---
_id: '14779'
abstract:
- lang: eng
text: The presence of a developed boundary layer decouples a glacier's response
from ambient conditions, suggesting that sensitivity to climate change is increased
by glacier retreat. To test this hypothesis, we explore six years of distributed
meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier
fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding
with notable frontal retreat, an observed switch from down‐glacier katabatic to
up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to
off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic
winds, sensible heat fluxes on the glacier are increasingly determined by the
conditions occurring outside the boundary layer of the glacier, sealing the glacier's
demise as the climate continues to warm and experience an increased frequency
of extreme summers.
acknowledgement: This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie
Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field
data by many parties since 2001, including those acknowledged for the cited works
on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg,
Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for
the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla)
and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision
and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem
and two anonymous reviewers whose comments have helped to improve the quality of
the manuscript.
article_number: e2023GL103043
article_processing_charge: No
article_type: original
author:
- first_name: Thomas E.
full_name: Shaw, Thomas E.
last_name: Shaw
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Michael
full_name: McCarthy, Michael
last_name: McCarthy
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Álvaro
full_name: Ayala, Álvaro
last_name: Ayala
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying
near‐surface boundary layer of a retreating alpine glacier. Geophysical Research
Letters. 2023;50(11). doi:10.1029/2023gl103043
apa: Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., & Pellicciotti,
F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier.
Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl103043
chicago: Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala,
and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating
Alpine Glacier.” Geophysical Research Letters. American Geophysical Union,
2023. https://doi.org/10.1029/2023gl103043.
ieee: T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti,
“The decaying near‐surface boundary layer of a retreating alpine glacier,” Geophysical
Research Letters, vol. 50, no. 11. American Geophysical Union, 2023.
ista: Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The
decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical
Research Letters. 50(11), e2023GL103043.
mla: Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating
Alpine Glacier.” Geophysical Research Letters, vol. 50, no. 11, e2023GL103043,
American Geophysical Union, 2023, doi:10.1029/2023gl103043.
short: T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical
Research Letters 50 (2023).
date_created: 2024-01-10T09:28:34Z
date_published: 2023-06-16T00:00:00Z
date_updated: 2024-01-16T08:42:36Z
day: '16'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1029/2023gl103043
external_id:
isi:
- '000999436400001'
file:
- access_level: open_access
checksum: 391a3005c95340a0ae129ce4fbdf2bae
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T08:35:02Z
date_updated: 2024-01-16T08:35:02Z
file_id: '14805'
file_name: 2023_GeophysicalResearchLetter_Shaw.pdf
file_size: 2529327
relation: main_file
success: 1
file_date_updated: 2024-01-16T08:35:02Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '11'
keyword:
- General Earth and Planetary Sciences
- Geophysics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Geophysical Research Letters
publication_identifier:
eissn:
- 1944-8007
issn:
- 0094-8276
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: The decaying near‐surface boundary layer of a retreating alpine glacier
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: 50
year: '2023'
...
---
_id: '14780'
abstract:
- lang: eng
text: In this paper, we study the eigenvalues and eigenvectors of the spiked invariant
multiplicative models when the randomness is from Haar matrices. We establish
the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩
for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence
rates. Moreover, we prove that the non-outlier eigenvalues stick with those of
the unspiked matrices and the non-outlier eigenvectors are delocalized. The results
also hold near the so-called BBP transition and for degenerate spikes. On one
hand, our results can be regarded as a refinement of the counterparts of [12]
under additional regularity conditions. On the other hand, they can be viewed
as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar
random matrix.
acknowledgement: The authors would like to thank the editor, the associated editor
and two anonymous referees for their many critical suggestions which have significantly
improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee
for many helpful discussions. The first author also wants to thank Hari Bercovici
for many useful comments. The first author is partially supported by National Science
Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant
“RMTBeyond” No. 101020331.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Xiucai
full_name: Ding, Xiucai
last_name: Ding
- first_name: Hong Chang
full_name: Ji, Hong Chang
id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d
last_name: Ji
citation:
ama: Ding X, Ji HC. Spiked multiplicative random matrices and principal components.
Stochastic Processes and their Applications. 2023;163:25-60. doi:10.1016/j.spa.2023.05.009
apa: Ding, X., & Ji, H. C. (2023). Spiked multiplicative random matrices and
principal components. Stochastic Processes and Their Applications. Elsevier.
https://doi.org/10.1016/j.spa.2023.05.009
chicago: Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices
and Principal Components.” Stochastic Processes and Their Applications.
Elsevier, 2023. https://doi.org/10.1016/j.spa.2023.05.009.
ieee: X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal
components,” Stochastic Processes and their Applications, vol. 163. Elsevier,
pp. 25–60, 2023.
ista: Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components.
Stochastic Processes and their Applications. 163, 25–60.
mla: Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and
Principal Components.” Stochastic Processes and Their Applications, vol.
163, Elsevier, 2023, pp. 25–60, doi:10.1016/j.spa.2023.05.009.
short: X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023)
25–60.
date_created: 2024-01-10T09:29:25Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2024-01-16T08:49:51Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1016/j.spa.2023.05.009
ec_funded: 1
external_id:
arxiv:
- '2302.13502'
isi:
- '001113615900001'
file:
- access_level: open_access
checksum: 46a708b0cd5569a73d0f3d6c3e0a44dc
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T08:47:31Z
date_updated: 2024-01-16T08:47:31Z
file_id: '14806'
file_name: 2023_StochasticProcAppl_Ding.pdf
file_size: 1870349
relation: main_file
success: 1
file_date_updated: 2024-01-16T08:47:31Z
has_accepted_license: '1'
intvolume: ' 163'
isi: 1
keyword:
- Applied Mathematics
- Modeling and Simulation
- Statistics and Probability
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 25-60
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Stochastic Processes and their Applications
publication_identifier:
eissn:
- 1879-209X
issn:
- 0304-4149
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Spiked multiplicative random matrices and principal components
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: 163
year: '2023'
...
---
_id: '14781'
abstract:
- lang: eng
text: Germ granules, condensates of phase-separated RNA and protein, are organelles
that are essential for germline development in different organisms. The patterning
of the granules and their relevance for germ cell fate are not fully understood.
Combining three-dimensional in vivo structural and functional analyses, we study
the dynamic spatial organization of molecules within zebrafish germ granules.
We find that the localization of RNA molecules to the periphery of the granules,
where ribosomes are localized, depends on translational activity at this location.
In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential
for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the
absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into
the granule interior, away from the ribosomes, a process that is correlated with
the loss of germ cell fate. These findings highlight the relevance of sub-granule
compartmentalization for post-transcriptional control and its importance for preserving
germ cell totipotency.
acknowledgement: We thank Celeste Brennecka for editing and Michal Reichman-Fried
for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt,
and Ines Sandbote for technical assistance. This work was supported by funding from
the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the
Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation
grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the
National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees
for insightful comments that helped improve the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Kim Joana
full_name: Westerich, Kim Joana
last_name: Westerich
- first_name: Katsiaryna
full_name: Tarbashevich, Katsiaryna
last_name: Tarbashevich
- first_name: Jan
full_name: Schick, Jan
last_name: Schick
- first_name: Antra
full_name: Gupta, Antra
last_name: Gupta
- first_name: Mingzhao
full_name: Zhu, Mingzhao
last_name: Zhu
- first_name: Kenneth
full_name: Hull, Kenneth
last_name: Hull
- first_name: Daniel
full_name: Romo, Daniel
last_name: Romo
- first_name: Dagmar
full_name: Zeuschner, Dagmar
last_name: Zeuschner
- first_name: Mohammad
full_name: Goudarzi, Mohammad
id: 3384113A-F248-11E8-B48F-1D18A9856A87
last_name: Goudarzi
- first_name: Theresa
full_name: Gross-Thebing, Theresa
last_name: Gross-Thebing
- first_name: Erez
full_name: Raz, Erez
last_name: Raz
citation:
ama: Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function
of RNA molecules within phase-separated condensates in zebrafish are controlled
by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009
apa: Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K.,
… Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated
condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2023.06.009
chicago: Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta,
Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function
of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled
by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.
ieee: K. J. Westerich et al., “Spatial organization and function of RNA molecules
within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental
Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.
ista: Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner
D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function
of RNA molecules within phase-separated condensates in zebrafish are controlled
by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.
mla: Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules
within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental
Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.
short: K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D.
Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell
58 (2023) 1578–1592.e5.
date_created: 2024-01-10T09:41:21Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2024-01-16T08:56:36Z
day: '11'
department:
- _id: Bio
doi: 10.1016/j.devcel.2023.06.009
external_id:
pmid:
- '37463577'
intvolume: ' 58'
issue: '17'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2023.07.09.548244
month: '09'
oa: 1
oa_version: Preprint
page: 1578-1592.e5
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Spatial organization and function of RNA molecules within phase-separated condensates
in zebrafish are controlled by Dnd1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2023'
...
---
_id: '14782'
abstract:
- lang: eng
text: The actin cortex is a complex cytoskeletal machinery that drives and responds
to changes in cell shape. It must generate or adapt to plasma membrane curvature
to facilitate diverse functions such as cell division, migration, and phagocytosis.
Due to the complex molecular makeup of the actin cortex, it remains unclear whether
actin networks are inherently able to sense and generate membrane curvature, or
whether they rely on their diverse binding partners to accomplish this. Here,
we show that curvature sensing is an inherent capability of branched actin networks
nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside
giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface
of the GUV membrane. We show that actin forms a uniform and thin cortical layer
when present at high concentration and distinct patches associated with negative
membrane curvature at low concentration. Serendipitously, we find that the GUV
production method also produces dumbbell-shaped GUVs, which we explain using mathematical
modeling in terms of membrane hemifusion of nested GUVs. We find that branched
actin networks preferentially assemble at the neck of the dumbbells, which possess
a micrometer-range convex curvature comparable with the curvature of the actin
patches found in spherical GUVs. Minimal branched actin networks can thus sense
membrane curvature, which may help mammalian cells to robustly recruit actin to
curved membranes to facilitate diverse cellular functions such as cytokinesis
and migration.
acknowledgement: We thank Jeffrey den Haan for protein purification, Kristina Ganzinger
(AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago)
for the CP constructs, and Michael Way (Crick Institute) for providing purified
human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation
experiments that formed the basis for establishing the eDICE method, to Federico
Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE,
and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling.
Lennard van Buren is thanked for his help with image analysis to quantify actin
concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform
pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with
the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher
for insightful and inspiring discussions. We acknowledge financial support from
The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program
Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding
from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lucia
full_name: Baldauf, Lucia
last_name: Baldauf
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
- first_name: Marcos
full_name: Arribas Perez, Marcos
last_name: Arribas Perez
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
citation:
ama: Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin
cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal.
2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018
apa: Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G.
H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature.
Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018
chicago: Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje
H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane
Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018.
ieee: L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink,
“Branched actin cortices reconstituted in vesicles sense membrane curvature,”
Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.
ista: Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched
actin cortices reconstituted in vesicles sense membrane curvature. Biophysical
Journal. 122(11), 2311–2324.
mla: Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense
Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023,
pp. 2311–24, doi:10.1016/j.bpj.2023.02.018.
short: L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical
Journal 122 (2023) 2311–2324.
date_created: 2024-01-10T09:45:48Z
date_published: 2023-06-06T00:00:00Z
date_updated: 2024-01-16T09:20:03Z
day: '06'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.bpj.2023.02.018
external_id:
isi:
- '001016792600001'
pmid:
- '36806830'
file:
- access_level: open_access
checksum: 70566e54cd95ea6df340909ad44c5cd5
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:09:29Z
date_updated: 2024-01-16T09:09:29Z
file_id: '14807'
file_name: 2023_BiophysicalJournal_Baldauf.pdf
file_size: 3285810
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:09:29Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 2311-2324
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BioSoftMatterGroup/actin-curvature-sensing
status: public
title: Branched actin cortices reconstituted in vesicles sense membrane curvature
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: 122
year: '2023'
...
---
_id: '14783'
abstract:
- lang: eng
text: Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic
astroglial processes and plays major roles in synaptic transmission. We have previously
found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent
glutamine release to sustain physiological synaptic transmissions and cognitiogns.
However, whether Cx43 is important for the release of synaptic vesicles, which
is a critical component of synaptic efficacy, remains unanswered. Here, using
transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate
whether and how astrocytes regulate the release of synaptic vesicles from hippocampal
synapses. We report that CA1 pyramidal neurons and their synapses develop normally
in the absence of astroglial Cx43. However, a significant impairment in synaptic
vesicle distribution and release dynamics were observed. In particular, the FM1-43
assays performed using two-photon live imaging and combined with multi-electrode
array stimulation in acute hippocampal slices, revealed a slower rate of synaptic
vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that
synaptic vesicle release probability was also reduced and is dependent on glutamine
supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for
Cx43 in regulating presynaptic functions by controlling the rate and probability
of synaptic vesicle release. Our findings further highlight the significance of
astroglial Cx43 in synaptic transmission and efficacy.
acknowledgement: 'This research was funded by grants from the European Research Council
(Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation
program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD)
to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career
development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie
Teillon for support with setting up the MEA system for the two-photon microscope.
We would also like to thank Tayfun Palaz for their technical assistance with the
EM preparations.'
article_number: '1133'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Oana
full_name: Chever, Oana
last_name: Chever
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
- first_name: Nicole
full_name: Quenech’du, Nicole
last_name: Quenech’du
- first_name: Pascal
full_name: Ezan, Pascal
last_name: Ezan
- first_name: Joachim H. R.
full_name: Lübke, Joachim H. R.
last_name: Lübke
- first_name: Nathalie
full_name: Rouach, Nathalie
last_name: Rouach
citation:
ama: Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates
synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133
apa: Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke,
J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle
release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133
chicago: Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du,
Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43
Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI,
2023. https://doi.org/10.3390/cells12081133.
ieee: G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle
release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.
ista: Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach
N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal
synapses. Cells. 12(8), 1133.
mla: Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle
Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023,
doi:10.3390/cells12081133.
short: G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke,
N. Rouach, Cells 12 (2023).
date_created: 2024-01-10T09:46:35Z
date_published: 2023-04-11T00:00:00Z
date_updated: 2024-01-16T09:29:35Z
day: '11'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/cells12081133
external_id:
isi:
- '000977445700001'
pmid:
- '37190042'
file:
- access_level: open_access
checksum: 6798cd75d8857976fbc58a43fd173d68
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:26:52Z
date_updated: 2024-01-16T09:26:52Z
file_id: '14808'
file_name: 2023_Cells_Cheung.pdf
file_size: 7931643
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:26:52Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
keyword:
- General Medicine
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cells
publication_identifier:
issn:
- 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses
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: 12
year: '2023'
...
---
_id: '14784'
abstract:
- lang: eng
text: The next steps of deep space exploration are manned missions to Moon and Mars.
For safe space missions for crew members, it is important to understand the impact
of space flight on the immune system. We studied the effects of 21 days dry immersion
(DI) exposure on the transcriptomes of T cells isolated from blood samples of
eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14,
and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed
transcriptional alterations across all time points, with most changes occurring
14 days after DI exposure. At day 21, T cells showed evidence of adaptation with
a transcriptional profile resembling that of 7 days before DI. At 7 days after
DI, T cells again changed their transcriptional profile. These data suggest that
T cells adapt by rewiring their transcriptomes in response to simulated weightlessness
and that remodeling cues persist when reexposed to normal gravity.
acknowledgement: This work was supported by a postdoctoral fellowship from the Swedish
Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W.,
a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from
Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the
program of fundamental research (theme 65.1) of the Institute for Biomedical Problems
of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K.,
D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research
Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB)
to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National
Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation,
and Karolinska Institutet to L.S.W.
article_number: adg1610
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlos J.
full_name: Gallardo-Dodd, Carlos J.
last_name: Gallardo-Dodd
- first_name: Christian
full_name: Oertlin, Christian
last_name: Oertlin
- first_name: Julien
full_name: Record, Julien
last_name: Record
- first_name: Rômulo G.
full_name: Galvani, Rômulo G.
last_name: Galvani
- first_name: Christian
full_name: Sommerauer, Christian
last_name: Sommerauer
- first_name: Nikolai V.
full_name: Kuznetsov, Nikolai V.
last_name: Kuznetsov
- first_name: Evangelos
full_name: Doukoumopoulos, Evangelos
last_name: Doukoumopoulos
- first_name: Liaqat
full_name: Ali, Liaqat
last_name: Ali
- first_name: Mariana M. S.
full_name: Oliveira, Mariana M. S.
last_name: Oliveira
- first_name: Christina
full_name: Seitz, Christina
last_name: Seitz
- first_name: Mathias
full_name: Percipalle, Mathias
id: 45adb726-eb97-11eb-a6c2-c7c3d3caabe9
last_name: Percipalle
- first_name: Tijana
full_name: Nikić, Tijana
last_name: Nikić
- first_name: Anastasia A.
full_name: Sadova, Anastasia A.
last_name: Sadova
- first_name: Sofia M.
full_name: Shulgina, Sofia M.
last_name: Shulgina
- first_name: Vjacheslav A.
full_name: Shmarov, Vjacheslav A.
last_name: Shmarov
- first_name: Olga V.
full_name: Kutko, Olga V.
last_name: Kutko
- first_name: Daria D.
full_name: Vlasova, Daria D.
last_name: Vlasova
- first_name: Kseniya D.
full_name: Orlova, Kseniya D.
last_name: Orlova
- first_name: Marina P.
full_name: Rykova, Marina P.
last_name: Rykova
- first_name: John
full_name: Andersson, John
last_name: Andersson
- first_name: Piergiorgio
full_name: Percipalle, Piergiorgio
last_name: Percipalle
- first_name: Claudia
full_name: Kutter, Claudia
last_name: Kutter
- first_name: Sergey A.
full_name: Ponomarev, Sergey A.
last_name: Ponomarev
- first_name: Lisa S.
full_name: Westerberg, Lisa S.
last_name: Westerberg
citation:
ama: Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity
by dry immersion bed over 21 days results in gene expression changes and adaptation
of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610
apa: Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer,
C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity
by dry immersion bed over 21 days results in gene expression changes and adaptation
of T cells. Science Advances. American Association for the Advancement
of Science. https://doi.org/10.1126/sciadv.adg1610
chicago: Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani,
Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure
of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene
Expression Changes and Adaptation of T Cells.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.
ieee: C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity
by dry immersion bed over 21 days results in gene expression changes and adaptation
of T cells,” Science Advances, vol. 9, no. 34. American Association for
the Advancement of Science, 2023.
ista: Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov
NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova
AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson
J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers
to microgravity by dry immersion bed over 21 days results in gene expression changes
and adaptation of T cells. Science Advances. 9(34), adg1610.
mla: Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by
Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation
of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association
for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.
short: C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V.
Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle,
T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova,
K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev,
L.S. Westerberg, Science Advances 9 (2023).
date_created: 2024-01-10T09:48:01Z
date_published: 2023-08-25T00:00:00Z
date_updated: 2024-01-16T09:38:58Z
day: '25'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1126/sciadv.adg1610
external_id:
isi:
- '001054596800007'
pmid:
- '37624890'
file:
- access_level: open_access
checksum: b9072e20e2d5d9d34d2c53319bafee41
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:35:28Z
date_updated: 2024-01-16T09:35:28Z
file_id: '14809'
file_name: 2023_ScienceAdvances_GallardoDodd.pdf
file_size: 1596639
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:35:28Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '34'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Exposure of volunteers to microgravity by dry immersion bed over 21 days results
in gene expression changes and adaptation of T 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: 9
year: '2023'
...
---
_id: '14785'
abstract:
- lang: eng
text: Small cryptic plasmids have no clear effect on the host fitness and their
functional repertoire remains obscure. The naturally competent cyanobacterium
Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their
evolution with this species is supported by horizontal transfer remains understudied.
Here, we show that the small cryptic plasmid DNA is transferred in the population
exclusively by natural transformation, where the transfer frequency of plasmid‐encoded
genes is similar to that of chromosome‐encoded genes. Establishing a system to
follow gene transfer, we compared the transfer frequency of genes encoded in cryptic
plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations
of two Synechocystis sp. PCC 6803 labtypes (termed
Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends
on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake
in the Sevilla labtype ranged among the lowest detected transfer rates in our
experiments. Our study indicates that horizontal DNA transfer via natural transformation
is frequent in the evolution of small cryptic plasmids that reside in naturally
competent organisms. Furthermore, we suggest that the contribution of natural
transformation to cryptic plasmid persistence in Synechocystis is limited.
acknowledgement: "We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla,
Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab
of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful
discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann,
FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National
Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft,
Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber:
101043835"
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Fabian
full_name: Nies, Fabian
last_name: Nies
- first_name: Tanita
full_name: Wein, Tanita
last_name: Wein
- first_name: Dustin M.
full_name: Hanke, Dustin M.
last_name: Hanke
- first_name: Benjamin L
full_name: Springstein, Benjamin L
id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083
last_name: Springstein
orcid: 0000-0002-3461-5391
- first_name: Jaime
full_name: Alcorta, Jaime
last_name: Alcorta
- first_name: Claudia
full_name: Taubenheim, Claudia
last_name: Taubenheim
- first_name: Tal
full_name: Dagan, Tal
last_name: Dagan
citation:
ama: Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution
of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology
Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203
apa: Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim,
C., & Dagan, T. (2023). Role of natural transformation in the evolution of
small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology
Reports. Wiley. https://doi.org/10.1111/1758-2229.13203
chicago: Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime
Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in
the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental
Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203.
ieee: F. Nies et al., “Role of natural transformation in the evolution of
small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology
Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023.
ista: Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T.
2023. Role of natural transformation in the evolution of small cryptic plasmids
in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.
mla: Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small
Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology
Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.
short: F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim,
T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.
date_created: 2024-01-10T10:41:07Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-16T09:46:12Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1111/1758-2229.13203
external_id:
isi:
- '001080203100001'
pmid:
- '37794696'
file:
- access_level: open_access
checksum: d09ebb68fee61f4e2e09ec286c9cf1d3
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:42:10Z
date_updated: 2024-01-16T09:42:10Z
file_id: '14810'
file_name: 2023_EnvirMicroBiolReports_Nies.pdf
file_size: 1518350
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:42:10Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '6'
keyword:
- Agricultural and Biological Sciences (miscellaneous)
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 656-668
pmid: 1
publication: Environmental Microbiology Reports
publication_identifier:
eissn:
- 1758-2229
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Role of natural transformation in the evolution of small cryptic plasmids in
Synechocystis sp. PCC 6803
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14786'
abstract:
- lang: eng
text: Acanthocephalans, intestinal parasites of vertebrates, are characterised by
orders of magnitude higher metal accumulation than free-living organisms, but
the mechanism of such effective metal accumulation is still unknown. The aim of
our study was to gain new insights into the high-resolution localization of elements
in the bodies of acanthocephalans, thus taking an initial step towards elucidating
metal uptake and accumulation in organisms under real environmental conditions.
For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used
for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S,
Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis
receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite
of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the
same body parts were examined using transmission electron microscopy (TEM) and
correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS
confirmed higher accumulation in D. truttae than in the fish intestine. The chemical
composition of the acanthocephalan body showed the highest density of C, Ca, N,
Na, O, S, as important and constitutive elements in living cells in all studied
structures, while Fe was predominant among trace elements. In general, higher
element density was found in trunk spines and tegument, as body structures responsible
for substance absorption in parasites. The results obtained with NanoSIMS and
TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements
at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans
and generally provide a contribution for further application of this technique
in all parasite species.
acknowledgement: 'The authors thank the Czech Science Foundation (project No. 19-28399X)
and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to
the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure,
ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological
Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms
(Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.'
article_number: '164010'
article_processing_charge: No
article_type: original
author:
- first_name: Vlatka
full_name: Filipović Marijić, Vlatka
last_name: Filipović Marijić
- first_name: Maria Angels
full_name: Subirana, Maria Angels
last_name: Subirana
- first_name: Dirk
full_name: Schaumlöffel, Dirk
last_name: Schaumlöffel
- first_name: Josip
full_name: Barišić, Josip
last_name: Barišić
- first_name: Etienne
full_name: Gontier, Etienne
last_name: Gontier
- first_name: Nesrete
full_name: Krasnici, Nesrete
id: cb5852d4-287f-11ed-baf0-bc1dd2d5c745
last_name: Krasnici
- first_name: Tatjana
full_name: Mijošek, Tatjana
last_name: Mijošek
- first_name: Jesús S.
full_name: Hernández-Orts, Jesús S.
last_name: Hernández-Orts
- first_name: Tomáš
full_name: Scholz, Tomáš
last_name: Scholz
- first_name: Marijana
full_name: Erk, Marijana
last_name: Erk
citation:
ama: Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element
localisation in different body parts of the acanthocephalan Dentitruncus truttae
using TEM and NanoSIMS. Science of The Total Environment. 2023;887. doi:10.1016/j.scitotenv.2023.164010
apa: Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier,
E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different
body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS.
Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2023.164010
chicago: Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip
Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts,
Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different
Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.”
Science of The Total Environment. Elsevier, 2023. https://doi.org/10.1016/j.scitotenv.2023.164010.
ieee: V. Filipović Marijić et al., “First insight in element localisation
in different body parts of the acanthocephalan Dentitruncus truttae using TEM
and NanoSIMS,” Science of The Total Environment, vol. 887. Elsevier, 2023.
ista: Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici
N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element
localisation in different body parts of the acanthocephalan Dentitruncus truttae
using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.
mla: Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in
Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and
NanoSIMS.” Science of The Total Environment, vol. 887, 164010, Elsevier,
2023, doi:10.1016/j.scitotenv.2023.164010.
short: V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier,
N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The
Total Environment 887 (2023).
date_created: 2024-01-10T10:43:08Z
date_published: 2023-08-20T00:00:00Z
date_updated: 2024-01-16T10:04:57Z
day: '20'
department:
- _id: LifeSc
doi: 10.1016/j.scitotenv.2023.164010
external_id:
isi:
- '001002645100001'
pmid:
- '37169189'
intvolume: ' 887'
isi: 1
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: First insight in element localisation in different body parts of the acanthocephalan
Dentitruncus truttae using TEM and NanoSIMS
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 887
year: '2023'
...
---
_id: '14787'
abstract:
- lang: eng
text: Understanding the phenotypic and genetic architecture of reproductive isolation
is a long‐standing goal of speciation research. In several systems, large‐effect
loci contributing to barrier phenotypes have been characterized, but such causal
connections are rarely known for more complex genetic architectures. In this study,
we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward
an integrated understanding of speciation across a monkeyflower hybrid zone. Previous
work suggests that pollinator visitation acts as a primary barrier to gene flow
between two divergent red‐ and yellow‐flowered ecotypes ofMimulus
aurantiacus. Several candidate isolating traits and anonymous single
nucleotide polymorphism loci under divergent selection have been identified, but
their genomic positions remain unknown. Here, we report findings from demographic
analyses that indicate this hybrid zone formed by secondary contact, but that
subsequent gene flow was restricted by widespread barrier loci across the genome.
Using a novel, geographic cline‐based genome scan, we demonstrate that candidate
barrier loci are broadly distributed across the genome, rather than mapping to
one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals
that most floral traits are highly polygenic, with little evidence that QTL colocalize,
indicating that most traits are genetically independent. Finally, we find little
evidence that QTL and candidate barrier loci overlap, suggesting that some loci
contribute to other forms of reproductive isolation. Our findings highlight the
challenges of understanding the genetic architecture of reproductive isolation
and reveal that barriers to gene flow other than pollinator isolation may play
an important role in this system.
acknowledgement: We thank Julian Catchen for making modifications to Stacks to aid
this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and
Nicholas H. Barton provided advice, stimulating discussion and critical feedback.
The project was supported by National Science Foundation grant DEB-1258199.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Madeline A.
full_name: Chase, Madeline A.
last_name: Chase
- first_name: Hanna
full_name: McIntosh, Hanna
last_name: McIntosh
- first_name: Matthew A.
full_name: Streisfeld, Matthew A.
last_name: Streisfeld
citation:
ama: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and
bottom‐up approaches to understand the genetic architecture of speciation across
a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849
apa: Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023).
Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16849
chicago: Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld.
“Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture
of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley,
2023. https://doi.org/10.1111/mec.16849.
ieee: S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating
top‐down and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8.
Wiley, pp. 2041–2054, 2023.
ista: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down
and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.
mla: Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to
Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid
Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.
short: S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology
32 (2023) 2041–2054.
date_created: 2024-01-10T10:44:45Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2024-01-16T10:10:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.16849
external_id:
isi:
- '000919244600001'
pmid:
- '36651268'
intvolume: ' 32'
isi: 1
issue: '8'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.01.28.478139
month: '04'
oa: 1
oa_version: Preprint
page: 2041-2054
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '14788'
abstract:
- lang: eng
text: "Eukaryotic cells use clathrin-mediated endocytosis to take up a large range
of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma
membrane, but it remains controversial when and how it is remodeled into a spherical
vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise
geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal
sorting, we determine the average trajectory of clathrin remodeling during endocytosis.
We find that clathrin coats assemble first on flat membranes to 50% of the coat
area before they become rapidly and continuously bent, and this mechanism is confirmed
in three cell lines. We introduce the cooperative curvature model, which is based
on positive feedback for curvature generation. It accurately describes the measured
shapes and dynamics of the clathrin coat and could represent a general mechanism
for clathrin coat remodeling on the plasma membrane."
acknowledgement: We thank the entire Ries and Kaksonen labs for fruitful discussions
and support. This work was supported by the European Research Council (ERC CoG-724489
to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant
U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the
EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND
(Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund,
A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant
310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent
of the Miriam Berman Presidential Development Chair.
article_number: e202206038
article_processing_charge: No
article_type: original
author:
- first_name: Markus
full_name: Mund, Markus
last_name: Mund
- first_name: Aline
full_name: Tschanz, Aline
last_name: Tschanz
- first_name: Yu-Le
full_name: Wu, Yu-Le
last_name: Wu
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Johanna L.
full_name: Mehl, Johanna L.
last_name: Mehl
- first_name: Marko
full_name: Kaksonen, Marko
last_name: Kaksonen
- first_name: Ori
full_name: Avinoam, Ori
last_name: Avinoam
- first_name: Ulrich S.
full_name: Schwarz, Ulrich S.
last_name: Schwarz
- first_name: Jonas
full_name: Ries, Jonas
last_name: Ries
citation:
ama: Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and
subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3).
doi:10.1083/jcb.202206038
apa: Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., …
Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during
endocytosis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038
chicago: Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko
Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially
Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology.
Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.
ieee: M. Mund et al., “Clathrin coats partially preassemble and subsequently
bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller
University Press, 2023.
ista: Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz
US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during
endocytosis. Journal of Cell Biology. 222(3), e202206038.
mla: Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently
Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038,
Rockefeller University Press, 2023, doi:10.1083/jcb.202206038.
short: M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam,
U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).
date_created: 2024-01-10T10:45:55Z
date_published: 2023-02-03T00:00:00Z
date_updated: 2024-01-16T10:17:05Z
day: '03'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1083/jcb.202206038
external_id:
isi:
- '000978065000001'
pmid:
- '36734980'
file:
- access_level: open_access
checksum: 505d5cac36c14b073b68c7fed1a92bd3
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T10:15:09Z
date_updated: 2024-01-16T10:15:09Z
file_id: '14811'
file_name: 2023_JCB_Mund.pdf
file_size: 5678069
relation: main_file
success: 1
file_date_updated: 2024-01-16T10:15:09Z
has_accepted_license: '1'
intvolume: ' 222'
isi: 1
issue: '3'
keyword:
- Cell Biology
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
status: public
title: Clathrin coats partially preassemble and subsequently bend during endocytosis
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: 222
year: '2023'
...
---
_id: '14798'
abstract:
- lang: eng
text: 'A faithful reproduction of gloss is inherently difficult because of the limited
dynamic range, peak luminance, and 3D capabilities of display devices. This work
investigates how the display capabilities affect gloss appearance with respect
to a real-world reference object. To this end, we employ an accurate imaging pipeline
to achieve a perceptual gloss match between a virtual and real object presented
side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display,
which has not been previously attained to this extent. Based on this precise gloss
reproduction, we conduct a series of gloss matching experiments to study how gloss
perception degrades based on individual factors: object albedo, display luminance,
dynamic range, stereopsis, and tone mapping. We support the study with a detailed
analysis of individual factors, followed by an in-depth discussion on the observed
perceptual effects. Our experiments demonstrate that stereoscopic presentation
has a limited effect on the gloss matching task on our HDR display. However, both
reduced luminance and dynamic range of the display reduce the perceived gloss.
This means that the visual system cannot compensate for the changes in gloss appearance
across luminance (lack of gloss constancy), and the tone mapping operator should
be carefully selected when reproducing gloss on a low dynamic range (LDR) display.'
acknowledgement: "This work is supported by FWF Lise Meitner (Grant M 3319), Spanish
Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant
no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür
Yöntem for building the turntable for our experiment."
article_number: '90'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Akshay
full_name: Jindal, Akshay
last_name: Jindal
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Hans Peter
full_name: Seidel, Hans Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
- first_name: Rafał K.
full_name: Mantiuk, Rafał K.
last_name: Mantiuk
citation:
ama: 'Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on
the gloss consistency between real and virtual objects. In: Proceedings of
the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery; 2023.
doi:10.1145/3610548.3618226'
apa: 'Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., …
Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency
between real and virtual objects. In Proceedings of the SIGGRAPH Asia 2023
Conference. Sydney, Australia: Association for Computing Machinery. https://doi.org/10.1145/3610548.3618226'
chicago: Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel,
Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect
of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.”
In Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing
Machinery, 2023. https://doi.org/10.1145/3610548.3618226.
ieee: B. Chen et al., “The effect of display capabilities on the gloss consistency
between real and virtual objects,” in Proceedings of the SIGGRAPH Asia 2023
Conference, Sydney, Australia, 2023.
ista: 'Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano
A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency
between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference.
SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.'
mla: Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency
between Real and Virtual Objects.” Proceedings of the SIGGRAPH Asia 2023 Conference,
90, Association for Computing Machinery, 2023, doi:10.1145/3610548.3618226.
short: B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski,
A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference,
Association for Computing Machinery, 2023.
conference:
end_date: 2023-12-15
location: Sydney, Australia
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-12-12
date_created: 2024-01-14T23:00:57Z
date_published: 2023-12-10T00:00:00Z
date_updated: 2024-01-17T08:38:35Z
day: '10'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3610548.3618226
file:
- access_level: open_access
checksum: 8abe27432ed222b50d1af9b3388db1b0
content_type: application/pdf
creator: dernst
date_created: 2024-01-17T08:33:06Z
date_updated: 2024-01-17T08:33:06Z
file_id: '14823'
file_name: 2023_SA_Chen.pdf
file_size: 95967451
relation: main_file
success: 1
file_date_updated: 2024-01-17T08:33:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: Proceedings of the SIGGRAPH Asia 2023 Conference
publication_identifier:
isbn:
- '9798400703157'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: The effect of display capabilities on the gloss consistency between real and
virtual objects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14799'
abstract:
- lang: eng
text: "A round-robin study has been carried out to estimate the impact of the human
element in small-angle scattering data analysis. Four corrected datasets were
provided to participants ready for analysis. All datasets were measured on samples
containing spherical scatterers, with two datasets in dilute dispersions and two
from powders. Most of the 46 participants correctly identified the number of populations
in the dilute dispersions, with half of the population\r\nmean entries within
1.5% and half of the population width entries within 40%. Due to the added complexity
of the structure factor, far fewer people submitted answers on the powder datasets.
For those that did, half of the entries for the means and widths were within 44
and 86%, respectively. This round-robin experiment highlights several causes for
the discrepancies, for which solutions are proposed."
acknowledgement: "KT acknowledges the NIST–NRC postdoctoral fellowship program for
support. This work was partially funded through the European Metrology Programme
for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment,
instruments, materials or software are identified in this article in order to specify
the experimental procedure adequately. Such identification is not intended to imply
recommendation or endorsement by NIST, nor is it intended to imply that the materials
or equipment identified are necessarily the best available for the purpose. Open
access funding enabled and organized by Projekt DEAL."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Brian R.
full_name: Pauw, Brian R.
last_name: Pauw
- first_name: Glen J.
full_name: Smales, Glen J.
last_name: Smales
- first_name: Andy S.
full_name: Anker, Andy S.
last_name: Anker
- first_name: Venkatasamy
full_name: Annadurai, Venkatasamy
last_name: Annadurai
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Ralf
full_name: Bienert, Ralf
last_name: Bienert
- first_name: Wim G.
full_name: Bouwman, Wim G.
last_name: Bouwman
- first_name: Ingo
full_name: Breßler, Ingo
last_name: Breßler
- first_name: Joachim
full_name: Breternitz, Joachim
last_name: Breternitz
- first_name: Erik S.
full_name: Brok, Erik S.
last_name: Brok
- first_name: Gary
full_name: Bryant, Gary
last_name: Bryant
- first_name: Andrew J.
full_name: Clulow, Andrew J.
last_name: Clulow
- first_name: Erin R.
full_name: Crater, Erin R.
last_name: Crater
- first_name: Frédéric
full_name: De Geuser, Frédéric
last_name: De Geuser
- first_name: Alessandra Del
full_name: Giudice, Alessandra Del
last_name: Giudice
- first_name: Jérôme
full_name: Deumer, Jérôme
last_name: Deumer
- first_name: Sabrina
full_name: Disch, Sabrina
last_name: Disch
- first_name: Shankar
full_name: Dutt, Shankar
last_name: Dutt
- first_name: Kilian
full_name: Frank, Kilian
last_name: Frank
- first_name: Emiliano
full_name: Fratini, Emiliano
last_name: Fratini
- first_name: Paulo R.A.F.
full_name: Garcia, Paulo R.A.F.
last_name: Garcia
- first_name: Elliot P.
full_name: Gilbert, Elliot P.
last_name: Gilbert
- first_name: Marc B.
full_name: Hahn, Marc B.
last_name: Hahn
- first_name: James
full_name: Hallett, James
last_name: Hallett
- first_name: Max
full_name: Hohenschutz, Max
last_name: Hohenschutz
- first_name: Martin
full_name: Hollamby, Martin
last_name: Hollamby
- first_name: Steven
full_name: Huband, Steven
last_name: Huband
- first_name: Jan
full_name: Ilavsky, Jan
last_name: Ilavsky
- first_name: Johanna K.
full_name: Jochum, Johanna K.
last_name: Jochum
- first_name: Mikkel
full_name: Juelsholt, Mikkel
last_name: Juelsholt
- first_name: Bradley W.
full_name: Mansel, Bradley W.
last_name: Mansel
- first_name: Paavo
full_name: Penttilä, Paavo
last_name: Penttilä
- first_name: Rebecca K.
full_name: Pittkowski, Rebecca K.
last_name: Pittkowski
- first_name: Giuseppe
full_name: Portale, Giuseppe
last_name: Portale
- first_name: Lilo D.
full_name: Pozzo, Lilo D.
last_name: Pozzo
- first_name: Leonhard
full_name: Rochels, Leonhard
last_name: Rochels
- first_name: Julian M.
full_name: Rosalie, Julian M.
last_name: Rosalie
- first_name: Patrick E.J.
full_name: Saloga, Patrick E.J.
last_name: Saloga
- first_name: Susanne
full_name: Seibt, Susanne
last_name: Seibt
- first_name: Andrew J.
full_name: Smith, Andrew J.
last_name: Smith
- first_name: Gregory N.
full_name: Smith, Gregory N.
last_name: Smith
- first_name: Glenn A.
full_name: Spiering, Glenn A.
last_name: Spiering
- first_name: Tomasz M.
full_name: Stawski, Tomasz M.
last_name: Stawski
- first_name: Olivier
full_name: Taché, Olivier
last_name: Taché
- first_name: Andreas F.
full_name: Thünemann, Andreas F.
last_name: Thünemann
- first_name: Kristof
full_name: Toth, Kristof
last_name: Toth
- first_name: Andrew E.
full_name: Whitten, Andrew E.
last_name: Whitten
- first_name: Joachim
full_name: Wuttke, Joachim
last_name: Wuttke
citation:
ama: 'Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle
scattering data analysis round robin. Journal of Applied Crystallography.
2023;56(6):1618-1629. doi:10.1107/S1600576723008324'
apa: 'Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert,
R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering
data analysis round robin. Journal of Applied Crystallography. https://doi.org/10.1107/S1600576723008324'
chicago: 'Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai,
Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results
of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied
Crystallography, 2023. https://doi.org/10.1107/S1600576723008324.'
ieee: 'B. R. Pauw et al., “The human factor: Results of a small-angle scattering
data analysis round robin,” Journal of Applied Crystallography, vol. 56,
no. 6. pp. 1618–1629, 2023.'
ista: 'Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG,
Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F,
Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert
EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum
JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels
L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM,
Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results
of a small-angle scattering data analysis round robin. Journal of Applied Crystallography.
56(6), 1618–1629.'
mla: 'Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering
Data Analysis Round Robin.” Journal of Applied Crystallography, vol. 56,
no. 6, 2023, pp. 1618–29, doi:10.1107/S1600576723008324.'
short: B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert,
W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R.
Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E.
Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz,
M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P.
Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J.
Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché,
A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography
56 (2023) 1618–1629.
date_created: 2024-01-14T23:00:57Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-17T07:49:52Z
day: '01'
ddc:
- '540'
department:
- _id: LifeSc
doi: 10.1107/S1600576723008324
external_id:
arxiv:
- '2303.03772'
file:
- access_level: open_access
checksum: dab30d4556360f2cecf99f4b7efb0ee9
content_type: application/pdf
creator: dernst
date_created: 2024-01-17T07:47:35Z
date_updated: 2024-01-17T07:47:35Z
file_id: '14822'
file_name: 2023_JourApplCrystallography_Pauw.pdf
file_size: 2165864
relation: main_file
success: 1
file_date_updated: 2024-01-17T07:47:35Z
has_accepted_license: '1'
intvolume: ' 56'
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1618-1629
publication: Journal of Applied Crystallography
publication_identifier:
eissn:
- 1600-5767
issn:
- 0021-8898
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The human factor: Results of a small-angle scattering data analysis round
robin'
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: 56
year: '2023'
...
---
_id: '14812'
abstract:
- lang: eng
text: This repository contains the code and VCF files needed to conduct the analyses
in our MS. Each folder contains a readMe document explaining the nature of each
file and dataset and the results and analyses that they relate to. The same anlaysis
code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995'
apa: 'Stankowski, S. (2023). Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995'
chicago: 'Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.'
ieee: 'S. Stankowski, “Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails.” Zenodo, 2023.'
ista: 'Stankowski S. 2023. Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.'
mla: 'Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.'
short: S. Stankowski, (2023).
contributor:
- first_name: Zusanna
last_name: Zagrodzka
- first_name: Martin
last_name: Garlovsky
- first_name: Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Hila
id: d6ab5470-2fb3-11ed-8633-986a9b84edac
last_name: Lifchitz
- first_name: Alan
last_name: Le Moan
- first_name: Erica
last_name: Leder
- first_name: James
last_name: Reeve
- first_name: Kerstin
last_name: Johannesson
- first_name: Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
last_name: Butlin
date_created: 2024-01-16T10:23:01Z
date_published: 2023-09-05T00:00:00Z
date_updated: 2025-08-12T09:04:30Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8318995
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8318995
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14796'
relation: used_in_publication
status: for_moderation
status: public
title: 'Data and code for: The genetic architecture of a recent transition to live-bearing
in marine snails'
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14815'
abstract:
- lang: eng
text: In the last few years, various communication compression techniques have emerged
as an indispensable tool helping to alleviate the communication bottleneck in
distributed learning. However, despite the fact biased compressors often show
superior performance in practice when compared to the much more studied and understood
unbiased compressors, very little is known about them. In this work we study three
classes of biased compression operators, two of which are new, and their performance
when applied to (stochastic) gradient descent and distributed (stochastic) gradient
descent. We show for the first time that biased compressors can lead to linear
convergence rates both in the single node and distributed settings. We prove that
distributed compressed SGD method, employed with error feedback mechanism, enjoys
the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter
which grows when more compression is applied, L and μ are the smoothness and strong
convexity constants, C captures stochastic gradient noise (C=0 if full gradients
are computed on each node) and D captures the variance of the gradients at the
optimum (D=0 for over-parameterized models). Further, via a theoretical study
of several synthetic and empirical distributions of communicated gradients, we
shed light on why and by how much biased compressors outperform their unbiased
variants. Finally, we propose several new biased compressors with promising theoretical
guarantees and practical performance.
acknowledgement: 'The work in Sections 1-5 was conducted while A. Beznosikov was a
research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at
KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The
work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by
Ministry of Science and Higher Education grant No. 075-10-2021-068. '
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Aleksandr
full_name: Beznosikov, Aleksandr
last_name: Beznosikov
- first_name: Samuel
full_name: Horvath, Samuel
last_name: Horvath
- first_name: Peter
full_name: Richtarik, Peter
last_name: Richtarik
- first_name: Mher
full_name: Safaryan, Mher
id: dd546b39-0804-11ed-9c55-ef075c39778d
last_name: Safaryan
citation:
ama: Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for
distributed learning. Journal of Machine Learning Research. 2023;24:1-50.
apa: Beznosikov, A., Horvath, S., Richtarik, P., & Safaryan, M. (2023). On biased
compression for distributed learning. Journal of Machine Learning Research.
Journal of Machine Learning Research.
chicago: Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan.
“On Biased Compression for Distributed Learning.” Journal of Machine Learning
Research. Journal of Machine Learning Research, 2023.
ieee: A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression
for distributed learning,” Journal of Machine Learning Research, vol. 24.
Journal of Machine Learning Research, pp. 1–50, 2023.
ista: Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression
for distributed learning. Journal of Machine Learning Research. 24, 1–50.
mla: Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.”
Journal of Machine Learning Research, vol. 24, Journal of Machine Learning
Research, 2023, pp. 1–50.
short: A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine
Learning Research 24 (2023) 1–50.
date_created: 2024-01-16T12:13:36Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-17T09:14:13Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '2002.12410'
isi:
- '001111578500001'
file:
- access_level: open_access
checksum: c50f2b9db53938b755e30a085f464059
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T12:13:27Z
date_updated: 2024-01-16T12:13:27Z
file_id: '14816'
file_name: 2023_JMLR_Beznosikov.pdf
file_size: 1510993
relation: main_file
success: 1
file_date_updated: 2024-01-16T12:13:27Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1-50
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- 1533-7928
publication_status: published
publisher: Journal of Machine Learning Research
quality_controlled: '1'
status: public
title: On biased compression for distributed learning
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: 24
year: '2023'
...
---
_id: '14827'
abstract:
- lang: eng
text: Understanding complex living systems, which are fundamentally constrained
by physical phenomena, requires combining experimental data with theoretical physical
and mathematical models. To develop such models, collaborations between experimental
cell biologists and theoreticians are increasingly important but these two groups
often face challenges achieving mutual understanding. To help navigate these challenges,
this Perspective discusses different modelling approaches, including bottom-up
hypothesis-driven and top-down data-driven models, and highlights their strengths
and applications. Using cell mechanics as an example, we explore the integration
of specific physical models with experimental data from the molecular, cellular
and tissue level up to multiscale input. We also emphasize the importance of constraining
model complexity and outline strategies for crosstalk between experimental design
and model development. Furthermore, we highlight how physical models can provide
conceptual insights and produce unifying and generalizable frameworks for biological
phenomena. Overall, this Perspective aims to promote fruitful collaborations that
advance our understanding of complex biological systems.
acknowledgement: "We thank Prisca Liberali and Edouard Hannezo for many inspiring
discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical
reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3.
We would also like to thank The Company of Biologists for the opportunity to attend
the 2023 workshop on Collective Cell Migration, and all workshop participants for
discussions.\r\nC.S. was supported by a European Molecular Biology Organization
(EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program
(HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS
Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022)."
article_number: jcs.261515
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
citation:
ama: Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue
mechanics. Journal of Cell Science. 2023;136(24). doi:10.1242/jcs.261515
apa: Schwayer, C., & Brückner, D. (2023). Connecting theory and experiment in
cell and tissue mechanics. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.261515
chicago: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment
in Cell and Tissue Mechanics.” Journal of Cell Science. The Company of
Biologists, 2023. https://doi.org/10.1242/jcs.261515.
ieee: C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and
tissue mechanics,” Journal of Cell Science, vol. 136, no. 24. The Company
of Biologists, 2023.
ista: Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and
tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.
mla: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in
Cell and Tissue Mechanics.” Journal of Cell Science, vol. 136, no. 24,
jcs. 261515, The Company of Biologists, 2023, doi:10.1242/jcs.261515.
short: C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).
date_created: 2024-01-17T12:46:55Z
date_published: 2023-12-27T00:00:00Z
date_updated: 2024-01-22T13:35:48Z
day: '27'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1242/jcs.261515
external_id:
pmid:
- '38149871'
intvolume: ' 136'
issue: '24'
keyword:
- Cell Biology
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Connecting theory and experiment in cell and tissue mechanics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...
---
_id: '14829'
abstract:
- lang: eng
text: 'This paper explores a modular design architecture aimed at helping blockchains
(and other SMR implementation) to scale to a very large number of processes. This
comes in contrast to existing monolithic architectures that interleave transaction
dissemination, ordering, and execution in a single functionality. To achieve this
we first split the monolith to multiple layers which can use existing distributed
computing primitives. The exact specifications of the data dissemination part
are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction.
Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes”
information into the network and another that “pulls” this information. Regarding
the latter, there is a dearth of research literature which is rectified in this
paper. We present a family of pulling sub-protocols and rigorously analyze them.
Extensive simulations support the theoretical claims of efficiency and robustness
in case of a very large number of players. Finally, actual implementation and
deployment on a small number of machines (roughly the size of several industrial
systems) demonstrates the viability of the architecture’s paradigm.'
acknowledgement: 'This work is partially supported by Meta. Eleftherios Kokoris-Kogias
is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen
is supported by the Adams Fellowship Program of the Israel Academy of Sciences and
Humanities.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Shir
full_name: Cohen, Shir
last_name: Cohen
- first_name: Guy
full_name: Goren, Guy
last_name: Goren
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
citation:
ama: 'Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability
and retrieval in a modular blockchain architecture. In: 27th International
Conference on Financial Cryptography and Data Security. Vol 13951. Springer
Nature; 2023:36-53. doi:10.1007/978-3-031-47751-5_3'
apa: 'Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A.
(2023). Proof of availability and retrieval in a modular blockchain architecture.
In 27th International Conference on Financial Cryptography and Data Security
(Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47751-5_3'
chicago: Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and
Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain
Architecture.” In 27th International Conference on Financial Cryptography and
Data Security, 13951:36–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47751-5_3.
ieee: S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof
of availability and retrieval in a modular blockchain architecture,” in 27th
International Conference on Financial Cryptography and Data Security, Bol,
Brac, Croatia, 2023, vol. 13951, pp. 36–53.
ista: 'Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof
of availability and retrieval in a modular blockchain architecture. 27th International
Conference on Financial Cryptography and Data Security. FC: Financial Cryptography
and Data Security, LNCS, vol. 13951, 36–53.'
mla: Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain
Architecture.” 27th International Conference on Financial Cryptography and
Data Security, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:10.1007/978-3-031-47751-5_3.
short: S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th
International Conference on Financial Cryptography and Data Security, Springer
Nature, 2023, pp. 36–53.
conference:
end_date: 2023-05-05
location: Bol, Brac, Croatia
name: 'FC: Financial Cryptography and Data Security'
start_date: 2023-05-01
date_created: 2024-01-18T07:41:12Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-22T13:58:07Z
day: '01'
department:
- _id: ElKo
doi: 10.1007/978-3-031-47751-5_3
intvolume: ' 13951'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://fc23.ifca.ai/preproceedings/150.pdf
month: '12'
oa: 1
oa_version: Submitted Version
page: 36-53
project:
- _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f
grant_number: F8512
name: Secure Network and Hardware for Efficient Blockchains
publication: 27th International Conference on Financial Cryptography and Data Security
publication_identifier:
eisbn:
- '9783031477515'
eissn:
- 1611-3349
isbn:
- '9783031477508'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proof of availability and retrieval in a modular blockchain architecture
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13951
year: '2023'
...
---
_id: '14830'
abstract:
- lang: eng
text: We study the problem of learning controllers for discrete-time non-linear
stochastic dynamical systems with formal reach-avoid guarantees. This work presents
the first method for providing formal reach-avoid guarantees, which combine and
generalize stability and safety guarantees, with a tolerable probability threshold
p in [0,1] over the infinite time horizon. Our method leverages advances in machine
learning literature and it represents formal certificates as neural networks.
In particular, we learn a certificate in the form of a reach-avoid supermartingale
(RASM), a novel notion that we introduce in this work. Our RASMs provide reachability
and avoidance guarantees by imposing constraints on what can be viewed as a stochastic
extension of level sets of Lyapunov functions for deterministic systems. Our approach
solves several important problems -- it can be used to learn a control policy
from scratch, to verify a reach-avoid specification for a fixed control policy,
or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification.
We validate our approach on 3 stochastic non-linear reinforcement learning tasks.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, ERC
CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies
for stochastic systems with reach-avoid guarantees. In: Proceedings of the
37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the
Advancement of Artificial Intelligence; 2023:11926-11935. doi:10.1609/aaai.v37i10.26407'
apa: 'Zikelic, D., Lechner, M., Henzinger, T. A., & Chatterjee, K. (2023). Learning
control policies for stochastic systems with reach-avoid guarantees. In Proceedings
of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 11926–11935).
Washington, DC, United States: Association for the Advancement of Artificial Intelligence.
https://doi.org/10.1609/aaai.v37i10.26407'
chicago: Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee.
“Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.”
In Proceedings of the 37th AAAI Conference on Artificial Intelligence,
37:11926–35. Association for the Advancement of Artificial Intelligence, 2023.
https://doi.org/10.1609/aaai.v37i10.26407.
ieee: D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control
policies for stochastic systems with reach-avoid guarantees,” in Proceedings
of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United
States, 2023, vol. 37, no. 10, pp. 11926–11935.
ista: 'Zikelic D, Lechner M, Henzinger TA, Chatterjee K. 2023. Learning control
policies for stochastic systems with reach-avoid guarantees. Proceedings of the
37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial
Intelligence vol. 37, 11926–11935.'
mla: Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with
Reach-Avoid Guarantees.” Proceedings of the 37th AAAI Conference on Artificial
Intelligence, vol. 37, no. 10, Association for the Advancement of Artificial
Intelligence, 2023, pp. 11926–35, doi:10.1609/aaai.v37i10.26407.
short: D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, in:, Proceedings of
the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement
of Artificial Intelligence, 2023, pp. 11926–11935.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2024-01-18T07:44:31Z
date_published: 2023-06-26T00:00:00Z
date_updated: 2025-07-14T09:10:02Z
day: '26'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i10.26407
ec_funded: 1
external_id:
arxiv:
- '2210.05308'
intvolume: ' 37'
issue: '10'
keyword:
- General Medicine
language:
- iso: eng
month: '06'
oa_version: Preprint
page: 11926-11935
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
issn:
- 2159-5399
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
related_material:
record:
- id: '14600'
relation: earlier_version
status: public
status: public
title: Learning control policies for stochastic systems with reach-avoid guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14831'
abstract:
- lang: eng
text: Catalysis, the acceleration of product formation by a substance that is left
unchanged, typically results from multiple elementary processes, including diffusion
of the reactants toward the catalyst, chemical steps, and release of the products.
While efforts to design catalysts are often focused on accelerating the chemical
reaction on the catalyst, catalysis is a global property of the catalytic cycle
that involves all processes. These are controlled by both intrinsic parameters
such as the composition and shape of the catalyst and extrinsic parameters such
as the concentration of the chemical species at play. We examine here the conditions
that catalysis imposes on the different steps of a reaction cycle and the respective
role of intrinsic and extrinsic parameters of the system on the emergence of catalysis
by using an approach based on first-passage times. We illustrate this approach
for various decompositions of a catalytic cycle into elementary steps, including
non-Markovian decompositions, which are useful when the presence and nature of
intermediate states are a priori unknown. Our examples cover different types of
reactions and clarify the constraints on elementary steps and the impact of species
concentrations on catalysis.
acknowledgement: We acknowledge funding from ANR-22-CE06-0037-02. This work has received
funding from the European Unions Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie grant agreement No. 754387.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yann
full_name: Sakref, Yann
last_name: Sakref
- first_name: Maitane
full_name: Muñoz Basagoiti, Maitane
id: 1a8a7950-82cd-11ed-bd4f-9624c913a607
last_name: Muñoz Basagoiti
orcid: 0000-0003-1483-1457
- first_name: Zorana
full_name: Zeravcic, Zorana
last_name: Zeravcic
- first_name: Olivier
full_name: Rivoire, Olivier
last_name: Rivoire
citation:
ama: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627
apa: Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., & Rivoire, O. (2023). On
kinetic constraints that catalysis imposes on elementary processes. The Journal
of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627
chicago: Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire.
“On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The
Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627.
ieee: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints
that catalysis imposes on elementary processes,” The Journal of Physical Chemistry
B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.
ista: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 127(51), 10950–10959.
mla: Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary
Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American
Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627.
short: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical
Chemistry B 127 (2023) 10950–10959.
date_created: 2024-01-18T07:47:11Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2024-01-23T07:58:27Z
day: '13'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.3c04627
external_id:
arxiv:
- '2312.15940'
isi:
- '001134068000001'
intvolume: ' 127'
isi: 1
issue: '51'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2312.15940
month: '12'
oa: 1
oa_version: Preprint
page: 10950-10959
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: On kinetic constraints that catalysis imposes on elementary processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2023'
...
---
_id: '14833'
abstract:
- lang: eng
text: Understanding the factors that have shaped the current distributions and diversity
of species is a central and longstanding aim of evolutionary biology. The recent
inclusion of genomic data into phylogeographic studies has dramatically improved
our understanding in organisms where evolutionary relationships have been challenging
to infer. We used whole-genome sequences to study the phylogeography of the intertidal
snail Littorina saxatilis, which has successfully colonized and diversified across
a broad range of coastal environments in the Northern Hemisphere amid repeated
cycles of glaciation. Building on past studies based on short DNA sequences, we
used genome-wide data to provide a clearer picture of the relationships among
samples spanning most of the species natural range. Our results confirm the trans-Atlantic
colonization of North America from Europe, and have allowed us to identify rough
locations of glacial refugia and to infer likely routes of colonization within
Europe. We also investigated the signals in different datasets to account for
the effects of genomic architecture and non-neutral evolution, which provides
new insights about diversification of four ecotypes of L. saxatilis (the crab,
wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we
provide a much clearer picture of the biogeography of L. saxatilis, providing
a foundation for more detailed phylogenomic and demographic studies.
acknowledgement: Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and
Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen
kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development
of bioinformatic pipelines. The analysis of genomic data was conducted on the University
of Sheffield high-performance computing cluster, ShARC. Funding was provided by
the Natural Environment Research Council (NERC) and the European Research Council
(ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio
de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).
article_number: kzad002
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Zuzanna B
full_name: Zagrodzka, Zuzanna B
last_name: Zagrodzka
- first_name: Juan
full_name: Galindo, Juan
last_name: Galindo
- first_name: Mauricio
full_name: Montaño-Rendón, Mauricio
last_name: Montaño-Rendón
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Natalia
full_name: Mikhailova, Natalia
last_name: Mikhailova
- first_name: April M H
full_name: Blakeslee, April M H
last_name: Blakeslee
- first_name: Einar
full_name: Arnason, Einar
last_name: Arnason
- first_name: Thomas
full_name: Broquet, Thomas
last_name: Broquet
- first_name: Hernán E
full_name: Morales, Hernán E
last_name: Morales
- first_name: John W
full_name: Grahame, John W
last_name: Grahame
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
citation:
ama: Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of
the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean
Society. 2023;2(1). doi:10.1093/evolinnean/kzad002
apa: Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R.,
Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal
snail Littorina saxatilis. Evolutionary Journal of the Linnean Society.
Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002
chicago: Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón,
Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography
of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean
Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.
ieee: S. Stankowski et al., “Whole-genome phylogeography of the intertidal
snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society,
vol. 2, no. 1. Oxford University Press, 2023.
ista: Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova
N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson
K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina
saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.
mla: Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail
Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol.
2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.
short: S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N.
Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame,
A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean
Society 2 (2023).
date_created: 2024-01-18T07:54:10Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2024-01-23T08:13:43Z
day: '17'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolinnean/kzad002
file:
- access_level: open_access
checksum: ba6f9102d3a9fe6631c4fa398c5e4313
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:10:00Z
date_updated: 2024-01-23T08:10:00Z
file_id: '14875'
file_name: 2023_EvolJourLinneanSociety_Stankowski.pdf
file_size: 3408944
relation: main_file
success: 1
file_date_updated: 2024-01-23T08:10:00Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Evolutionary Journal of the Linnean Society
publication_identifier:
eissn:
- 2752-938X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Whole-genome phylogeography of the intertidal snail Littorina saxatilis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2023'
...
---
_id: '14835'
abstract:
- lang: ger
text: Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von
Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen.
Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β
Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung
und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der
aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern
starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von
Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche
sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen
Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten
Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung
der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen
Cross‐β‐Amyloidstruktur hervorgeht.
acknowledgement: Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen.
Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318
an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center
(ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural
Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural
Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität
Bordeaux.
article_number: e202219314
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- 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: Mélanie
full_name: Berbon, Mélanie
last_name: Berbon
- first_name: Alicia
full_name: Vallet, Alicia
last_name: Vallet
- first_name: Axelle
full_name: Grelard, Axelle
last_name: Grelard
- first_name: Estelle
full_name: Morvan, Estelle
last_name: Morvan
- first_name: Benjamin
full_name: Bardiaux, Benjamin
last_name: Bardiaux
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Antoine
full_name: Loquet, Antoine
last_name: Loquet
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche
von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen
Resten. Angewandte Chemie. 2023;135(19). doi:10.1002/ange.202219314
apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B.,
… Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen
– Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte
Chemie. Wiley. https://doi.org/10.1002/ange.202219314
chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle
Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet,
and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen
– Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte
Chemie. Wiley, 2023. https://doi.org/10.1002/ange.202219314.
ieee: L. M. Becker et al., “Der starre Kern und die flexible Oberfläche von
Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,”
Angewandte Chemie, vol. 135, no. 19. Wiley, 2023.
ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker
R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche
von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen
Resten. Angewandte Chemie. 135(19), e202219314.
mla: Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von
Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.”
Angewandte Chemie, vol. 135, no. 19, e202219314, Wiley, 2023, doi:10.1002/ange.202219314.
short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R.
Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).
date_created: 2024-01-18T10:01:01Z
date_published: 2023-05-02T00:00:00Z
date_updated: 2024-01-23T12:23:35Z
day: '02'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1002/ange.202219314
file:
- access_level: open_access
checksum: 98e68d370159f7be52a3d7c8a8ee1198
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:57:01Z
date_updated: 2024-01-23T08:57:01Z
file_id: '14876'
file_name: 2023_AngewChem_Becker.pdf
file_size: 1004676
relation: main_file
success: 1
file_date_updated: 2024-01-23T08:57:01Z
has_accepted_license: '1'
intvolume: ' 135'
issue: '19'
keyword:
- General Medicine
language:
- iso: ger
month: '05'
oa: 1
oa_version: Published Version
publication: Angewandte Chemie
publication_identifier:
eissn:
- 1521-3757
issn:
- 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning
NMR Spektroskopie von aromatischen Resten
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2023'
...