Annual ACM Symposium, Association for Computing
Machinery, 2021, pp. 954–71, doi:10.1145/3472749.3474798.
short: D. Degraen, M. Piovarci, B. Bickel, A. Kruger, in:, 34th Annual ACM Symposium,
Association for Computing Machinery, 2021, pp. 954–971.
conference:
end_date: 2021-10-14
location: Virtual
name: 'UIST: User Interface Software and Technology'
start_date: 2021-10-10
date_created: 2021-10-18T07:36:11Z
date_published: 2021-10-10T00:00:00Z
date_updated: 2021-10-19T19:29:06Z
day: '10'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3472749.3474798
ec_funded: 1
file:
- access_level: open_access
checksum: b0b26464df79b3a59e8ed82e4e19ab15
content_type: application/pdf
creator: bbickel
date_created: 2021-10-18T07:36:03Z
date_updated: 2021-10-18T07:36:03Z
file_id: '10149'
file_name: degraen-UIST2021_Texture_Appropriation_CR_preprint.pdf
file_size: 29796364
relation: main_file
file_date_updated: 2021-10-18T07:36:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
page: 954-971
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: 34th Annual ACM Symposium
publication_identifier:
isbn:
- 978-1-4503-8635-7
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Capturing tactile properties of real surfaces for haptic reproduction
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10153'
abstract:
- lang: eng
text: "Gradual typing is a principled means for mixing typed and untyped code. But
typed and untyped code often exhibit different programming patterns. There is
already substantial research investigating gradually giving types to code exhibiting
typical untyped patterns, and some research investigating gradually removing types
from code exhibiting typical typed patterns. This paper investigates how to extend
these established gradual-typing concepts to give formal guarantees not only about
how to change types as code evolves but also about how to change such programming
patterns as well.\r\n\r\nIn particular, we explore mixing untyped \"structural\"
code with typed \"nominal\" code in an object-oriented language. But whereas previous
work only allowed \"nominal\" objects to be treated as \"structural\" objects,
we also allow \"structural\" objects to dynamically acquire certain nominal types,
namely interfaces. We present a calculus that supports such \"cross-paradigm\"
code migration and interoperation in a manner satisfying both the static and dynamic
gradual guarantees, and demonstrate that the calculus can be implemented efficiently."
acknowledgement: "We thank the reviewers for their valuable suggestions towards improving
the paper. We also \r\nthank Mae Milano and Adrian Sampson, as well as the members
of the Programming Languages Discussion Group at Cornell University and of the Programming
Research Laboratory at Northeastern University, for their helpful feedback on preliminary
findings of this work.\r\n\r\nThis material is based upon work supported in part
by the National Science Foundation (NSF) through grant CCF-1350182 and the Austrian
Science Fund (FWF) through grant Z211-N23 (Wittgenstein~Award).\r\nAny opinions,
findings, and conclusions or recommendations expressed in this material are those
of the authors and do not necessarily reflect the views of the NSF or the FWF."
article_number: '127'
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Ross
full_name: Tate, Ross
last_name: Tate
citation:
ama: Mühlböck F, Tate R. Transitioning from structural to nominal code with efficient
gradual typing. Proceedings of the ACM on Programming Languages. 2021;5.
doi:10.1145/3485504
apa: 'Mühlböck, F., & Tate, R. (2021). Transitioning from structural to nominal
code with efficient gradual typing. Proceedings of the ACM on Programming Languages.
Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3485504'
chicago: Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal
Code with Efficient Gradual Typing.” Proceedings of the ACM on Programming
Languages. Association for Computing Machinery, 2021. https://doi.org/10.1145/3485504.
ieee: F. Mühlböck and R. Tate, “Transitioning from structural to nominal code with
efficient gradual typing,” Proceedings of the ACM on Programming Languages,
vol. 5. Association for Computing Machinery, 2021.
ista: Mühlböck F, Tate R. 2021. Transitioning from structural to nominal code with
efficient gradual typing. Proceedings of the ACM on Programming Languages. 5,
127.
mla: Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal
Code with Efficient Gradual Typing.” Proceedings of the ACM on Programming
Languages, vol. 5, 127, Association for Computing Machinery, 2021, doi:10.1145/3485504.
short: F. Mühlböck, R. Tate, Proceedings of the ACM on Programming Languages 5 (2021).
conference:
end_date: 2021-10-23
location: Chicago, IL, United States
name: 'OOPSLA: Object-Oriented Programming, Systems, Languages, and Applications'
start_date: 2021-10-17
date_created: 2021-10-19T12:48:44Z
date_published: 2021-10-15T00:00:00Z
date_updated: 2021-11-12T11:30:07Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/3485504
file:
- access_level: open_access
checksum: 71011efd2da771cafdec7f0d9693f8c1
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-10-19T12:52:23Z
date_updated: 2021-10-19T12:52:23Z
file_id: '10154'
file_name: monnom-oopsla21.pdf
file_size: 770269
relation: main_file
success: 1
file_date_updated: 2021-10-19T12:52:23Z
has_accepted_license: '1'
intvolume: ' 5'
keyword:
- gradual typing
- gradual guarantee
- nominal
- structural
- call tags
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Transitioning from structural to nominal code with efficient gradual typing
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2021'
...
---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T08:02:31Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
- access_level: open_access
checksum: d99fcd51aebde19c21314e3de0148007
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
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: 12
year: '2021'
...
---
_id: '10166'
abstract:
- lang: eng
text: While sexual reproduction is widespread among many taxa, asexual lineages
have repeatedly evolved from sexual ancestors. Despite extensive research on the
evolution of sex, it is still unclear whether this switch represents a major transition
requiring major molecular reorganization, and how convergent the changes involved
are. In this study, we investigated the phylogenetic relationship and patterns
of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp,
to assess how gene expression patterns are affected by the transition to asexuality.
We find only a few genes that are consistently associated with the evolution of
asexuality, suggesting that this shift may not require an extensive overhauling
of the meiotic machinery. While genes with sex-biased expression have high rates
of expression divergence within Eurasian Artemia, neither female- nor male-biased
genes appear to show unusual evolutionary patterns after sexuality is lost, contrary
to theoretical expectations.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander
for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate
and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific
Computing Group for their support. This work was supported by the European Research
Council under the European Union's Horizon 2020 research and innovation program
(grant agreement no. 715257).
article_number: '20211720'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720'
apa: 'Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions
to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings
of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720'
chicago: 'Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso.
“Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”
Proceedings of the Royal Society B: Biological Sciences. The Royal Society,
2021. https://doi.org/10.1098/rspb.2021.1720.'
ieee: 'A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp,” Proceedings of the
Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society,
2021.'
ista: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 288(1959), 20211720.'
mla: 'Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene
Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological
Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720.'
short: 'A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal
Society B: Biological Sciences 288 (2021).'
date_created: 2021-10-21T07:46:06Z
date_published: 2021-09-22T00:00:00Z
date_updated: 2024-02-21T12:40:29Z
day: '22'
ddc:
- '595'
department:
- _id: BeVi
doi: 10.1098/rspb.2021.1720
ec_funded: 1
external_id:
isi:
- '000697643700001'
pmid:
- '34547909'
file:
- access_level: open_access
checksum: 76e7f253b7040bca2ad76f82bd7c45c0
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-22T11:48:02Z
date_updated: 2021-10-22T11:48:02Z
file_id: '10172'
file_name: 2021_ProRoSocBBioSci_Huylmans.pdf
file_size: 995806
relation: main_file
success: 1
file_date_updated: 2021-10-22T11:48:02Z
has_accepted_license: '1'
intvolume: ' 288'
isi: 1
issue: '1959'
keyword:
- asexual reproduction
- parthenogenesis
- sex-biased genes
- sexual conflict
- automixis
- crustaceans
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://doi.org/10.6084/m9.figshare.c.5615488.v1
record:
- id: '9949'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Transitions to asexuality and evolution of gene expression in Artemia brine
shrimp
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: 288
year: '2021'
...
---
_id: '10167'
abstract:
- lang: eng
text: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic.
Different parts of their ZW sex chromosomes have stopped recombining in distinct
lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome
is well characterized at the genomic and molecular level, the W-chromosome has
remained largely unstudied from an evolutionary perspective, as only a few W-linked
genes have been detected outside of the model species Schistosoma mansoni. Here,
we characterize the gene content and evolution of the W-chromosomes of S. mansoni
and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based
pipeline to assemble around 100 candidate W-specific transcripts in each of the
species. About half of them map to known protein coding genes, the majority homologous
to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary
strata present in the two species (including characterizing a previously undetected
young stratum in S. japonicum) to infer patterns of sequence and expression evolution
of W-linked genes at different time points after recombination was lost. W-linked
genes show evidence of degeneration, including high rates of protein evolution
and reduced expression. Most are found in young lineage-specific strata, with
only a few high expression ancestral W-genes remaining, consistent with the progressive
erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands
out as a promising candidate for primary sex determination, opening new avenues
for understanding the molecular basis of the reproductive biology of this group.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors thank IT support at IST Austria for providing an optimal
environment for bioinformatic analyses. This work was supported by an Austrian Science
Foundation FWF grant (Project P28842) to B.V.
article_processing_charge: No
article_type: original
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Mikhail A.
full_name: Moldovan, Mikhail A.
id: c8bb7f32-3315-11ec-b58b-e5950e6c14a0
last_name: Moldovan
orcid: 0000-0002-8876-6494
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform
temporal dynamics of sex chromosome evolution and suggest candidate for sex determination.
Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178
apa: Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021).
Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
and suggest candidate for sex determination. Molecular Biology and Evolution.
Oxford University Press . https://doi.org/10.1093/molbev/msab178
chicago: Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz
Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome
Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and
Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178.
ieee: M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome
W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest
candidate for sex determination,” Molecular Biology and Evolution. Oxford
University Press , 2021.
ista: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked
genes inform temporal dynamics of sex chromosome evolution and suggest candidate
for sex determination. Molecular Biology and Evolution.
mla: Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics
of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular
Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178.
short: M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology
and Evolution (2021).
date_created: 2021-10-21T07:49:12Z
date_published: 2021-06-19T00:00:00Z
date_updated: 2023-08-14T08:03:06Z
day: '19'
ddc:
- '610'
department:
- _id: BeVi
doi: 10.1093/molbev/msab178
external_id:
isi:
- '000741368600009'
pmid:
- '34146097'
file:
- access_level: open_access
checksum: 1b096702fb356d9c0eb88e1b3fcff5f8
content_type: application/pdf
creator: dernst
date_created: 2022-05-06T09:47:18Z
date_updated: 2022-05-06T09:47:18Z
file_id: '11352'
file_name: 2021_MolecularBiolEvolution_Elkrewi.pdf
file_size: 1008594
relation: main_file
success: 1
file_date_updated: 2022-05-06T09:47:18Z
has_accepted_license: '1'
isi: 1
keyword:
- sex chromosomes
- evolutionary strata
- W-linked gene
- sex determining gene
- schistosome parasites
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: 'Oxford University Press '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
and suggest candidate for sex determination
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
year: '2021'
...
---
_id: '10174'
abstract:
- lang: eng
text: Quantitative stochastic homogenization of linear elliptic operators is by
now well-understood. In this contribution we move forward to the nonlinear setting
of monotone operators with p-growth. This first work is dedicated to a quantitative
two-scale expansion result. Fluctuations will be addressed in companion articles.
By treating the range of exponents 2≤p<∞ in dimensions d≤3, we are able to consider
genuinely nonlinear elliptic equations and systems such as −∇⋅A(x)(1+|∇u|p−2)∇u=f
(with A random, non-necessarily symmetric) for the first time. When going from
p=2 to p>2, the main difficulty is to analyze the associated linearized operator,
whose coefficients are degenerate, unbounded, and depend on the random input A
via the solution of a nonlinear equation. One of our main achievements is the
control of this intricate nonlinear dependence, leading to annealed Meyers' estimates
for the linearized operator, which are key to the quantitative two-scale expansion
result.
acknowledgement: The authors warmly thank Mitia Duerinckx for discussions on annealed
estimates, and Mathias Schäffner for pointing out that the conditions of [14] apply
to ̄a in the setting of Theorem 2.2 and for discussions on regularity theory for
operators with non-standard growth conditions. The authors received financial support
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (Grant Agreement n◦ 864066).
article_number: '2104.04263'
article_processing_charge: No
arxiv: 1
author:
- first_name: Nicolas
full_name: Clozeau, Nicolas
id: fea1b376-906f-11eb-847d-b2c0cf46455b
last_name: Clozeau
- first_name: Antoine
full_name: Gloria, Antoine
last_name: Gloria
citation:
ama: 'Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations.
arXiv.'
apa: 'Clozeau, N., & Gloria, A. (n.d.). Quantitative nonlinear homogenization:
control of oscillations. arXiv.'
chicago: 'Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization:
Control of Oscillations.” ArXiv, n.d.'
ieee: 'N. Clozeau and A. Gloria, “Quantitative nonlinear homogenization: control
of oscillations,” arXiv. .'
ista: 'Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations.
arXiv, 2104.04263.'
mla: 'Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization:
Control of Oscillations.” ArXiv, 2104.04263.'
short: N. Clozeau, A. Gloria, ArXiv (n.d.).
date_created: 2021-10-23T10:50:55Z
date_published: 2021-04-09T00:00:00Z
date_updated: 2021-10-28T15:44:05Z
day: '09'
department:
- _id: JuFi
external_id:
arxiv:
- '2104.04263'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.04263
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Quantitative nonlinear homogenization: control of oscillations'
type: preprint
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2021'
...
---
_id: '10176'
abstract:
- lang: eng
text: "We give a combinatorial model for r-spin surfaces with parameterized boundary
based on Novak (“Lattice topological field theories in two dimensions,” Ph.D.
thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of
ℤ\U0001D45F-valued indices assigned to the edges of a polygonal decomposition.
This combinatorial model is designed for our state-sum construction of two-dimensional
topological field theories on r-spin surfaces. We show that an example of such
a topological field theory computes the Arf-invariant of an r-spin surface as
introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka
J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant
is constant on orbits of the mapping class group, providing an alternative proof
of that fact."
acknowledgement: We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse,
Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and
Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG
Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum
Field Theory.”
article_number: '102302'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ingo
full_name: Runkel, Ingo
last_name: Runkel
- first_name: Lorant
full_name: Szegedy, Lorant
id: 7943226E-220E-11EA-94C7-D59F3DDC885E
last_name: Szegedy
orcid: 0000-0003-2834-5054
citation:
ama: Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant.
Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826
apa: Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces
and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing.
https://doi.org/10.1063/5.0037826
chicago: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces
and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing,
2021. https://doi.org/10.1063/5.0037826.
ieee: I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and
the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP
Publishing, 2021.
ista: Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and
the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.
mla: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces
and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10,
102302, AIP Publishing, 2021, doi:10.1063/5.0037826.
short: I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).
date_created: 2021-10-24T22:01:32Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-08-14T08:04:12Z
day: '01'
department:
- _id: MiLe
doi: 10.1063/5.0037826
external_id:
arxiv:
- '1802.09978'
isi:
- '000755638500010'
intvolume: ' 62'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.09978
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological field theory on r-spin surfaces and the Arf-invariant
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 62
year: '2021'
...
---
_id: '10177'
abstract:
- lang: eng
text: Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane
hyperbolic dispersion exhibit ray-like propagation with large wave vectors and
enhanced density of optical states along certain directions on a surface. As such,
they have raised a surge of interest, promising unprecedented manipulation of
infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing
of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end,
we developed metallic nanoantennas of convex geometries for both efficient launching
and focusing of the polaritons. The foci obtained exhibit enhanced near-field
confinement and absorption compared to foci produced by in-plane isotropic PhPs.
Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength
and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces
a first and most basic building block developing planar polariton optics using
in-plane anisotropic van der Waals materials.
acknowledgement: J.M.-S. acknowledges financial support from the Ramón y Cajal Program
of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of
Science and Innovation (State Plan for Scientific and Technical Research and Innovation
grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European
Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry
of Science and Innovation (State Plan for Scientific and Technical Research and
Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through
the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126).
G.A.-P. acknowledges support through the Severo Ochoa Program from the Government
of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge
the financial support from the Ministry of Science and Higher Education of the Russian
Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry
of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R
and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014).
R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation,
and Universities (national project number RTI2018-094830-B-100 and project number
MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque
Government (grant number IT1164-19).
article_number: abj0127
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Javier
full_name: Martín-Sánchez, Javier
last_name: Martín-Sánchez
- first_name: Jiahua
full_name: Duan, Jiahua
last_name: Duan
- first_name: Javier
full_name: Taboada-Gutiérrez, Javier
last_name: Taboada-Gutiérrez
- first_name: Gonzalo
full_name: Álvarez-Pérez, Gonzalo
last_name: Álvarez-Pérez
- first_name: Kirill V.
full_name: Voronin, Kirill V.
last_name: Voronin
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Weiliang
full_name: Ma, Weiliang
last_name: Ma
- first_name: Qiaoliang
full_name: Bao, Qiaoliang
last_name: Bao
- first_name: Valentyn S.
full_name: Volkov, Valentyn S.
last_name: Volkov
- first_name: Rainer
full_name: Hillenbrand, Rainer
last_name: Hillenbrand
- first_name: Alexey Y.
full_name: Nikitin, Alexey Y.
last_name: Nikitin
- first_name: Pablo
full_name: Alonso-González, Pablo
last_name: Alonso-González
citation:
ama: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane
hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas.
Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127
apa: Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin,
K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane
hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas.
Science Advances. American Association for the Advancement of Science.
https://doi.org/10.1126/sciadv.abj0127
chicago: Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo
Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing
of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared
Nanoantennas.” Science Advances. American Association for the Advancement
of Science, 2021. https://doi.org/10.1126/sciadv.abj0127.
ieee: J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons
in van der Waals crystals with tailored infrared nanoantennas,” Science Advances,
vol. 7, no. 41. American Association for the Advancement of Science, 2021.
ista: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV,
Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González
P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals
with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.
mla: Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons
in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances,
vol. 7, no. 41, abj0127, American Association for the Advancement of Science,
2021, doi:10.1126/sciadv.abj0127.
short: J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V.
Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y.
Nikitin, P. Alonso-González, Science Advances 7 (2021).
date_created: 2021-10-24T22:01:33Z
date_published: 2021-10-08T00:00:00Z
date_updated: 2023-08-14T08:04:42Z
day: '08'
ddc:
- '530'
department:
- _id: NanoFab
doi: 10.1126/sciadv.abj0127
external_id:
arxiv:
- '2103.10852'
isi:
- '000704912700024'
file:
- access_level: open_access
checksum: 0a470ef6a47d2b8a96ede4c4d28cfacd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T14:16:06Z
date_updated: 2021-10-27T14:16:06Z
file_id: '10189'
file_name: 2021_ScienceAdv_Martin-Sanchez.pdf
file_size: 2441163
relation: main_file
success: 1
file_date_updated: 2021-10-27T14:16:06Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '41'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored
infrared nanoantennas
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2021'
...
---
_id: '10178'
abstract:
- lang: eng
text: In dense biological tissues, cell types performing different roles remain
segregated by maintaining sharp interfaces. To better understand the mechanisms
for such sharp compartmentalization, we study the effect of an imposed heterotypic
tension at the interface between two distinct cell types in a fully 3D Voronoi
model for confluent tissues. We find that cells rapidly sort and self-organize
to generate a tissue-scale interface between cell types, and cells adjacent to
this interface exhibit signature geometric features including nematic-like ordering,
bimodal facet areas, and registration, or alignment, of cell centers on either
side of the two-tissue interface. The magnitude of these features scales directly
with the magnitude of the imposed tension, suggesting that biologists can estimate
the magnitude of tissue surface tension between two tissue types simply by segmenting
a 3D tissue. To uncover the underlying physical mechanisms driving these geometric
features, we develop two minimal, ordered models using two different underlying
lattices that identify an energetic competition between bulk cell shapes and tissue
interface area. When the interface area dominates, changes to neighbor topology
are costly and occur less frequently, which generates the observed geometric features.
acknowledgement: "We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina
Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing
and sharing the original version of the 3D Voronoi code. This work was primarily
funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics
at the National Science Foundation. PS and MLM acknowledge additional support from
Simons Grant No. 454947.\r\n"
article_number: '093043'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Preeti
full_name: Sahu, Preeti
id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E
last_name: Sahu
- first_name: J. M.
full_name: Schwarz, J. M.
last_name: Schwarz
- first_name: M. Lisa
full_name: Manning, M. Lisa
last_name: Manning
citation:
ama: Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension
in a three-dimensional model of confluent tissue. New Journal of Physics.
2021;23(9). doi:10.1088/1367-2630/ac23f1
apa: Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures
of tissue surface tension in a three-dimensional model of confluent tissue. New
Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1
chicago: Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures
of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New
Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1.
ieee: P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue
surface tension in a three-dimensional model of confluent tissue,” New Journal
of Physics, vol. 23, no. 9. IOP Publishing, 2021.
ista: Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface
tension in a three-dimensional model of confluent tissue. New Journal of Physics.
23(9), 093043.
mla: Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional
Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043,
IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1.
short: P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).
date_created: 2021-10-24T22:01:34Z
date_published: 2021-09-29T00:00:00Z
date_updated: 2023-08-14T08:10:31Z
day: '29'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1088/1367-2630/ac23f1
external_id:
arxiv:
- '2102.05397'
isi:
- '000702042400001'
file:
- access_level: open_access
checksum: ace603e8f0962b3ba55f23fa34f57764
content_type: application/pdf
creator: cziletti
date_created: 2021-10-28T12:06:01Z
date_updated: 2021-10-28T12:06:01Z
file_id: '10193'
file_name: 2021_NewJPhys_Sahu.pdf
file_size: 2215016
relation: main_file
success: 1
file_date_updated: 2021-10-28T12:06:01Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: New Journal of Physics
publication_identifier:
eissn:
- '13672630'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometric signatures of tissue surface tension in a three-dimensional model
of confluent tissue
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: 23
year: '2021'
...
---
_id: '10179'
abstract:
- lang: eng
text: Inhibitory GABAergic interneurons migrate over long distances from their extracortical
origin into the developing cortex. In humans, this process is uniquely slow and
prolonged, and it is unclear whether guidance cues unique to humans govern the
various phases of this complex developmental process. Here, we use fused cerebral
organoids to identify key roles of neurotransmitter signaling pathways in guiding
the migratory behavior of human cortical interneurons. We use scRNAseq to reveal
expression of GABA, glutamate, glycine, and serotonin receptors along distinct
maturation trajectories across interneuron migration. We develop an image analysis
software package, TrackPal, to simultaneously assess 48 parameters for entire
migration tracks of individual cells. By chemical screening, we show that different
modes of interneuron migration depend on distinct neurotransmitter signaling pathways,
linking transcriptional maturation of interneurons with their migratory behavior.
Altogether, our study provides a comprehensive quantitative analysis of human
interneuron migration and its functional modulation by neurotransmitter signaling.
acknowledgement: We thank all Knoblich laboratory members for continued support and
discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek,
Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service,
in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas
Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in
particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility,
notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon
Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance
with slice culture setups, Oliver L. Eichmueller for discussions and assistance
with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical
assistance regarding generation of cerebral organoids. This project received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in
J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education,
Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research
Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European
Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020
program (grant agreement no. 695642).
article_number: e108714
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sunanjay
full_name: Bajaj, Sunanjay
last_name: Bajaj
- first_name: Joshua A.
full_name: Bagley, Joshua A.
last_name: Bagley
- 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: Abel
full_name: Vertesy, Abel
last_name: Vertesy
- first_name: Sakurako
full_name: Nagumo Wong, Sakurako
last_name: Nagumo Wong
- first_name: Veronica
full_name: Krenn, Veronica
last_name: Krenn
- first_name: Julie
full_name: Lévi-Strauss, Julie
last_name: Lévi-Strauss
- first_name: Juergen A.
full_name: Knoblich, Juergen A.
last_name: Knoblich
citation:
ama: Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates
distinct phases of multimodal human interneuron migration. EMBO Journal.
2021;40(23). doi:10.15252/embj.2021108714
apa: Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn,
V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases
of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714
chicago: Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako
Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter
Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.”
EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714.
ieee: S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases
of multimodal human interneuron migration,” EMBO Journal, vol. 40, no.
23. Embo Press, 2021.
ista: Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss
J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of
multimodal human interneuron migration. EMBO Journal. 40(23), e108714.
mla: Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases
of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no.
23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714.
short: S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn,
J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).
date_created: 2021-10-24T22:01:34Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2023-08-14T08:05:23Z
day: '18'
ddc:
- '610'
department:
- _id: Bio
doi: 10.15252/embj.2021108714
external_id:
isi:
- '000708012800001'
pmid:
- '34661293'
file:
- access_level: open_access
checksum: 78d2d02e775322297e774f72810a41a4
content_type: application/pdf
creator: alisjak
date_created: 2021-12-13T14:54:14Z
date_updated: 2021-12-13T14:54:14Z
file_id: '10541'
file_name: 2021_EMBO_Bajaj.pdf
file_size: 7819881
relation: main_file
success: 1
file_date_updated: 2021-12-13T14:54:14Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '23'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neurotransmitter signaling regulates distinct phases of multimodal human interneuron
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: 40
year: '2021'
...
---
_id: '10180'
abstract:
- lang: eng
text: The growing energy and performance costs of deep learning have driven the
community to reduce the size of neural networks by selectively pruning components.
Similarly to their biological counterparts, sparse networks generalize just as
well, sometimes even better than, the original dense networks. Sparsity promises
to reduce the memory footprint of regular networks to fit mobile devices, as well
as shorten training time for ever growing networks. In this paper, we survey prior
work on sparsity in deep learning and provide an extensive tutorial of sparsification
for both inference and training. We describe approaches to remove and add elements
of neural networks, different training strategies to achieve model sparsity, and
mechanisms to exploit sparsity in practice. Our work distills ideas from more
than 300 research papers and provides guidance to practitioners who wish to utilize
sparsity today, as well as to researchers whose goal is to push the frontier forward.
We include the necessary background on mathematical methods in sparsification,
describe phenomena such as early structure adaptation, the intricate relations
between sparsity and the training process, and show techniques for achieving acceleration
on real hardware. We also define a metric of pruned parameter efficiency that
could serve as a baseline for comparison of different sparse networks. We close
by speculating on how sparsity can improve future workloads and outline major
open problems in the field.
acknowledgement: "We thank Doug Burger, Steve Scott, Marco Heddes, and the respective
teams at Microsoft for inspiring discussions on the topic. We thank Angelika Steger
for uplifting debates about the connections to biological brains, Sidak Pal Singh
for his support regarding experimental results, and Utku Evci as well as Xin Wang
for comments on previous versions of this\r\nwork. Special thanks go to Bernhard
Schölkopf, our JMLR editor Samy Bengio, and the three anonymous reviewers who provided
excellent comprehensive, pointed, and deep review comments that improved the quality
of our manuscript significantly."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Tal
full_name: Ben-Nun, Tal
last_name: Ben-Nun
- first_name: Nikoli
full_name: Dryden, Nikoli
last_name: Dryden
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
citation:
ama: 'Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. Sparsity in deep
learning: Pruning and growth for efficient inference and training in neural networks.
Journal of Machine Learning Research. 2021;22(241):1-124.'
apa: 'Hoefler, T., Alistarh, D.-A., Ben-Nun, T., Dryden, N., & Peste, E.-A.
(2021). Sparsity in deep learning: Pruning and growth for efficient inference
and training in neural networks. Journal of Machine Learning Research.
Journal of Machine Learning Research.'
chicago: 'Hoefler, Torsten, Dan-Adrian Alistarh, Tal Ben-Nun, Nikoli Dryden, and
Elena-Alexandra Peste. “Sparsity in Deep Learning: Pruning and Growth for Efficient
Inference and Training in Neural Networks.” Journal of Machine Learning Research.
Journal of Machine Learning Research, 2021.'
ieee: 'T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, and E.-A. Peste, “Sparsity
in deep learning: Pruning and growth for efficient inference and training in neural
networks,” Journal of Machine Learning Research, vol. 22, no. 241. Journal
of Machine Learning Research, pp. 1–124, 2021.'
ista: 'Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. 2021. Sparsity in
deep learning: Pruning and growth for efficient inference and training in neural
networks. Journal of Machine Learning Research. 22(241), 1–124.'
mla: 'Hoefler, Torsten, et al. “Sparsity in Deep Learning: Pruning and Growth for
Efficient Inference and Training in Neural Networks.” Journal of Machine Learning
Research, vol. 22, no. 241, Journal of Machine Learning Research, 2021, pp.
1–124.'
short: T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, E.-A. Peste, Journal of
Machine Learning Research 22 (2021) 1–124.
date_created: 2021-10-24T22:01:34Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2022-05-13T09:36:08Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '2102.00554'
file:
- access_level: open_access
checksum: 3389d9d01fc58f8fb4c1a53e14a8abbf
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T15:34:18Z
date_updated: 2021-10-27T15:34:18Z
file_id: '10192'
file_name: 2021_JMachLearnRes_Hoefler.pdf
file_size: 3527521
relation: main_file
success: 1
file_date_updated: 2021-10-27T15:34:18Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '241'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.jmlr.org/papers/v22/21-0366.html
month: '09'
oa: 1
oa_version: Published Version
page: 1-124
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
issn:
- 1532-4435
publication_status: published
publisher: Journal of Machine Learning Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Sparsity in deep learning: Pruning and growth for efficient inference and
training in neural networks'
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: 22
year: '2021'
...
---
_id: '10181'
abstract:
- lang: eng
text: In this article we study some geometric properties of proximally smooth sets.
First, we introduce a modification of the metric projection and prove its existence.
Then we provide an algorithm for constructing a rectifiable curve between two
sufficiently close points of a proximally smooth set in a uniformly convex and
uniformly smooth Banach space, with the moduli of smoothness and convexity of
power type. Our algorithm returns a reasonably short curve between two sufficiently
close points of a proximally smooth set, is iterative and uses our modification
of the metric projection. We estimate the length of the constructed curve and
its deviation from the segment with the same endpoints. These estimates coincide
up to a constant factor with those for the geodesics in a proximally smooth set
in a Hilbert space.
acknowledgement: Theorem 2 was obtained at Steklov Mathematical Institute RAS and
supported by Russian Science Foundation, grant N 19-11-00087.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Mariana S.
full_name: Lopushanski, Mariana S.
last_name: Lopushanski
citation:
ama: Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued
and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1
apa: Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally
smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1
chicago: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally
Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021.
https://doi.org/10.1007/s11228-021-00612-1.
ieee: G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth
sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.
ista: Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets.
Set-Valued and Variational Analysis.
mla: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally
Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021,
doi:10.1007/s11228-021-00612-1.
short: G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).
date_created: 2021-10-24T22:01:35Z
date_published: 2021-10-09T00:00:00Z
date_updated: 2023-08-14T08:11:38Z
day: '09'
department:
- _id: UlWa
doi: 10.1007/s11228-021-00612-1
external_id:
arxiv:
- '2012.10691'
isi:
- '000705774800001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.10691
month: '10'
oa: 1
oa_version: Published Version
publication: Set-Valued and Variational Analysis
publication_identifier:
eissn:
- 1877-0541
issn:
- 0927-6947
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rectifiable curves in proximally smooth sets
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10184'
abstract:
- lang: eng
text: "We introduce a novel technique to automatically decompose an input object’s
volume into a set of parts that can be represented by two opposite height fields.
Such decomposition enables the manufacturing of individual parts using two-piece
reusable rigid molds. Our decomposition strategy relies on a new energy formulation
that utilizes a pre-computed signal on the mesh volume representing the accessibility
for a predefined set of extraction directions. Thanks to this novel formulation,
our method allows for efficient optimization of a fabrication-aware partitioning
of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our
approach by generating valid volume partitionings for a wide range of complex
objects and physically reproducing several of them."
acknowledgement: 'The authors thank Marco Callieri for all his precious help with
the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning
Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research
was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent
fabrication-oriented computational design and modeling (grant no. 715767).'
article_number: '272'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
citation:
ama: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6).
doi:10.1145/3478513.3480555
apa: Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021).
Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics.
Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555
chicago: Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico
Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions
on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555.
ieee: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition
for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no.
6. Association for Computing Machinery, 2021.
ista: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.
mla: Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.”
ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing
Machinery, 2021, doi:10.1145/3478513.3480555.
short: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-10-27T07:08:19Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-02-28T12:52:48Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3478513.3480555
ec_funded: 1
external_id:
isi:
- '000729846700077'
file:
- access_level: open_access
checksum: 384ece7a9ad1026787ba9560b04336d5
content_type: application/pdf
creator: bbickel
date_created: 2021-10-27T07:08:07Z
date_updated: 2021-10-27T07:08:07Z
file_id: '10185'
file_name: rigidmolds-authorversion.pdf
file_size: 107708317
relation: main_file
file_date_updated: 2021-10-27T07:08:07Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://vcg.isti.cnr.it/Publications/2021/AMBCP21
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '1557-7368 '
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Volume decomposition for two-piece rigid casting
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2021'
...
---
_id: '10191'
abstract:
- lang: eng
text: "In this work we solve the algorithmic problem of consistency verification
for the TSO and PSO memory models given a reads-from map, denoted VTSO-rf and
VPSO-rf, respectively. For an execution of n events over k threads and d variables,
we establish novel bounds that scale as nk+1 for TSO and as nk+1· min(nk2, 2k·
d) for PSO. Moreover, based on our solution to these problems, we develop an SMC
algorithm under TSO and PSO that uses the RF equivalence. The algorithm is exploration-optimal,
in the sense that it is guaranteed to explore each class of the RF partitioning
exactly once, and spends polynomial time per class when k is bounded. Finally,
we implement all our algorithms in the SMC tool Nidhugg, and perform a large number
of experiments over benchmarks from existing literature. Our experimental results
show that our algorithms for VTSO-rf and VPSO-rf provide significant scalability
improvements over standard alternatives. Moreover, when used for SMC, the RF partitioning
is often much coarser than the standard Shasha-Snir partitioning for TSO/PSO,
which yields a significant speedup in the model checking task.\r\n\r\n"
acknowledgement: "The research was partially funded by the ERC CoG 863818 (ForM-SMArt)
and the Vienna Science\r\nand Technology Fund (WWTF) through project ICT15-003."
article_number: '164'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Truc Lam
full_name: Bui, Truc Lam
last_name: Bui
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tushar
full_name: Gautam, Tushar
last_name: Gautam
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. The reads-from equivalence
for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages.
2021;5(OOPSLA). doi:10.1145/3485541
apa: Bui, T. L., Chatterjee, K., Gautam, T., Pavlogiannis, A., & Toman, V. (2021).
The reads-from equivalence for the TSO and PSO memory models. Proceedings of
the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3485541
chicago: Bui, Truc Lam, Krishnendu Chatterjee, Tushar Gautam, Andreas Pavlogiannis,
and Viktor Toman. “The Reads-from Equivalence for the TSO and PSO Memory Models.”
Proceedings of the ACM on Programming Languages. Association for Computing
Machinery, 2021. https://doi.org/10.1145/3485541.
ieee: T. L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, and V. Toman, “The reads-from
equivalence for the TSO and PSO memory models,” Proceedings of the ACM on Programming
Languages, vol. 5, no. OOPSLA. Association for Computing Machinery, 2021.
ista: Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. 2021. The reads-from
equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming
Languages. 5(OOPSLA), 164.
mla: Bui, Truc Lam, et al. “The Reads-from Equivalence for the TSO and PSO Memory
Models.” Proceedings of the ACM on Programming Languages, vol. 5, no. OOPSLA,
164, Association for Computing Machinery, 2021, doi:10.1145/3485541.
short: T.L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, V. Toman, Proceedings
of the ACM on Programming Languages 5 (2021).
date_created: 2021-10-27T15:05:34Z
date_published: 2021-10-15T00:00:00Z
date_updated: 2025-07-14T09:10:16Z
day: '15'
ddc:
- '000'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1145/3485541
ec_funded: 1
external_id:
arxiv:
- '2011.11763'
file:
- access_level: open_access
checksum: 9d6dce7b611853c529bb7b1915ac579e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-04T07:24:48Z
date_updated: 2021-11-04T07:24:48Z
file_id: '10215'
file_name: 2021_ProcACMPL_Bui.pdf
file_size: 2903485
relation: main_file
success: 1
file_date_updated: 2021-11-04T07:24:48Z
has_accepted_license: '1'
intvolume: ' 5'
issue: OOPSLA
keyword:
- safety
- risk
- reliability and quality
- software
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '10199'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The reads-from equivalence for the TSO and PSO memory models
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: 5
year: '2021'
...
---
_id: '10199'
abstract:
- lang: eng
text: The design and verification of concurrent systems remains an open challenge
due to the non-determinism that arises from the inter-process communication. In
particular, concurrent programs are notoriously difficult both to be written correctly
and to be analyzed formally, as complex thread interaction has to be accounted
for. The difficulties are further exacerbated when concurrent programs get executed
on modern-day hardware, which contains various buffering and caching mechanisms
for efficiency reasons. This causes further subtle non-determinism, which can
often produce very unintuitive behavior of the concurrent programs. Model checking
is at the forefront of tackling the verification problem, where the task is to
decide, given as input a concurrent system and a desired property, whether the
system satisfies the property. The inherent state-space explosion problem in model
checking of concurrent systems causes naïve explicit methods not to scale, thus
more inventive methods are required. One such method is stateless model checking
(SMC), which explores in memory-efficient manner the program executions rather
than the states of the program. State-of-the-art SMC is typically coupled with
partial order reduction (POR) techniques, which argue that certain executions
provably produce identical system behavior, thus limiting the amount of executions
one needs to explore in order to cover all possible behaviors. Another method
to tackle the state-space explosion is symbolic model checking, where the considered
techniques operate on a succinct implicit representation of the input system rather
than explicitly accessing the system. In this thesis we present new techniques
for verification of concurrent systems. We present several novel POR methods for
SMC of concurrent programs under various models of semantics, some of which account
for write-buffering mechanisms. Additionally, we present novel algorithms for
symbolic model checking of finite-state concurrent systems, where the desired
property of the systems is to ensure a formally defined notion of fairness.
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199
apa: Toman, V. (2021). Improved verification techniques for concurrent systems.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199
chicago: Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.
ieee: V. Toman, “Improved verification techniques for concurrent systems,” Institute
of Science and Technology Austria, 2021.
ista: Toman V. 2021. Improved verification techniques for concurrent systems. Institute
of Science and Technology Austria.
mla: Toman, Viktor. Improved Verification Techniques for Concurrent Systems.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.
short: V. Toman, Improved Verification Techniques for Concurrent Systems, Institute
of Science and Technology Austria, 2021.
date_created: 2021-10-29T20:09:01Z
date_published: 2021-10-31T00:00:00Z
date_updated: 2025-07-14T09:10:16Z
day: '31'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrCh
doi: 10.15479/at:ista:10199
ec_funded: 1
file:
- access_level: open_access
checksum: 4f412a1ee60952221b499a4b1268df35
content_type: application/pdf
creator: vtoman
date_created: 2021-11-08T14:12:22Z
date_updated: 2021-11-08T14:12:22Z
file_id: '10225'
file_name: toman_th_final.pdf
file_size: 2915234
relation: main_file
- access_level: closed
checksum: 9584943f99127be2dd2963f6784c37d4
content_type: application/zip
creator: vtoman
date_created: 2021-11-08T14:12:46Z
date_updated: 2021-11-09T09:00:50Z
file_id: '10226'
file_name: toman_thesis.zip
file_size: 8616056
relation: source_file
file_date_updated: 2021-11-09T09:00:50Z
has_accepted_license: '1'
keyword:
- concurrency
- verification
- model checking
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '166'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10190'
relation: part_of_dissertation
status: public
- id: '9987'
relation: part_of_dissertation
status: public
- id: '141'
relation: part_of_dissertation
status: public
- id: '10191'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Improved verification techniques for concurrent systems
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10202'
abstract:
- lang: eng
text: Zygotic genome activation (ZGA) initiates regionalized transcription underlying
distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture
sculpted by conserved DNA-binding proteins. However, the direct mechanistic link
between the onset of ZGA and the tissue-specific transcription remains unclear.
Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating
both processes during zebrafish embryogenesis. Integrative analysis of transcriptome,
genome-wide occupancy and chromatin accessibility reveals contrasting molecular
activities of maternally deposited and zygotically synthesized Satb2. Maternal
Satb2 prevents premature transcription of zygotic genes by influencing the interplay
between the pluripotency factors. By contrast, zygotic Satb2 activates transcription
of the same group of genes during neural crest development and organogenesis.
Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores
how these antithetical activities are temporally coordinated and functionally
implemented highlighting the evolutionary implications of the biphasic and bimodal
regulation of landmark developmental transitions by a single determinant.
acknowledgement: 'We are grateful to the members of C.-P.H. and SG lab for discussions.
Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful
to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10:
GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish
S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments.
We would also like to thank Chaitanya Dingare for valuable suggestions. We thank
Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the
manuscript. This work was supported by the Centre of Excellence in Epigenetics program
of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07)
to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship
(JCB/2019/000013) from Science and Engineering Research Board, Government of India
to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The
work using animal models was partly supported by the infrastructure support grants
from the Department of Biotechnology (National Facility for Laboratory Model Organisms:
BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism
to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015).
S.J.P. was supported by Fellowship from the Council of Scientific and Industrial
Research, India and travel fellowship from the Company of Biologists, UK. P.C.R.
was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance
(IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India.
M.S. was supported by core funding from the Tata Institute of Fundamental Research
(TIFR 12P-121).'
article_number: '6094'
article_processing_charge: Yes
article_type: original
author:
- first_name: Saurabh J.
full_name: Pradhan, Saurabh J.
last_name: Pradhan
- first_name: Puli Chandramouli
full_name: Reddy, Puli Chandramouli
last_name: Reddy
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Ankita
full_name: Sharma, Ankita
last_name: Sharma
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Meghana S.
full_name: Oak, Meghana S.
last_name: Oak
- first_name: Rini
full_name: Shah, Rini
last_name: Shah
- first_name: Mrinmoy
full_name: Pal, Mrinmoy
last_name: Pal
- first_name: Ojas
full_name: Deshpande, Ojas
last_name: Deshpande
- first_name: Greg
full_name: Dsilva, Greg
last_name: Dsilva
- first_name: Yin
full_name: Tang, Yin
last_name: Tang
- first_name: Rakesh
full_name: Mishra, Rakesh
last_name: Mishra
- first_name: Girish
full_name: Deshpande, Girish
last_name: Deshpande
- first_name: Antonio J.
full_name: Giraldez, Antonio J.
last_name: Giraldez
- first_name: Mahendra
full_name: Sonawane, Mahendra
last_name: Sonawane
- 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
- first_name: Sanjeev
full_name: Galande, Sanjeev
last_name: Galande
citation:
ama: Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major
developmental transitions during early vertebrate embryogenesis. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-26234-7
apa: Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S.,
… Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions
during early vertebrate embryogenesis. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-021-26234-7
chicago: Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma,
Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for
Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature
Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.
ieee: S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental
transitions during early vertebrate embryogenesis,” Nature Communications,
vol. 12, no. 1. Springer Nature, 2021.
ista: Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande
O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg
C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions
during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.
mla: Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental
Transitions during Early Vertebrate Embryogenesis.” Nature Communications,
vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.
short: S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah,
M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez,
M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).
date_created: 2021-10-31T23:01:29Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T10:32:48Z
day: '19'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1038/s41467-021-26234-7
external_id:
isi:
- '000709050300016'
pmid:
- '34667153'
file:
- access_level: open_access
checksum: c40a69ae94435ecd3a30c9874a11ef2b
content_type: application/pdf
creator: cziletti
date_created: 2021-11-09T13:59:26Z
date_updated: 2021-11-09T13:59:26Z
file_id: '10262'
file_name: 2021_NatureComm_Pradhan.pdf
file_size: 7144437
relation: main_file
success: 1
file_date_updated: 2021-11-09T13:59:26Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: Preprint
relation: earlier_version
url: 'https://doi.org/10.1101/2020.11.23.394171 '
scopus_import: '1'
status: public
title: Satb2 acts as a gatekeeper for major developmental transitions during early
vertebrate embryogenesis
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: 12
year: '2021'
...
---
_id: '10203'
abstract:
- lang: eng
text: Single photon emitters in atomically-thin semiconductors can be deterministically
positioned using strain induced by underlying nano-structures. Here, we couple
monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas
providing both optical enhancement and monolayer deformation. For single photon
emitters formed on such nano-antennas, we find very low (femto-Joule) saturation
pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed
on low-refractive-index SiO2 pillars. We show that the key to these observations
is the increase on average by a factor of 5 of the quantum efficiency of the emitters
coupled to the nano-antennas. This further allows us to gain new insights into
their photoluminescence dynamics, revealing the roles of the dark exciton reservoir
and Auger processes. We also find that the coherence time of such emitters is
limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas
as a platform for high-efficiency quantum light generation in monolayer semiconductors.
acknowledgement: L.S., P.G.Z., and A.I.T. thank the financial support of the European
Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1.
L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation
programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108.
P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation
programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C.,
S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P.,
A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1.
S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid
(SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.
article_number: '6063'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Luca
full_name: Sortino, Luca
last_name: Sortino
- first_name: Panaiot G.
full_name: Zotev, Panaiot G.
last_name: Zotev
- first_name: Catherine L.
full_name: Phillips, Catherine L.
last_name: Phillips
- first_name: Alistair J.
full_name: Brash, Alistair J.
last_name: Brash
- first_name: Javier
full_name: Cambiasso, Javier
last_name: Cambiasso
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: A. Mark
full_name: Fox, A. Mark
last_name: Fox
- first_name: Stefan A.
full_name: Maier, Stefan A.
last_name: Maier
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
- first_name: Alexander I.
full_name: Tartakovskii, Alexander I.
last_name: Tartakovskii
citation:
ama: Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with
enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3
apa: Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi,
E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced
quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3
chicago: Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash,
Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza,
and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum
Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.”
Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3.
ieee: L. Sortino et al., “Bright single photon emitters with enhanced quantum
efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,”
Nature Communications, vol. 12. Springer Nature, 2021.
ista: Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM,
Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with
enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric
nano-antennas. Nature Communications. 12, 6063.
mla: Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum
Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.”
Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3.
short: L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi,
A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12
(2021).
date_created: 2021-10-31T23:01:30Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2023-08-14T08:12:12Z
day: '18'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1038/s41467-021-26262-3
external_id:
arxiv:
- '2103.16986'
isi:
- '000708601800015'
file:
- access_level: open_access
checksum: 8580d128389860f732028c521cd5949e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-03T11:31:24Z
date_updated: 2021-11-03T11:31:24Z
file_id: '10212'
file_name: 2021_NatComm_Sortino.pdf
file_size: 1434201
relation: main_file
success: 1
file_date_updated: 2021-11-03T11:31:24Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bright single photon emitters with enhanced quantum efficiency in a two-dimensional
semiconductor coupled with dielectric nano-antennas
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: 12
year: '2021'
...
---
_id: '10204'
abstract:
- lang: eng
text: Two common representations of close packings of identical spheres consisting
of hexagonal layers, called Barlow stackings, appear abundantly in minerals and
metals. These motifs, however, occupy an identical portion of space and bear identical
first-order topological signatures as measured by persistent homology. Here we
present a novel method based on k-fold covers that unambiguously distinguishes
between these patterns. Moreover, our approach provides topological evidence that
the FCC motif is the more stable of the two in the context of evolving experimental
sphere packings during the transition from disordered to an ordered state. We
conclude that our approach can be generalised to distinguish between various Barlow
stackings manifested in minerals and metals.
acknowledgement: MS acknowledges the support by Australian Research Council funding
through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour
and N. Francois for their input and valuable discussions. This project has received
funding from the European Research Council (ERC) under the European Union's Horizon
2020 research and innovation programme, grant no. 788183 and from the Wittgenstein
Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.
article_processing_charge: No
article_type: original
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mohammad
full_name: Saadatfar, Mohammad
last_name: Saadatfar
citation:
ama: Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability
of hexagonal close packing and Barlow stackings. Soft Matter. 2021;17(40):9107-9115.
doi:10.1039/d1sm00774b
apa: Osang, G. F., Edelsbrunner, H., & Saadatfar, M. (2021). Topological signatures
and stability of hexagonal close packing and Barlow stackings. Soft Matter.
Royal Society of Chemistry . https://doi.org/10.1039/d1sm00774b
chicago: Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological
Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft
Matter. Royal Society of Chemistry , 2021. https://doi.org/10.1039/d1sm00774b.
ieee: G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and
stability of hexagonal close packing and Barlow stackings,” Soft Matter,
vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.
ista: Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability
of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.
mla: Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal
Close Packing and Barlow Stackings.” Soft Matter, vol. 17, no. 40, Royal
Society of Chemistry , 2021, pp. 9107–15, doi:10.1039/d1sm00774b.
short: G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115.
date_created: 2021-10-31T23:01:30Z
date_published: 2021-10-20T00:00:00Z
date_updated: 2023-10-03T09:24:27Z
day: '20'
ddc:
- '540'
department:
- _id: HeEd
doi: 10.1039/d1sm00774b
ec_funded: 1
external_id:
isi:
- '000700090000001'
pmid:
- '34569592'
file:
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checksum: b4da0c420530295e61b153960f6cb350
content_type: application/pdf
creator: dernst
date_created: 2023-10-03T09:21:42Z
date_updated: 2023-10-03T09:21:42Z
file_id: '14385'
file_name: 2021_SoftMatter_acceptedversion_Osang.pdf
file_size: 4678788
relation: main_file
success: 1
file_date_updated: 2023-10-03T09:21:42Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 9107-9115
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological signatures and stability of hexagonal close packing and Barlow
stackings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10206'
abstract:
- lang: eng
text: Neural-network classifiers achieve high accuracy when predicting the class
of an input that they were trained to identify. Maintaining this accuracy in dynamic
environments, where inputs frequently fall outside the fixed set of initially
known classes, remains a challenge. The typical approach is to detect inputs from
novel classes and retrain the classifier on an augmented dataset. However, not
only the classifier but also the detection mechanism needs to adapt in order to
distinguish between newly learned and yet unknown input classes. To address this
challenge, we introduce an algorithmic framework for active monitoring of a neural
network. A monitor wrapped in our framework operates in parallel with the neural
network and interacts with a human user via a series of interpretable labeling
queries for incremental adaptation. In addition, we propose an adaptive quantitative
monitor to improve precision. An experimental evaluation on a diverse set of benchmarks
with varying numbers of classes confirms the benefits of our active monitoring
framework in dynamic scenarios.
acknowledgement: We thank Christoph Lampert and Alex Greengold for fruitful discussions.
This research was supported in part by the Simons Institute for the Theory of Computing,
the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the
European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural
networks. In: 21st International Conference on Runtime Verification. Vol
12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3'
apa: 'Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown:
active monitoring of neural networks. In 21st International Conference on Runtime
Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3'
chicago: 'Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown:
Active Monitoring of Neural Networks.” In 21st International Conference on
Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3.'
ieee: 'A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring
of neural networks,” in 21st International Conference on Runtime Verification,
Virtual, 2021, vol. 12974, pp. 42–61.'
ista: 'Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring
of neural networks. 21st International Conference on Runtime Verification. RV:
Runtime Verification, LNCS, vol. 12974, 42–61.'
mla: 'Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.”
21st International Conference on Runtime Verification, vol. 12974, Springer
Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3.'
short: A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference
on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-31T23:01:31Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2024-01-30T12:06:56Z
day: '06'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_3
ec_funded: 1
external_id:
arxiv:
- '2009.06429'
isi:
- '000719383800003'
isi: 1
keyword:
- monitoring
- neural networks
- novelty detection
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06429
month: '10'
oa: 1
oa_version: Preprint
page: 42-61
place: Cham
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
publication: 21st International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 9-783-0308-8493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
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relation: extended_version
status: public
scopus_import: '1'
status: public
title: 'Into the unknown: active monitoring of neural networks'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12974 '
year: '2021'
...