---
_id: '12104'
abstract:
- lang: eng
text: We study ergodic decompositions of Dirichlet spaces under intertwining via
unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular
Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore,
every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces
is decomposable over their ergodic decompositions up to conjugation via an isomorphism
of the corresponding indexing spaces.
acknowledgement: Research supported by the Austrian Science Fund (FWF) grant F65 at
the Institute of Science and Technology Austria and by the European Research Council
(ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully
acknowledges funding of his current position by the Austrian Science Fund (FWF)
through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding
of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme
(Grant No. 156).
article_number: '9'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order
isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7
apa: Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet
forms under order isomorphisms. Journal of Evolution Equations. Springer
Nature. https://doi.org/10.1007/s00028-022-00859-7
chicago: Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of
Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations.
Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.
ieee: L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms
under order isomorphisms,” Journal of Evolution Equations, vol. 23, no.
1. Springer Nature, 2023.
ista: Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms
under order isomorphisms. Journal of Evolution Equations. 23(1), 9.
mla: Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet
Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23,
no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.
short: L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).
date_created: 2023-01-08T23:00:53Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-06-28T11:54:35Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00028-022-00859-7
ec_funded: 1
external_id:
isi:
- '000906214600004'
file:
- access_level: open_access
checksum: 1f34f3e2cb521033de6154f274ea3a4e
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T10:45:06Z
date_updated: 2023-01-20T10:45:06Z
file_id: '12325'
file_name: 2023_JourEvolutionEquations_DelloSchiavo.pdf
file_size: 422612
relation: main_file
success: 1
file_date_updated: 2023-01-20T10:45:06Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c
grant_number: E208
name: Configuration Spaces over Non-Smooth Spaces
- _id: 34c6ea2d-11ca-11ed-8bc3-c04f3c502833
grant_number: ESP156_N
name: Gradient flow techniques for quantum Markov semigroups
publication: Journal of Evolution Equations
publication_identifier:
eissn:
- 1424-3202
issn:
- 1424-3199
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ergodic decompositions of Dirichlet forms under order isomorphisms
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: 23
year: '2023'
...
---
_id: '12105'
abstract:
- lang: eng
text: Data-driven dimensionality reduction methods such as proper orthogonal decomposition
and dynamic mode decomposition have proven to be useful for exploring complex
phenomena within fluid dynamics and beyond. A well-known challenge for these techniques
is posed by the continuous symmetries, e.g. translations and rotations, of the
system under consideration, as drifts in the data dominate the modal expansions
without providing an insight into the dynamics of the problem. In the present
study, we address this issue for fluid flows in rectangular channels by formulating
a continuous symmetry reduction method that eliminates the translations in the
streamwise and spanwise directions simultaneously. We demonstrate our method by
computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows
of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille
flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity
of the invariant solutions with translation symmetries, i.e. travelling waves
and relative periodic orbits, whereas in the latter, our calculations reveal episodes
of turbulent time evolution that can be approximated by a low-dimensional linear
expansion.
acknowledgement: "E.M. acknowledges funding from the ISTplus fellowship programme.
G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH)."
article_number: A10
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition
of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001
apa: Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced
dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001
chicago: Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced
Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics.
Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.
ieee: E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic
mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics,
vol. 954. Cambridge University Press, 2023.
ista: Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode
decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.
mla: Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall
Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University
Press, 2023, doi:10.1017/jfm.2022.1001.
short: E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954
(2023).
date_created: 2023-01-08T23:00:53Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2023-08-01T12:53:23Z
day: '10'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2022.1001
external_id:
arxiv:
- '2101.07516'
isi:
- '000903336600001'
file:
- access_level: open_access
checksum: 9224f987caefe5dd85a70814d3cce65c
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T12:34:54Z
date_updated: 2023-02-02T12:34:54Z
file_id: '12489'
file_name: 2023_JourFluidMechanics_Marensi.pdf
file_size: 1931647
relation: main_file
success: 1
file_date_updated: 2023-02-02T12:34:54Z
has_accepted_license: '1'
intvolume: ' 954'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-reduced dynamic mode decomposition of near-wall turbulence
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: 954
year: '2023'
...
---
_id: '12106'
abstract:
- lang: eng
text: Regulation of chromatin states involves the dynamic interplay between different
histone modifications to control gene expression. Recent advances have enabled
mapping of histone marks in single cells, but most methods are constrained to
profile only one histone mark per cell. Here, we present an integrated experimental
and computational framework, scChIX-seq (single-cell chromatin immunocleavage
and unmixing sequencing), to map several histone marks in single cells. scChIX-seq
multiplexes two histone marks together in single cells, then computationally deconvolves
the signal using training data from respective histone mark profiles. This framework
learns the cell-type-specific correlation structure between histone marks, and
therefore does not require a priori assumptions of their genomic distributions.
Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single
cells across a range of mark combinations. Modeling dynamics of in vitro macrophage
differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq
unlocks systematic interrogation of the interplay between histone modifications
in single cells.
acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell
types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg
for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat
and O. Stegle for discussions on multinomial distributions. This work was supported
by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse
Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001)
and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early
Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie
Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term
Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is
part of the Oncode Institute which is financed partly by the Dutch Cancer Society.
article_processing_charge: No
article_type: original
author:
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Buys Anton
full_name: De Barbanson, Buys Anton
last_name: De Barbanson
- first_name: Max D.
full_name: Wellenstein, Max D.
last_name: Wellenstein
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
citation:
ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. scChIX-seq infers dynamic relationships between histone modifications in single
cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3
apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D.,
& Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between
histone modifications in single cells. Nature Biotechnology. Springer Nature.
https://doi.org/10.1038/s41587-022-01560-3
chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max
D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships
between Histone Modifications in Single Cells.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.
ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and
A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications
in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823,
2023.
ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. 2023. scChIX-seq infers dynamic relationships between histone modifications
in single cells. Nature Biotechnology. 41, 813–823.
mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone
Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer
Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.
short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A.
Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.
date_created: 2023-01-08T23:00:53Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-16T11:32:33Z
day: '01'
ddc:
- '570'
department:
- _id: ScienComp
doi: 10.1038/s41587-022-01560-3
external_id:
isi:
- '000909067600003'
file:
- access_level: open_access
checksum: 668447a1c8d360b68f8aaf9e08ed644f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:30:45Z
date_updated: 2023-08-16T11:30:45Z
file_id: '14066'
file_name: 2023_NatureBioTech_Yeung.pdf
file_size: 12040976
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:30:45Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 813–823
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: scChIX-seq infers dynamic relationships between histone modifications in single
cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2023'
...
---
_id: '12113'
abstract:
- lang: eng
text: The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate)
(PEDOT:PSS) film can be significantly improved by optimizing the oxidation level
of the film in oxidation and reduction processes. However, precise control over
the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly
sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture
of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence
to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity
EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid
conformational change in the PEDOT:PSS films. In particular, basic amino acid
Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation
during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment
further induces highly orientated lamellar stacking microstructures to increase
σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel
trigonal-shape thermoelectric device is designed and assembled by the as-prepared
PEDOT:PSS films in order to harvest heat via a vertical temperature gradient.
An output power density of 33 μW cm−2 is generated at a temperature difference
of 40 K, showing the potential application for low-grade wearable electronic devices.
acknowledgement: Scientific Research Program Funded by Shaanxi Provincial Education
Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi
(Grant No.2022JZ-31), Young Talent fund of University Association for Science and
Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation
(Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology
(Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry
and Technology for Chemical Industry, Ministry of Education, Shaanxi University
of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi
Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology,
Shaanxi University of Science and Technology (Grant No. KFKT2022-15).
article_number: '156101'
article_processing_charge: No
article_type: original
author:
- first_name: Li
full_name: Zhang, Li
last_name: Zhang
- first_name: Xingyu
full_name: Liu, Xingyu
last_name: Liu
- first_name: Ting
full_name: Wu, Ting
last_name: Wu
- first_name: Shengduo
full_name: Xu, Shengduo
id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f
last_name: Xu
- first_name: Guoquan
full_name: Suo, Guoquan
last_name: Suo
- first_name: Xiaohui
full_name: Ye, Xiaohui
last_name: Ye
- first_name: Xiaojiang
full_name: Hou, Xiaojiang
last_name: Hou
- first_name: Yanling
full_name: Yang, Yanling
last_name: Yang
- first_name: Qingfeng
full_name: Liu, Qingfeng
last_name: Liu
- first_name: Hongqiang
full_name: Wang, Hongqiang
last_name: Wang
citation:
ama: Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance
thermoelectric device with vertical temperature gradient. Applied Surface Science.
2023;613. doi:10.1016/j.apsusc.2022.156101
apa: Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step
post-treatment to deliver high performance thermoelectric device with vertical
temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101
chicago: Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang
Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment
to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.”
Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101.
ieee: L. Zhang et al., “Two-step post-treatment to deliver high performance
thermoelectric device with vertical temperature gradient,” Applied Surface
Science, vol. 613. Elsevier, 2023.
ista: Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023.
Two-step post-treatment to deliver high performance thermoelectric device with
vertical temperature gradient. Applied Surface Science. 613, 156101.
mla: Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric
Device with Vertical Temperature Gradient.” Applied Surface Science, vol.
613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101.
short: L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H.
Wang, Applied Surface Science 613 (2023).
date_created: 2023-01-12T11:55:02Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-14T11:47:06Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.apsusc.2022.156101
external_id:
isi:
- '000911497000001'
intvolume: ' 613'
isi: 1
keyword:
- Surfaces
- Coatings and Films
- Condensed Matter Physics
- Surfaces and Interfaces
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '03'
oa_version: None
publication: Applied Surface Science
publication_identifier:
issn:
- 0169-4332
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-step post-treatment to deliver high performance thermoelectric device with
vertical temperature gradient
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 613
year: '2023'
...
---
_id: '12114'
abstract:
- lang: eng
text: 'Probing the dynamics of aromatic side chains provides important insights
into the behavior of a protein because flips of aromatic rings in a protein’s
hydrophobic core report on breathing motion involving a large part of the protein.
Inherently invisible to crystallography, aromatic motions have been primarily
studied by solution NMR. The question how packing of proteins in crystals affects
ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning
NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a
protein in three different crystal packing environments to shed light onto possible
impact of packing on ring flips. The flips of the two Phe residues in ubiquitin,
both surface exposed, appear remarkably conserved in the different crystal forms,
even though the intermolecular packing is quite different: Phe4 flips on a ca.
10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to
µs motion. Our findings suggest that intramolecular influences are more important
for ring flips than intermolecular (packing) effects.'
acknowledgement: The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within
the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche)
CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research
Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the
Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI
(ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership
for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing
and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg
State University in a form of the grant 92425251 and the access to the MRR, MCT
and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact
that “tensor asymmetry” is better called “tensor biaxiality”.
article_number: '100079'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Olga O.
full_name: Lebedenko, Olga O.
last_name: Lebedenko
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079'
apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R.,
Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079'
chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman
Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in
Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal
of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.'
ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin
protein crystals from MAS NMR and MD,” Journal of Structural Biology: X,
vol. 7. Elsevier, 2023.'
ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR,
Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals
from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.'
mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin
Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X,
vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.'
short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R.
Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).'
date_created: 2023-01-12T11:55:38Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-16T09:37:25Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.yjsbx.2022.100079
external_id:
pmid:
- '36578472'
file:
- access_level: open_access
checksum: b4b1c10a31018aafe053b7d55a470e54
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T09:36:28Z
date_updated: 2023-08-16T09:36:28Z
file_id: '14064'
file_name: 2023_JourStrucBiologyX_Gauto.pdf
file_size: 5132322
relation: main_file
success: 1
file_date_updated: 2023-08-16T09:36:28Z
has_accepted_license: '1'
intvolume: ' 7'
keyword:
- Structural Biology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Structural Biology: X'
publication_identifier:
issn:
- 2590-1524
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS
NMR and MD
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12115'
acknowledgement: This work was supported by European Commission’s Seventh Framework
Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
full_name: Glajzer, Jacek
last_name: Glajzer
- first_name: Dan Cacsire
full_name: Castillo-Tong, Dan Cacsire
last_name: Castillo-Tong
- first_name: Rolf
full_name: Richter, Rolf
last_name: Richter
- first_name: Ignace
full_name: Vergote, Ignace
last_name: Vergote
- first_name: Hagen
full_name: Kulbe, Hagen
last_name: Kulbe
- first_name: Adriaan
full_name: Vanderstichele, Adriaan
last_name: Vanderstichele
- first_name: Ilary
full_name: Ruscito, Ilary
last_name: Ruscito
- first_name: Fabian
full_name: Trillsch, Fabian
last_name: Trillsch
- first_name: Alexander
full_name: Mustea, Alexander
last_name: Mustea
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Charlie
full_name: Gourley, Charlie
last_name: Gourley
- first_name: Hani
full_name: Gabra, Hani
last_name: Gabra
- first_name: Eliane T.
full_name: Taube, Eliane T.
last_name: Taube
- first_name: Oliver
full_name: Dorigo, Oliver
last_name: Dorigo
- first_name: David
full_name: Horst, David
last_name: Horst
- first_name: Carlotta
full_name: Keunecke, Carlotta
last_name: Keunecke
- first_name: Joanna
full_name: Baum, Joanna
last_name: Baum
- first_name: Timothy
full_name: Angelotti, Timothy
last_name: Angelotti
- first_name: Jalid
full_name: Sehouli, Jalid
last_name: Sehouli
- first_name: Elena Ioana
full_name: Braicu, Elena Ioana
last_name: Braicu
citation:
ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact
of BRCA mutation status on tumor dissemination pattern, surgical outcome, and
patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC).
A multicenter, retrospective study of the ovarian cancer therapy—innovative models
prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47.
doi:10.1245/s10434-022-12681-z'
apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome, and patient survival in primary
and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z'
chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract:
Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome,
and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer
(HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative
Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology.
Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.'
ieee: 'J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome, and patient survival in primary
and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective
study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS)
consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp.
46–47, 2023.'
ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern,
surgical outcome, and patient survival in primary and recurrent high-grade serous
ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer
therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical
Oncology. 30, 46–47.'
mla: 'Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status
on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary
and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective
Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS)
Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023,
pp. 46–47, doi:10.1245/s10434-022-12681-z.'
short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
Braicu, Annals of Surgical Oncology 30 (2023) 46–47.
date_created: 2023-01-12T11:56:22Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-05T15:18:36Z
day: '01'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12681-z
external_id:
isi:
- '000879151800001'
intvolume: ' 30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1245/s10434-022-12681-z
month: '01'
oa: 1
oa_version: Published Version
page: 46-47
publication: Annals of Surgical Oncology
publication_identifier:
eissn:
- 1534-4681
issn:
- 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12205'
relation: other
status: public
scopus_import: '1'
status: public
title: 'ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome, and patient survival in primary and recurrent high-grade
serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian
cancer therapy—innovative models prolong survival (OCTIPS) consortium'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2023'
...
---
_id: '12158'
abstract:
- lang: eng
text: 'Post-translational histone modifications modulate chromatin activity to affect
gene expression. How chromatin states underlie lineage choice in single cells
is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage
(sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3)
histone modifications in the mouse bone marrow. During differentiation, hematopoietic
stem and progenitor cells (HSPCs) acquire active chromatin states mediated by
cell-type-specifying transcription factors, which are unique for each lineage.
By contrast, most alterations in repressive marks during differentiation occur
independent of the final cell type. Chromatin trajectory analysis shows that lineage
choice at the chromatin level occurs at the progenitor stage. Joint profiling
of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage
have distinct active chromatin but share similar myeloid-specific heterochromatin
states. This implies a hierarchical regulation of chromatin during hematopoiesis:
heterochromatin dynamics distinguish differentiation trajectories and lineages,
while euchromatin dynamics reflect cell types within lineages.'
acknowledgement: We thank A. Giladi for sharing mRNA abundance tables of cell types
together with J. van den Berg for critical reading of the manuscript. We thank M.
Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich
Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973).
Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström
under CC-BY-SA 3.0 license. This work was supported by European Research Council
Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor
Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991),
HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z.
The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF
(ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which
is partly financed by the Dutch Cancer Society. The funders had no role in study
design, data collection and analysis, decision to publish or preparation of the
manuscript.
article_processing_charge: No
article_type: review
author:
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Helena
full_name: Viñas Gaza, Helena
last_name: Viñas Gaza
- first_name: Buys Anton
full_name: de Barbanson, Buys Anton
last_name: de Barbanson
- first_name: Vivek
full_name: Bhardwaj, Vivek
last_name: Bhardwaj
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Reinier
full_name: van der Linden, Reinier
last_name: van der Linden
- first_name: Alexander
full_name: van Oudenaarden, Alexander
last_name: van Oudenaarden
citation:
ama: Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345.
doi:10.1038/s41588-022-01260-3
apa: Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu,
M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature.
https://doi.org/10.1038/s41588-022-01260-3
chicago: Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson,
Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden.
“Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.”
Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.
ieee: P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin
dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature,
pp. 333–345, 2023.
ista: Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M,
van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.
mla: Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin
Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature,
2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.
short: P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu,
R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.
date_created: 2023-01-12T12:09:09Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-02-27T07:48:24Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: ScienComp
doi: 10.1038/s41588-022-01260-3
file:
- access_level: open_access
checksum: 6fdb8e34fbeea63edd0f2c6c2cc5823e
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:46:45Z
date_updated: 2023-02-27T07:46:45Z
file_id: '12688'
file_name: 2023_NatureGenetics_Zeller.pdf
file_size: 21484855
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success: 1
file_date_updated: 2023-02-27T07:46:45Z
has_accepted_license: '1'
intvolume: ' 55'
keyword:
- Genetics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 333-345
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis
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: 55
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
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: 32
year: '2023'
...
---
_id: '12162'
abstract:
- lang: eng
text: Homeostatic balance in the intestinal epithelium relies on a fast cellular
turnover, which is coordinated by an intricate interplay between biochemical signalling,
mechanical forces and organ geometry. We review recent modelling approaches that
have been developed to understand different facets of this remarkable homeostatic
equilibrium. Existing models offer different, albeit complementary, perspectives
on the problem. First, biomechanical models aim to explain the local and global
mechanical stresses driving cell renewal as well as tissue shape maintenance.
Second, compartmental models provide insights into the conditions necessary to
keep a constant flow of cells with well-defined ratios of cell types, and how
perturbations can lead to an unbalance of relative compartment sizes. A third
family of models address, at the cellular level, the nature and regulation of
stem fate choices that are necessary to fuel cellular turnover. We also review
how these different approaches are starting to be integrated together across scales,
to provide quantitative predictions and new conceptual frameworks to think about
the dynamics of cell renewal in complex tissues.
acknowledgement: "This work received funding from the ERC under the European Union’s
Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB.
C-M wants to acknowledge the support of the field of excellence Complexity of Life,
in Basic Research and Innovation of the University of Graz."
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis.
Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005
apa: Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of
mammalian gut homeostasis. Seminars in Cell & Developmental Biology.
Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005
chicago: Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics
of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology.
Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.
ieee: B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian
gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151.
Elsevier, pp. 58–65, 2023.
ista: Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian
gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.
mla: Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of
Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology,
vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.
short: B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology
150–151 (2023) 58–65.
date_created: 2023-01-12T12:09:47Z
date_published: 2023-12-02T00:00:00Z
date_updated: 2024-01-16T13:22:32Z
day: '02'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.semcdb.2022.11.005
ec_funded: 1
external_id:
isi:
- '001053522200001'
pmid:
- '36470715'
file:
- access_level: open_access
checksum: c619887cf130f4649bf3035417186004
content_type: application/pdf
creator: dernst
date_created: 2024-01-08T10:16:04Z
date_updated: 2024-01-08T10:16:04Z
file_id: '14741'
file_name: 2023_SeminarsCellDevBiology_CorominasMurtra.pdf
file_size: 1343750
relation: main_file
success: 1
file_date_updated: 2024-01-08T10:16:04Z
has_accepted_license: '1'
isi: 1
keyword:
- Cell Biology
- Developmental Biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 58-65
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Seminars in Cell & Developmental Biology
publication_identifier:
issn:
- 1084-9521
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modelling the dynamics of mammalian gut homeostasis
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: 150-151
year: '2023'
...
---
_id: '12163'
abstract:
- lang: eng
text: Small GTPases play essential roles in the organization of eukaryotic cells.
In recent years, it has become clear that their intracellular functions result
from intricate biochemical networks of the GTPase and their regulators that dynamically
bind to a membrane surface. Due to the inherent complexities of their interactions,
however, revealing the underlying mechanisms of action is often difficult to achieve
from in vivo studies. This review summarizes in vitro reconstitution approaches
developed to obtain a better mechanistic understanding of how small GTPase activities
are regulated in space and time.
acknowledgement: The authors acknowledge support from IST Austria and helpful comments
from the anonymous reviewers that helped to improve this manuscript. We apologize
to the authors of primary literature and outstanding research not cited here due
to space restraints.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: Hanifatul R
full_name: Budiman, Hanifatul R
id: 55380f95-15b2-11ec-abd3-aff8e230696b
last_name: Budiman
- first_name: Lukasz M
full_name: Kowalski, Lukasz M
id: e3a512e2-4bbe-11eb-a68a-e3857a7844c2
last_name: Kowalski
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
citation:
ama: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro
reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777.
doi:10.1002/1873-3468.14540
apa: Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic,
I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters.
Wiley. https://doi.org/10.1002/1873-3468.14540
chicago: Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz
M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.
ieee: M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic,
“In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol.
597, no. 6. Wiley, pp. 762–777, 2023.
ista: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In
vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.
mla: Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.
short: M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic,
FEBS Letters 597 (2023) 762–777.
date_created: 2023-01-12T12:09:58Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:32:29Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1002/1873-3468.14540
external_id:
isi:
- '000891573000001'
pmid:
- '36448231'
file:
- access_level: open_access
checksum: 7492244d3f9c5faa1347ef03f6e5bc84
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:31:04Z
date_updated: 2023-08-16T08:31:04Z
file_id: '14063'
file_name: 2023_FEBSLetters_Loose.pdf
file_size: 3148143
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:31:04Z
has_accepted_license: '1'
intvolume: ' 597'
isi: 1
issue: '6'
keyword:
- Cell Biology
- Genetics
- Molecular Biology
- Biochemistry
- Structural Biology
- Biophysics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 762-777
pmid: 1
publication: FEBS Letters
publication_identifier:
eissn:
- 1873-3468
issn:
- 0014-5793
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution of small GTPase regulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 597
year: '2023'
...
---
_id: '12164'
abstract:
- lang: eng
text: 'A shared-memory counter is a widely-used and well-studied concurrent object.
It supports two operations: An Inc operation that increases its value by 1 and
a Read operation that returns its current value. In Jayanti et al (SIAM J Comput,
30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case
step complexity of obstruction-free implementations, from read-write registers,
of a large class of shared objects that includes counters. The lower bound leaves
open the question of finding counter implementations with sub-linear amortized
step complexity. In this work, we address this gap. We show that n-process, wait-free
and linearizable counters can be implemented from read-write registers with O(log2n)
amortized step complexity. This is the first counter algorithm from read-write
registers that provides sub-linear amortized step complexity in executions of
arbitrary length. Since a logarithmic lower bound on the amortized step complexity
of obstruction-free counter implementations exists, our upper bound is within
a logarithmic factor of the optimal. The worst-case step complexity of the construction
remains linear, which is optimal. This is obtained thanks to a new max register
construction with O(logn) amortized step complexity in executions of arbitrary
length in which the value stored in the register does not grow too quickly. We
then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel
[1] in which we “plug” our max register implementation to show that it remains
linearizable while achieving O(log2n) amortized step complexity.'
acknowledgement: A preliminary version of this work appeared in DISC’19. Mirza Ahad
Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes
and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported
by the Israel Science Foundation (Grants 380/18 and 1425/22).
article_processing_charge: No
article_type: original
author:
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Danny
full_name: Hendler, Danny
last_name: Hendler
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5
apa: Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived
counters with polylogarithmic amortized step complexity. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00439-5
chicago: Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers.
“Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.
ieee: M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with
polylogarithmic amortized step complexity,” Distributed Computing, vol.
36. Springer Nature, pp. 29–43, 2023.
ista: Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic
amortized step complexity. Distributed Computing. 36, 29–43.
mla: Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized
Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023,
pp. 29–43, doi:10.1007/s00446-022-00439-5.
short: M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023)
29–43.
date_created: 2023-01-12T12:10:08Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:39:36Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00446-022-00439-5
external_id:
isi:
- '000890138700001'
intvolume: ' 36'
isi: 1
keyword:
- Computational Theory and Mathematics
- Computer Networks and Communications
- Hardware and Architecture
- Theoretical Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://drops.dagstuhl.de/opus/volltexte/2019/11310/
month: '03'
oa: 1
oa_version: Preprint
page: 29-43
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived counters with polylogarithmic amortized step complexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12165'
abstract:
- lang: eng
text: It may come as a surprise that a phenomenon as ubiquitous and prominent as
the transition from laminar to turbulent flow has resisted combined efforts by
physicists, engineers and mathematicians, and remained unresolved for almost one
and a half centuries. In recent years, various studies have proposed analogies
to directed percolation, a well-known universality class in statistical mechanics,
which describes a non-equilibrium phase transition from a fluctuating active phase
into an absorbing state. It is this unlikely relation between the multiscale,
high-dimensional dynamics that signify the transition process in virtually all
flows of practical relevance, and the arguably most basic non-equilibrium phase
transition, that so far has mainly been the subject of model studies, which I
review in this Perspective.
article_processing_charge: No
article_type: original
author:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Hof B. Directed percolation and the transition to turbulence. Nature Reviews
Physics. 2023;5:62-72. doi:10.1038/s42254-022-00539-y
apa: Hof, B. (2023). Directed percolation and the transition to turbulence. Nature
Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-022-00539-y
chicago: Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature
Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-022-00539-y.
ieee: B. Hof, “Directed percolation and the transition to turbulence,” Nature
Reviews Physics, vol. 5. Springer Nature, pp. 62–72, 2023.
ista: Hof B. 2023. Directed percolation and the transition to turbulence. Nature
Reviews Physics. 5, 62–72.
mla: Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature
Reviews Physics, vol. 5, Springer Nature, 2023, pp. 62–72, doi:10.1038/s42254-022-00539-y.
short: B. Hof, Nature Reviews Physics 5 (2023) 62–72.
date_created: 2023-01-12T12:10:18Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T12:50:48Z
day: '01'
department:
- _id: BjHo
doi: 10.1038/s42254-022-00539-y
external_id:
isi:
- '000890148700002'
intvolume: ' 5'
isi: 1
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '01'
oa_version: None
page: 62-72
publication: Nature Reviews Physics
publication_identifier:
eissn:
- 2522-5820
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directed percolation and the transition to turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2023'
...
---
_id: '12172'
abstract:
- lang: eng
text: In industrial reactors and equipment, non-ideality is quite a common phenomenon
rather than an exception. These deviations from ideality impact the process's
overall efficiency and the effectiveness of the equipment. To recognize the associated
non-ideality, one needs to have enough understanding of the formulation of the
equations and in-depth knowledge of the residence time distribution (RTD) data
of real reactors. In the current work, step input and pulse input were used to
create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the
aforementioned configuration, experiments were run at various flow rates to validate
the developed characteristic equations. To produce RTD data, distilled water was
utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior
of tracer concentration exits age distribution, and cumulative fraction for each
setup and each input was plotted and experimental results were compared with perfect
behavior. Deviation of concentration exit age distribution and cumulative fractional
distribution from ideal behavior is more in pulse input as compared to a step
input. For ideal cases, the exit age distribution curve and cumulative fraction
curves are independent of the type of input. But a significant difference was
observed for the two cases, which may be due to non-measurable fluctuations in
volumetric flow rate, non-achievement of instant injection of tracer in case of
pulse input, and slight variations in the sampling period. Further, with increasing
flow rate, concentration, exit age, and cumulative fractional curves shifted upward,
and this behavior matches with the actual case.
article_processing_charge: No
article_type: original
author:
- first_name: Bushra
full_name: Khatoon, Bushra
last_name: Khatoon
- first_name: Shoaib
full_name: Kamil, Shoaib
id: 185a19af-dc7d-11ea-9b2f-8eb2201959e9
last_name: Kamil
- first_name: Hitesh
full_name: Babu, Hitesh
last_name: Babu
- first_name: M.
full_name: Siraj Alam, M.
last_name: Siraj Alam
citation:
ama: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade
CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part
1):40-47. doi:10.1016/j.matpr.2022.11.037'
apa: 'Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental
analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings.
Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037'
chicago: 'Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental
Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings.
Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.'
ieee: 'B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis
of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings,
vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.'
ista: 'Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of
Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part
1), 40–47.'
mla: 'Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step
and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier,
2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.'
short: 'B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings
78 (2023) 40–47.'
date_created: 2023-01-12T12:11:26Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-08-16T09:08:11Z
day: '20'
department:
- _id: BjHo
doi: 10.1016/j.matpr.2022.11.037
intvolume: ' 78'
issue: Part 1
keyword:
- General Medicine
language:
- iso: eng
month: '03'
oa_version: None
page: 40-47
publication: 'Materials Today: Proceedings'
publication_identifier:
issn:
- 2214-7853
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental analysis of Cascade CSTRs with step and pulse inputs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2023'
...
---
_id: '12183'
abstract:
- lang: eng
text: We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with
Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii
regime, with an optimal bound on the condensate depletion. Moreover, our lower
bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann
bracketing) a lower bound for the ground state energy of N bosons in a large box
[−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.
acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 is gratefully acknowledged.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions.
Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3
apa: Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann
boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3
chicago: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.
ieee: C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary
conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560,
2023.
ista: Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary
conditions. Annales Henri Poincare. 24, 1505–1560.
mla: Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann
Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature,
2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.
short: C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.
date_created: 2023-01-15T23:00:52Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-08-16T11:34:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00023-022-01252-3
ec_funded: 1
external_id:
arxiv:
- '2205.15284'
isi:
- '000910751800002'
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.15284
month: '05'
oa: 1
oa_version: Preprint
page: 1505-1560
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bose Gas in a box with Neumann boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12205'
abstract:
- lang: eng
text: "Background: This study seeks to evaluate the impact of breast cancer (BRCA)
gene status on tumor dissemination pattern, surgical outcome and survival in a
multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian
cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data
from 190 patients were gathered retrospectively. All patients had surgery at pOC
and at least one further rOC surgery at four European high-volume centers. Patients
were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut)
and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor
presentation, surgical outcome and survival data were analyzed between the two
groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years
younger and had significantly more tumor involvement upon diagnosis. Patients
with BRCAmut disease showed higher debulking rates at all stages. Multivariate
analysis showed that only patient age had significant predictive value for complete
tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated
with optimal debulking. Patients with BRCAmut disease showed significantly prolonged
overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged
in the BRCAmut group at all stages as well, reaching statistical significance
during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a
more aggressive course of disease with earlier onset and more extensive tumor
dissemination at pOC. However, surgical outcome and OS were significantly better
in patients with BRCAmut disease compared with patients with BRCAwt disease. We
therefore propose to consider BRCAmut status in regard to patient selection for
cytoreductive surgery, especially in rOC."
acknowledgement: "E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a
participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin
Berlin and the Berlin Institute of Health. This work was supported by European Commission’s
Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen
Access funding enabled and organized by Projekt DEAL."
article_processing_charge: No
article_type: original
author:
- first_name: Jacek
full_name: Glajzer, Jacek
last_name: Glajzer
- first_name: Dan Cacsire
full_name: Castillo-Tong, Dan Cacsire
last_name: Castillo-Tong
- first_name: Rolf
full_name: Richter, Rolf
last_name: Richter
- first_name: Ignace
full_name: Vergote, Ignace
last_name: Vergote
- first_name: Hagen
full_name: Kulbe, Hagen
last_name: Kulbe
- first_name: Adriaan
full_name: Vanderstichele, Adriaan
last_name: Vanderstichele
- first_name: Ilary
full_name: Ruscito, Ilary
last_name: Ruscito
- first_name: Fabian
full_name: Trillsch, Fabian
last_name: Trillsch
- first_name: Alexander
full_name: Mustea, Alexander
last_name: Mustea
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Charlie
full_name: Gourley, Charlie
last_name: Gourley
- first_name: Hani
full_name: Gabra, Hani
last_name: Gabra
- first_name: Eliane T.
full_name: Taube, Eliane T.
last_name: Taube
- first_name: Oliver
full_name: Dorigo, Oliver
last_name: Dorigo
- first_name: David
full_name: Horst, David
last_name: Horst
- first_name: Carlotta
full_name: Keunecke, Carlotta
last_name: Keunecke
- first_name: Joanna
full_name: Baum, Joanna
last_name: Baum
- first_name: Timothy
full_name: Angelotti, Timothy
last_name: Angelotti
- first_name: Jalid
full_name: Sehouli, Jalid
last_name: Sehouli
- first_name: Elena Ioana
full_name: Braicu, Elena Ioana
last_name: Braicu
citation:
ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status
on tumor dissemination pattern, surgical outcome and patient survival in primary
and recurrent high-grade serous ovarian cancer: A multicenter retrospective study
by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium.
Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3'
apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele,
A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome and patient survival in primary and recurrent high-grade
serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical
Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3'
chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote,
Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation
Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in
Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective
Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.”
Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.'
ieee: 'J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination
pattern, surgical outcome and patient survival in primary and recurrent high-grade
serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of
Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.'
ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele
A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET,
Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023.
Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
and patient survival in primary and recurrent high-grade serous ovarian cancer:
A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.'
mla: 'Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination
Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade
Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer
Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of
Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.'
short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele,
I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T.
Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I.
Braicu, Annals of Surgical Oncology 30 (2023) 35–45.
date_created: 2023-01-16T09:44:36Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-09-05T15:18:37Z
day: '01'
ddc:
- '610'
department:
- _id: JoDa
doi: 10.1245/s10434-022-12459-3
external_id:
isi:
- '000852125500006'
file:
- access_level: open_access
checksum: 36a1200e1011f4b2155a8041d0308f34
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T13:01:20Z
date_updated: 2023-02-02T13:01:20Z
file_id: '12490'
file_name: 2023_AnnalsSurgicalOncology_Glajzer.pdf
file_size: 365865
relation: main_file
success: 1
file_date_updated: 2023-02-02T13:01:20Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
keyword:
- Oncology
- Surgery
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 35-45
publication: Annals of Surgical Oncology
publication_identifier:
eissn:
- 1534-4681
issn:
- 1068-9265
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12115'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome
and patient survival in primary and recurrent high-grade serous ovarian cancer:
A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models
Prolong Survival (OCTIPS) consortium'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2023'
...
---
_id: '12287'
abstract:
- lang: eng
text: We present criteria for establishing a triangulation of a manifold. Given
a manifold M, a simplicial complex A, and a map H from the underlying space of
A to M, our criteria are presented in local coordinate charts for M, and ensure
that H is a homeomorphism. These criteria do not require a differentiable structure,
or even an explicit metric on M. No Delaunay property of A is assumed. The result
provides a triangulation guarantee for algorithms that construct a simplicial
complex by working in local coordinate patches. Because the criteria are easily
verified in such a setting, they are expected to be of general use.
acknowledgement: "This work has been funded by the European Research Council under
the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations
of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan
Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh
was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by
the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken
also received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian
Science Fund (FWF): M-3073. A part of the results described in this paper were presented
at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science
Fund (FWF)."
article_processing_charge: No
article_type: original
author:
- first_name: Jean-Daniel
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Ramsay
full_name: Dyer, Ramsay
last_name: Dyer
- first_name: Arijit
full_name: Ghosh, Arijit
last_name: Ghosh
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating
general manifolds. Discrete & Computational Geometry. 2023;69:156-191.
doi:10.1007/s00454-022-00431-7
apa: Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local
criteria for triangulating general manifolds. Discrete & Computational
Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7
chicago: Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken.
“Local Criteria for Triangulating General Manifolds.” Discrete & Computational
Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.
ieee: J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for
triangulating general manifolds,” Discrete & Computational Geometry,
vol. 69. Springer Nature, pp. 156–191, 2023.
ista: Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating
general manifolds. Discrete & Computational Geometry. 69, 156–191.
mla: Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.”
Discrete & Computational Geometry, vol. 69, Springer Nature, 2023,
pp. 156–91, doi:10.1007/s00454-022-00431-7.
short: J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational
Geometry 69 (2023) 156–191.
date_created: 2023-01-16T10:04:06Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T12:47:32Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-022-00431-7
ec_funded: 1
external_id:
isi:
- '000862193600001'
file:
- access_level: open_access
checksum: 46352e0ee71e460848f88685ca852681
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T11:01:10Z
date_updated: 2023-02-02T11:01:10Z
file_id: '12488'
file_name: 2023_DiscreteCompGeometry_Boissonnat.pdf
file_size: 582850
relation: main_file
success: 1
file_date_updated: 2023-02-02T11:01:10Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
keyword:
- Computational Theory and Mathematics
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Theoretical Computer Science
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 156-191
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local criteria for triangulating general manifolds
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: 69
year: '2023'
...
---
_id: '12313'
abstract:
- lang: eng
text: Let P be a nontorsion point on an elliptic curve defined over a number field
K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that
every term of the sequence of the Bn has a primitive divisor for n greater than
an effectively computable constant that we will explicitly compute. This constant
will depend only on the model defining the curve.
acknowledgement: "This paper is part of the author’s PhD thesis at Università of Pisa.
Moreover, this\r\nproject has received funding from the European Union’s Horizon
2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant
Agreement\r\nNo. 101034413. I thank the referee for many helpful comments."
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: Verzobio M. Some effectivity results for primitive divisors of elliptic divisibility
sequences. Pacific Journal of Mathematics. 2023;325(2):331-351. doi:10.2140/pjm.2023.325.331
apa: Verzobio, M. (2023). Some effectivity results for primitive divisors of elliptic
divisibility sequences. Pacific Journal of Mathematics. Mathematical Sciences
Publishers. https://doi.org/10.2140/pjm.2023.325.331
chicago: Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic
Divisibility Sequences.” Pacific Journal of Mathematics. Mathematical
Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.325.331.
ieee: M. Verzobio, “Some effectivity results for primitive divisors of elliptic
divisibility sequences,” Pacific Journal of Mathematics, vol. 325, no.
2. Mathematical Sciences Publishers, pp. 331–351, 2023.
ista: Verzobio M. 2023. Some effectivity results for primitive divisors of elliptic
divisibility sequences. Pacific Journal of Mathematics. 325(2), 331–351.
mla: Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic
Divisibility Sequences.” Pacific Journal of Mathematics, vol. 325, no.
2, Mathematical Sciences Publishers, 2023, pp. 331–51, doi:10.2140/pjm.2023.325.331.
short: M. Verzobio, Pacific Journal of Mathematics 325 (2023) 331–351.
date_created: 2023-01-16T11:46:19Z
date_published: 2023-11-03T00:00:00Z
date_updated: 2023-12-13T11:18:14Z
day: '03'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.2140/pjm.2023.325.331
ec_funded: 1
external_id:
arxiv:
- '2001.02987'
isi:
- '001104766900001'
file:
- access_level: open_access
checksum: b6218d16a72742d8bb38d6fc3c9bb8c6
content_type: application/pdf
creator: dernst
date_created: 2023-11-13T09:50:41Z
date_updated: 2023-11-13T09:50:41Z
file_id: '14525'
file_name: 2023_PacificJourMaths_Verzobio.pdf
file_size: 389897
relation: main_file
success: 1
file_date_updated: 2023-11-13T09:50:41Z
has_accepted_license: '1'
intvolume: ' 325'
isi: 1
issue: '2'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 331-351
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Pacific Journal of Mathematics
publication_identifier:
eissn:
- 0030-8730
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Some effectivity results for primitive divisors of elliptic divisibility sequences
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: 325
year: '2023'
...
---
_id: '12329'
abstract:
- lang: eng
text: In this article, we develop two independent and new approaches to model epidemic
spread in a network. Contrary to the most studied models, those developed here
allow for contacts with different probabilities of transmitting the disease (transmissibilities).
We then examine each of these models using some mean field type approximations.
The first model looks at the late-stage effects of an epidemic outbreak and allows
for the computation of the probability that a given vertex was infected. This
computation is based on a mean field approximation and only depends on the number
of contacts and their transmissibilities. This approach shares many similarities
with percolation models in networks. The second model we develop is a dynamic
model which we analyze using a mean field approximation which highly reduces the
dimensionality of the system. In particular, the original system which individually
analyses each vertex of the network is reduced to one with as many equations as
different transmissibilities. Perhaps the greatest contribution of this article
is the observation that, in both these models, the existence and size of an epidemic
outbreak are linked to the properties of a matrix which we call the R-matrix.
This is a generalization of the basic reproduction number which more precisely
characterizes the main routes of infection.
acknowledgement: Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira
1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through
the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.
article_number: '468'
article_processing_charge: No
article_type: original
author:
- first_name: Arturo
full_name: Gómez, Arturo
last_name: Gómez
- first_name: Goncalo
full_name: Oliveira, Goncalo
id: 58abbde8-f455-11eb-a497-98c8fd71b905
last_name: Oliveira
citation:
ama: Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific
Reports. 2023;13. doi:10.1038/s41598-022-19827-9
apa: Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on
networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9
chicago: Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling
on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9.
ieee: A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,”
Scientific Reports, vol. 13. Springer Nature, 2023.
ista: Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks.
Scientific Reports. 13, 468.
mla: Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on
Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.
short: A. Gómez, G. Oliveira, Scientific Reports 13 (2023).
date_created: 2023-01-22T23:00:55Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2023-08-01T12:31:40Z
day: '10'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1038/s41598-022-19827-9
external_id:
isi:
- '001003345000051'
file:
- access_level: open_access
checksum: a8b83739f4a951e83e0b2a778f03b327
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T07:53:23Z
date_updated: 2023-01-23T07:53:23Z
file_id: '12336'
file_name: 2023_ScientificReports_Gomez.pdf
file_size: 2167792
relation: main_file
success: 1
file_date_updated: 2023-01-23T07:53:23Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: New approaches to epidemic modeling on 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2023'
...
---
_id: '12330'
abstract:
- lang: eng
text: 'The design and implementation of efficient concurrent data structures has
seen significant attention. However, most of this work has focused on concurrent
data structures providing good worst-case guarantees, although, in real workloads,
objects are often accessed at different rates. Efficient distribution-adaptive
data structures, such as splay-trees, are known in the sequential case; however,
they often are hard to translate efficiently to the concurrent case. We investigate
distribution-adaptive concurrent data structures, and propose a new design called
the splay-list. At a high level, the splay-list is similar to a standard skip-list,
with the key distinction that the height of each element adapts dynamically to
its access rate: popular elements “move up,” whereas rarely-accessed elements
decrease in height. We show that the splay-list provides order-optimal amortized
complexity bounds for a subset of operations, while being amenable to efficient
concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity
for performance, and can outperform the only previously-known distribution-adaptive
concurrent design in certain workloads.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- 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: Alexandra
full_name: Drozdova, Alexandra
last_name: Drozdova
- first_name: Amirkeivan
full_name: Mohtashami, Amirkeivan
last_name: Mohtashami
citation:
ama: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive
concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x'
apa: 'Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The
splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-022-00441-x'
chicago: 'Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan
Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed
Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.'
ieee: 'V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list:
A distribution-adaptive concurrent skip-list,” Distributed Computing, vol.
36. Springer Nature, pp. 395–418, 2023.'
ista: 'Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list:
A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.'
mla: 'Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent
Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp.
395–418, doi:10.1007/s00446-022-00441-x.'
short: V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing
36 (2023) 395–418.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-07-22T14:06:00Z
day: '01'
department:
- _id: DaAl
doi: 10.1007/s00446-022-00441-x
external_id:
arxiv:
- '2008.01009'
isi:
- '000913424000001'
oaworkID:
- w4390499170
intvolume: ' 36'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2008.01009
month: '09'
oa: 1
oa_version: Preprint
oaworkID: 1
page: 395-418
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The splay-list: A distribution-adaptive concurrent skip-list'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '12331'
abstract:
- lang: eng
text: High carrier mobility is critical to improving thermoelectric performance
over a broad temperature range. However, traditional doping inevitably deteriorates
carrier mobility. Herein, we develop a strategy for fine tuning of defects to
improve carrier mobility. To begin, n-type PbTe is created by compensating for
the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering,
resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is
introduced to compensate for the remaining intrinsic Pb vacancies. We find that
excess Ag exhibits a dynamic doping process with increasing temperatures, increasing
both the carrier concentration and carrier mobility throughout a wide temperature
range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained
for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier
concentration suppresses the bipolar thermal conductivity at high temperatures.
The final step is using iodine to optimize the carrier concentration to ∼1019
cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of
∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings
demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance
carrier mobility and improve thermoelectric performance.
acknowledgement: The National Key Research and Development Program of China (2018YFA0702100),
the Basic Science Center Project of the National Natural Science Foundation of China
(51788104), the National Natural Science Foundation of China (51571007 and 51772012),
the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the
National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise
Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian
Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Siqi
full_name: Wang, Siqi
last_name: Wang
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Shulin
full_name: Bai, Shulin
last_name: Bai
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Yingcai
full_name: Zhu, Yingcai
last_name: Zhu
- first_name: Shaoping
full_name: Zhan, Shaoping
last_name: Zhan
- first_name: Junqing
full_name: Zheng, Junqing
last_name: Zheng
- first_name: Shuwei
full_name: Tang, Shuwei
last_name: Tang
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier
mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry
of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542
apa: Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023).
Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe. Chemistry of Materials. American Chemical Society.
https://doi.org/10.1021/acs.chemmater.2c03542
chicago: Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping
Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables
High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.”
Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.
ieee: S. Wang et al., “Fine tuning of defects enables high carrier mobility
and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials,
vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.
ista: Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023.
Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.
mla: Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and
Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials,
vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.
short: S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D.
Zhao, Chemistry of Materials 35 (2023) 755–763.
date_created: 2023-01-22T23:00:55Z
date_published: 2023-01-24T00:00:00Z
date_updated: 2023-08-14T12:57:44Z
day: '24'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acs.chemmater.2c03542
external_id:
isi:
- '000914749700001'
file:
- access_level: open_access
checksum: b21dca2aa7a80c068bc256bdd1fea9df
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T12:57:25Z
date_updated: 2023-08-14T12:57:25Z
file_id: '14055'
file_name: 2023_ChemistryMaterials_Wang.pdf
file_size: 2961043
relation: main_file
success: 1
file_date_updated: 2023-08-14T12:57:25Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 755-763
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Chemistry of Materials
publication_identifier:
eissn:
- 1520-5002
issn:
- 0897-4756
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fine tuning of defects enables high carrier mobility and enhanced thermoelectric
performance of n-type PbTe
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)
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...