---
_id: '9813'
abstract:
- lang: eng
text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
S2 contains the code required for a stochastic simulation of the SLF system with
an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
material for Bodova et al., 2018.” Genetics Society of America, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.
mla: Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018.
Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-11T13:57:42Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
record:
- id: '316'
relation: used_in_publication
status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '5780'
abstract:
- lang: eng
text: Bioluminescence is found across the entire tree of life, conferring a spectacular
set of visually oriented functions from attracting mates to scaring off predators.
Half a dozen different luciferins, molecules that emit light when enzymatically
oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis
has been described in full, which is found only in bacteria. Here, we report identification
of the fungal luciferase and three other key enzymes that together form the biosynthetic
cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite.
Introduction of the identified genes into the genome of the yeast Pichia pastoris
along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent
in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis
cycle and found that fungal bioluminescence emerged through a series of events
that included two independent gene duplications. The retention of the duplicated
enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication
was followed by functional sequence divergence of enzymes of at least one gene
in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence
proceeded through several closely related stepping stone nonluminescent biochemical
reactions with adaptive roles. The availability of a complete eukaryotic luciferin
biosynthesis pathway provides several applications in biomedicine and bioengineering.
article_processing_charge: No
author:
- first_name: Alexey A.
full_name: Kotlobay, Alexey A.
last_name: Kotlobay
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Yuliana A.
full_name: Mokrushina, Yuliana A.
last_name: Mokrushina
- first_name: Marina
full_name: Marcet-Houben, Marina
last_name: Marcet-Houben
- first_name: Ekaterina O.
full_name: Serebrovskaya, Ekaterina O.
last_name: Serebrovskaya
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Andrey Y.
full_name: Gorokhovatsky, Andrey Y.
last_name: Gorokhovatsky
- first_name: Andrey
full_name: Vvedensky, Andrey
last_name: Vvedensky
- first_name: Konstantin V.
full_name: Purtov, Konstantin V.
last_name: Purtov
- first_name: Valentin N.
full_name: Petushkov, Valentin N.
last_name: Petushkov
- first_name: Natalja S.
full_name: Rodionova, Natalja S.
last_name: Rodionova
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Liliia
full_name: Fakhranurova, Liliia
last_name: Fakhranurova
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Rustam
full_name: Ziganshin, Rustam
last_name: Ziganshin
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Zinaida M.
full_name: Kaskova, Zinaida M.
last_name: Kaskova
- first_name: Victoria
full_name: Shender, Victoria
last_name: Shender
- first_name: Maxim
full_name: Abakumov, Maxim
last_name: Abakumov
- first_name: Tatiana O.
full_name: Abakumova, Tatiana O.
last_name: Abakumova
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Fedor M.
full_name: Eroshkin, Fedor M.
last_name: Eroshkin
- first_name: Andrey G.
full_name: Zaraisky, Andrey G.
last_name: Zaraisky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Tatiana Y.
full_name: Mitiouchkina, Tatiana Y.
last_name: Mitiouchkina
- first_name: Eugene P.
full_name: Kopantzev, Eugene P.
last_name: Kopantzev
- first_name: Hans E.
full_name: Waldenmaier, Hans E.
last_name: Waldenmaier
- first_name: Anderson G.
full_name: Oliveira, Anderson G.
last_name: Oliveira
- first_name: Yuichi
full_name: Oba, Yuichi
last_name: Oba
- first_name: Ekaterina
full_name: Barsova, Ekaterina
last_name: Barsova
- first_name: Ekaterina A.
full_name: Bogdanova, Ekaterina A.
last_name: Bogdanova
- first_name: Toni
full_name: Gabaldón, Toni
last_name: Gabaldón
- first_name: Cassius V.
full_name: Stevani, Cassius V.
last_name: Stevani
- first_name: Sergey
full_name: Lukyanov, Sergey
last_name: Lukyanov
- first_name: Ivan V.
full_name: Smirnov, Ivan V.
last_name: Smirnov
- first_name: Josef I.
full_name: Gitelson, Josef I.
last_name: Gitelson
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
citation:
ama: Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115
apa: Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya,
E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115
chicago: Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben,
Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et
al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.
ieee: A. A. Kotlobay et al., “Genetically encodable bioluminescent system
from fungi,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732,
2018.
ista: Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO,
Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov
VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova
AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin
FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier
HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov
S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable
bioluminescent system from fungi. Proceedings of the National Academy of Sciences
of the United States of America. 115(50), 12728–12732.
mla: Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from
Fungi.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32,
doi:10.1073/pnas.1803615115.
short: A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya,
N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov,
V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya,
R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova,
I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y.
Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova,
E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson,
F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences
of the United States of America 115 (2018) 12728–12732.
date_created: 2018-12-23T22:59:18Z
date_published: 2018-12-11T00:00:00Z
date_updated: 2023-09-11T14:04:05Z
day: '11'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1073/pnas.1803615115
external_id:
isi:
- '000452866000068'
file:
- access_level: open_access
checksum: 46b2c12185eb2ddb598f4c7b4bd267bf
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T15:21:40Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5926'
file_name: 2018_PNAS_Kotlobay.pdf
file_size: 1271988
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 12728-12732
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encodable bioluminescent system from fungi
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '428'
abstract:
- lang: eng
text: The plant hormone gibberellic acid (GA) is a crucial regulator of growth and
development. The main paradigm of GA signaling puts forward transcriptional regulation
via the degradation of DELLA transcriptional repressors. GA has also been shown
to regulate tropic responses by modulation of the plasma membrane incidence of
PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular
and molecular mechanisms by which GA redirects protein trafficking and thus regulates
cell surface functionality. Photoconvertible reporters revealed that GA balances
the protein traffic between the vacuole degradation route and recycling back to
the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple
cargos, including PIN proteins, whereas high GA levels promote their recycling
to the plasma membrane. This GA effect requires components of the retromer complex,
such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated
protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates
the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton
is essential for the GA effect on trafficking. This GA cellular action occurs
through DELLA proteins that regulate the MT and retromer presumably via their
interaction partners Prefoldins (PFDs). Our study identified a branching of the
GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating
transcription, also target by a nontranscriptional mechanism the retromer complex
acting at the intersection of the degradation and recycling trafficking routes.
By this mechanism, GA can redirect receptors and transporters to the cell surface,
thus coregulating multiple processes, including PIN-dependent auxin fluxes during
tropic responses.
acknowledgement: "We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular
y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and
Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology,
Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central
European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for
Science), and Y. Gu (Penn State University) for making available the materials used
in this study;\r\n...funding from the European Research Council (ERC) under the
European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement
282300.\r\nCC BY NC ND"
article_processing_charge: No
author:
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Kaori
full_name: Tabata, Kaori
id: 7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0
last_name: Tabata
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets
the retromer complex to redirect protein trafficking to the plasma membrane. PNAS.
2018;115(14):3716-3721. doi:10.1073/pnas.1721760115
apa: Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc,
M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex
to redirect protein trafficking to the plasma membrane. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1721760115
chicago: Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi
Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the
Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS.
National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.
ieee: Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer
complex to redirect protein trafficking to the plasma membrane,” PNAS,
vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.
ista: Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml
J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect
protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.
mla: Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer
Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS,
vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.
short: Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc,
J. Friml, PNAS 115 (2018) 3716–3721.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-04-03T00:00:00Z
date_updated: 2023-09-11T14:06:34Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1721760115
ec_funded: 1
external_id:
isi:
- '000429012500073'
file:
- access_level: open_access
checksum: 1fcf7223fb8f99559cfa80bd6f24ce44
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:30:14Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5700'
file_name: 2018_PNAS_Salanenka.pdf
file_size: 1924101
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: ' 3716 - 3721'
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7395'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gibberellin DELLA signaling targets the retromer complex to redirect protein
trafficking to the plasma membrane
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '62'
abstract:
- lang: eng
text: Imaging is a dominant strategy for data collection in neuroscience, yielding
stacks of images that often scale to gigabytes of data for a single experiment.
Machine learning algorithms from computer vision can serve as a pair of virtual
eyes that tirelessly processes these images, automatically detecting and identifying
microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction
of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual
clues and requires no training. This approach generalizes across different modalities,
including serially-sectioned scanning electron microscopy (sSEM) of genetically
labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe)
microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue
volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets,
demonstrating the high biological fidelity of the pipeline’s reconstructions.
FLoRIN reconstructions are of sufficient quality for preliminary biological study,
for example examining the distribution and morphology of cells or extracting single
axons from functional data. Compared to existing supervised learning methods,
FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions
that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.
acknowledgement: 'Equipment was generously donated by the NVIDIA Corporation, and
made available by the National Science Foundation (NSF) through grant #CNS-1629914.
This research used resources of the Argonne Leadership Computing Facility, which
is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.'
article_number: '14247'
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Shabazi, Ali
last_name: Shabazi
- first_name: Jeffery
full_name: Kinnison, Jeffery
last_name: Kinnison
- first_name: Rafael
full_name: Vescovi, Rafael
last_name: Vescovi
- first_name: Ming
full_name: Du, Ming
last_name: Du
- first_name: Robert
full_name: Hill, Robert
last_name: Hill
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Marc
full_name: Takeno, Marc
last_name: Takeno
- first_name: Hongkui
full_name: Zeng, Hongkui
last_name: Zeng
- first_name: Nuno
full_name: Da Costa, Nuno
last_name: Da Costa
- first_name: Jaime
full_name: Grutzendler, Jaime
last_name: Grutzendler
- first_name: Narayanan
full_name: Kasthuri, Narayanan
last_name: Kasthuri
- first_name: Walter
full_name: Scheirer, Walter
last_name: Scheirer
citation:
ama: Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation
and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3
apa: Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer,
W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3
chicago: Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian
A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018.
https://doi.org/10.1038/s41598-018-32628-3.
ieee: A. Shabazi et al., “Flexible learning-free segmentation and reconstruction
of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing
Group, 2018.
ista: Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H,
Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free
segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.
mla: Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing
Group, 2018, doi:10.1038/s41598-018-32628-3.
short: A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno,
H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports
8 (2018).
date_created: 2018-12-11T11:44:25Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2023-09-11T14:02:55Z
day: '24'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-018-32628-3
external_id:
isi:
- '000445336600015'
file:
- access_level: open_access
checksum: 1a14ae0666b82fbaa04bef110e3f6bf2
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:22:24Z
date_updated: 2020-07-14T12:47:24Z
file_id: '5699'
file_name: 2018_ScientificReports_Shahbazi.pdf
file_size: 4141645
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7992'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: http://doi.org/10.1038/s41598-018-36220-7
scopus_import: '1'
status: public
title: Flexible learning-free segmentation and reconstruction of neural volumes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '437'
abstract:
- lang: eng
text: Dendritic cells (DCs) are sentinels of the adaptive immune system that reside
in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation
and up-regulate the chemokine receptor CCR7 that guides them along gradients of
its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs
present peripherally acquired antigen to naïve T cells, thereby triggering adaptive
immunity.
acknowledged_ssus:
- _id: SSU
acknowledgement: "This work was supported by grants of the European Research Council
(ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific
support units at IST Austria for excellent technical support.\r\nWe thank the scientific
\ support units at IST Austria for excellent technical support. "
article_processing_charge: Yes (via OA deal)
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Hans
full_name: Haecker, Hans
last_name: Haecker
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast
and efficient genetic engineering of hematopoietic precursor cells for the study
of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077.
doi:10.1002/eji.201747358
apa: Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., &
Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor
cells for the study of dendritic cell migration. European Journal of Immunology.
Wiley-Blackwell. https://doi.org/10.1002/eji.201747358
chicago: Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild,
Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.
ieee: A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M.
K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells
for the study of dendritic cell migration,” European Journal of Immunology,
vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.
ista: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018.
Fast and efficient genetic engineering of hematopoietic precursor cells for the
study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.
mla: Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.
short: A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K.
Sixt, European Journal of Immunology 48 (2018) 1074–1077.
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-09-11T14:01:18Z
day: '13'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1002/eji.201747358
ec_funded: 1
external_id:
isi:
- '000434963700016'
file:
- access_level: open_access
checksum: 9d5b74cd016505aeb9a4c2d33bbedaeb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5044'
file_name: IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf
file_size: 590106
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1074 - 1077
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: European Journal of Immunology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7386'
pubrep_id: '1067'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and efficient genetic engineering of hematopoietic precursor cells for
the study of dendritic cell migration
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2018'
...
---
_id: '617'
abstract:
- lang: eng
text: Insects are exposed to a variety of potential pathogens in their environment,
many of which can severely impact fitness and health. Consequently, hosts have
evolved resistance and tolerance strategies to suppress or cope with infections.
Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads,
and hosts utilizing tolerance reduce harmful fitness effects per pathogen load.
To understand variation in, and selective pressures on, resistance and tolerance,
we asked to what degree they are shaped by host genetic background, whether plasticity
in these responses depends upon dietary environment, and whether there are interactions
between these two factors. Females from ten wild-type Drosophila melanogaster
genotypes were kept on high- or low-protein (yeast) diets and infected with one
of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila.
We measured host resistance as the inverse of bacterial load in the early infection
phase. The relationship (slope) between fly fecundity and individual-level bacteria
load provided our fecundity tolerance measure. Genotype and dietary yeast determined
host fecundity and strongly affected survival after infection with pathogenic
P. entomophila. There was considerable genetic variation in host resistance, a
commonly found phenomenon resulting from for example varying resistance costs
or frequency-dependent selection. Despite this variation and the reproductive
cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes.
The absence of genetic variation in tolerance may suggest that at this early infection
stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are
not expressed under these infection conditions.
acknowledgement: 'We would like to thank Susann Wicke for performing the genome-wide
SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara
Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical
help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the
Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for
their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG)
priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR
872/1-1). '
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival,
and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
2018;31(1):159-171. doi:10.1111/jeb.13211
apa: Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect
resistance, survival, and fecundity but not fecundity tolerance. Journal of
Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect
Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of
Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.
ieee: M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary
Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.
ista: Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
31(1), 159–171.
mla: Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity
but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31,
no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.
short: M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018)
159–171.
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T14:06:04Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/jeb.13211
external_id:
isi:
- '000419307000014'
pmid:
- '29150962'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13211
month: '01'
oa: 1
oa_version: Published Version
page: 159 - 171
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '7187'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genotype and diet affect resistance, survival, and fecundity but not fecundity
tolerance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 31
year: '2018'
...
---
_id: '5888'
abstract:
- lang: eng
text: "Despite the remarkable number of scientific breakthroughs of the last 100
years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum
disorder, intellectual disability) remains a great challenge. Recent advancements
in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists
to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given
the few hundred risk genes that have been discovered,\r\nthe etiological variability
and the heterogeneous clinical presentation, the need for genotype — along with
phenotype-\r\nbased diagnosis of individual patients has become a requisite. In
this review we look at recent advancements in\r\ngenomic analysis and their translation
into clinical practice."
article_number: '100'
article_processing_charge: No
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an
avenue to personalized medicine. Experimental & Molecular Medicine.
2018;50(8). doi:10.1038/s12276-018-0129-7'
apa: 'Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental
disorders: an avenue to personalized medicine. Experimental & Molecular
Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7'
chicago: 'Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental
Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular
Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.'
ieee: 'D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders:
an avenue to personalized medicine,” Experimental & Molecular Medicine,
vol. 50, no. 8. Springer Nature, 2018.'
ista: 'Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders:
an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8),
100.'
mla: 'Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental
Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular
Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.'
short: D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50
(2018).
date_created: 2019-01-27T22:59:11Z
date_published: 2018-08-07T00:00:00Z
date_updated: 2023-09-11T14:04:41Z
day: '07'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1038/s12276-018-0129-7
external_id:
isi:
- '000441266700006'
pmid:
- '30089840'
file:
- access_level: open_access
checksum: 4498301c8c53097c9a1a8ef990936eb5
content_type: application/pdf
creator: dernst
date_created: 2019-01-28T15:18:02Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5893'
file_name: 2018_EMM_Tarlungeanu.pdf
file_size: 1237482
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Experimental & Molecular Medicine
publication_identifier:
issn:
- 2092-6413
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomics in neurodevelopmental disorders: an avenue to personalized medicine'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '295'
abstract:
- lang: eng
text: We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional
anyon gas. Our bounds are extensive in the particle number, as for fermions, and
linear in the statistics parameter (Formula presented.). The lower bounds extend
to Lieb–Thirring inequalities for all anyons except bosons.
acknowledgement: Financial support from the Swedish Research Council, grant no. 2013-4734
(D. L.), the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No 694227, R. S.), and by
the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully
acknowledged.
article_processing_charge: No
author:
- first_name: Douglas
full_name: Lundholm, Douglas
last_name: Lundholm
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in
Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y
apa: Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons.
Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y
chicago: Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.”
Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y.
ieee: D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters
in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.
ista: Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters
in Mathematical Physics. 108(11), 2523–2541.
mla: Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.”
Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp.
2523–41, doi:10.1007/s11005-018-1091-y.
short: D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.
date_created: 2018-12-11T11:45:40Z
date_published: 2018-05-11T00:00:00Z
date_updated: 2023-09-11T14:01:57Z
day: '11'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-018-1091-y
ec_funded: 1
external_id:
arxiv:
- '1712.06218'
isi:
- '000446491500008'
file:
- access_level: open_access
checksum: 8beb9632fa41bbd19452f55f31286a31
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:14:17Z
date_updated: 2020-07-14T12:45:55Z
file_id: '5698'
file_name: 2018_LettMathPhys_Lundholm.pdf
file_size: 551996
relation: main_file
file_date_updated: 2020-07-14T12:45:55Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
issue: '11'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2523-2541
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '7586'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fermionic behavior of ideal anyons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 108
year: '2018'
...
---
_id: '555'
abstract:
- lang: eng
text: Conventional wisdom has it that proteins fold and assemble into definite structures,
and that this defines their function. Glycosaminoglycans (GAGs) are different.
In most cases the structures they form have a low degree of order, even when interacting
with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity,
charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich
matrices. By integrating soft matter physics concepts (e.g. polymer brushes and
phase separation) with our molecular understanding of GAG–protein interactions,
we can better comprehend how GAG-rich matrices assemble, what their properties
are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix
enveloping neurons — as a relevant example, we propose that microphase separation
determines the holey PNN anatomy that is pivotal to PNN functions.
acknowledgement: "This work was supported by the European Research Council [Starting
Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation
[MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering
and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1,
to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15,
to JCFK] and the European Union, the Operational Programme Research, Development
and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’
[CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis
Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on
GAG–protein interactions.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Ralf
full_name: Richter, Ralf
last_name: Richter
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Anthony
full_name: Day, Anthony
last_name: Day
- first_name: Jessica
full_name: Kwok, Jessica
last_name: Kwok
citation:
ama: 'Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets? Current Opinion in Structural Biology.
2018;50:65-74. doi:10.1016/j.sbi.2017.12.002'
apa: 'Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans
in extracellular matrix organisation: Are concepts from soft matter physics key
to understanding the formation of perineuronal nets? Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002'
chicago: 'Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans
in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key
to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural
Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.'
ieee: 'R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets?,” Current Opinion in Structural Biology,
vol. 50. Elsevier, pp. 65–74, 2018.'
ista: 'Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets? Current Opinion in Structural Biology. 50,
65–74.'
mla: 'Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation:
Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal
Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018,
pp. 65–74, doi:10.1016/j.sbi.2017.12.002.'
short: R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural
Biology 50 (2018) 65–74.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-11T14:07:03Z
day: '01'
department:
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doi: 10.1016/j.sbi.2017.12.002
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month: '06'
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page: 65 - 74
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '7259'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Glycosaminoglycans in extracellular matrix organisation: Are concepts from
soft matter physics key to understanding the formation of perineuronal nets?'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '448'
abstract:
- lang: eng
text: Around 150 million years ago, eusocial termites evolved from within the cockroaches,
50 million years before eusocial Hymenoptera, such as bees and ants, appeared.
Here, we report the 2-Gb genome of the German cockroach, Blattella germanica,
and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary
signatures of termite eusociality by comparing the genomes and transcriptomes
of three termites and the cockroach against the background of 16 other eusocial
and non-eusocial insects. Dramatic adaptive changes in genes underlying the production
and perception of pheromones confirm the importance of chemical communication
in the termites. These are accompanied by major changes in gene regulation and
the molecular evolution of caste determination. Many of these results parallel
molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific
solutions are remarkably different, thus revealing a striking case of convergence
in one of the major evolutionary transitions in biological complexity.
acknowledgement: We thank O. Niehuis for allowing use of the unpublished E. danica
genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J.
Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks
Charles Darwin University (Australia), especially S. Garnett and the Horticulture
and Aquaculture team, for providing logistic support to collect C. secundus. The
Parks and Wildlife Commission, Northern Territory, the Department of the Environment,
Water, Heritage and the Arts gave permission to collect (Permit number 36401) and
export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider
and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B.
J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and
M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251
and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds,
and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US
Department of Housing and Urban Development (NCHHU-0017-13), the National Science
Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National
Institute of Environmental Health Sciences (P30ES025128) to the Center for Human
Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported
by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).
article_processing_charge: No
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full_name: Harrison, Mark
last_name: Harrison
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Hugh
full_name: Robertson, Hugh
last_name: Robertson
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Tristan
full_name: Bitard Feildel, Tristan
last_name: Bitard Feildel
- first_name: Hsu
full_name: Chao, Hsu
last_name: Chao
- first_name: Christopher
full_name: Childers, Christopher
last_name: Childers
- first_name: Huyen
full_name: Dinh, Huyen
last_name: Dinh
- first_name: Harshavardhan
full_name: Doddapaneni, Harshavardhan
last_name: Doddapaneni
- first_name: Shannon
full_name: Dugan, Shannon
last_name: Dugan
- first_name: Johannes
full_name: Gowin, Johannes
last_name: Gowin
- first_name: Carolin
full_name: Greiner, Carolin
last_name: Greiner
- first_name: Yi
full_name: Han, Yi
last_name: Han
- first_name: Haofu
full_name: Hu, Haofu
last_name: Hu
- first_name: Daniel
full_name: Hughes, Daniel
last_name: Hughes
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Karsten
full_name: Kemena, Karsten
last_name: Kemena
- first_name: Lukas
full_name: Kremer, Lukas
last_name: Kremer
- first_name: Sandra
full_name: Lee, Sandra
last_name: Lee
- first_name: Alberto
full_name: López Ezquerra, Alberto
last_name: López Ezquerra
- first_name: Ludovic
full_name: Mallet, Ludovic
last_name: Mallet
- first_name: Jose
full_name: Monroy Kuhn, Jose
last_name: Monroy Kuhn
- first_name: Annabell
full_name: Moser, Annabell
last_name: Moser
- first_name: Shwetha
full_name: Murali, Shwetha
last_name: Murali
- first_name: Donna
full_name: Muzny, Donna
last_name: Muzny
- first_name: Saria
full_name: Otani, Saria
last_name: Otani
- first_name: Maria
full_name: Piulachs, Maria
last_name: Piulachs
- first_name: Monica
full_name: Poelchau, Monica
last_name: Poelchau
- first_name: Jiaxin
full_name: Qu, Jiaxin
last_name: Qu
- first_name: Florentine
full_name: Schaub, Florentine
last_name: Schaub
- first_name: Ayako
full_name: Wada Katsumata, Ayako
last_name: Wada Katsumata
- first_name: Kim
full_name: Worley, Kim
last_name: Worley
- first_name: Qiaolin
full_name: Xie, Qiaolin
last_name: Xie
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Michael
full_name: Poulsen, Michael
last_name: Poulsen
- first_name: Richard
full_name: Gibbs, Richard
last_name: Gibbs
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
citation:
ama: Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal
molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566.
doi:10.1038/s41559-017-0459-1
apa: Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T.,
Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular
basis of termite eusociality. Nature Ecology and Evolution. Springer Nature.
https://doi.org/10.1038/s41559-017-0459-1
chicago: Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan
Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes
Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution.
Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.
ieee: M. Harrison et al., “Hemimetabolous genomes reveal molecular basis
of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer
Nature, pp. 557–566, 2018.
ista: Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H,
Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes
D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy
Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub
F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards
S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular
basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.
mla: Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite
Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature,
2018, pp. 557–66, doi:10.1038/s41559-017-0459-1.
short: M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H.
Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y.
Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra,
L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs,
M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla,
M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer,
Nature Ecology and Evolution 2 (2018) 557–566.
date_created: 2018-12-11T11:46:32Z
date_published: 2018-02-05T00:00:00Z
date_updated: 2023-09-11T14:10:57Z
day: '05'
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doi: 10.1038/s41559-017-0459-1
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oa: 1
oa_version: Published Version
page: 557-566
publication: Nature Ecology and Evolution
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publisher: Springer Nature
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pubrep_id: '969'
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related_material:
record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Hemimetabolous genomes reveal molecular basis of termite eusociality
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
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volume: 2
year: '2018'
...
---
_id: '723'
abstract:
- lang: eng
text: Escaping local optima is one of the major obstacles to function optimisation.
Using the metaphor of a fitness landscape, local optima correspond to hills separated
by fitness valleys that have to be overcome. We define a class of fitness valleys
of tunable difficulty by considering their length, representing the Hamming path
between the two optima and their depth, the drop in fitness. For this function
class we present a runtime comparison between stochastic search algorithms using
different search strategies. The (1+1) EA is a simple and well-studied evolutionary
algorithm that has to jump across the valley to a point of higher fitness because
it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm
and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population
genetics, are both able to cross the fitness valley by accepting worsening moves.
We show that the runtime of the (1+1) EA depends critically on the length of the
valley while the runtimes of the non-elitist algorithms depend crucially on the
depth of the valley. Moreover, we show that both SSWM and Metropolis can also
efficiently optimise a rugged function consisting of consecutive valleys.
article_processing_charge: No
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape
local optima in black box optimisation when non elitism outperforms elitism. Algorithmica.
2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2
apa: Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B.
(2018). How to escape local optima in black box optimisation when non elitism
outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora
Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism
Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.
ieee: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How
to escape local optima in black box optimisation when non elitism outperforms
elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.
ista: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to
escape local optima in black box optimisation when non elitism outperforms elitism.
Algorithmica. 80(5), 1604–1633.
mla: Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation
When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer,
2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.
short: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica
80 (2018) 1604–1633.
date_created: 2018-12-11T11:48:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:11:35Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-017-0369-2
ec_funded: 1
external_id:
isi:
- '000428239300010'
file:
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checksum: 7d92f5d7be81e387edeec4f06442791c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:14Z
date_updated: 2020-07-14T12:47:54Z
file_id: '4674'
file_name: IST-2018-1014-v1+1_2018_Paixao_Escape.pdf
file_size: 691245
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file_date_updated: 2020-07-14T12:47:54Z
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issue: '5'
language:
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month: '05'
oa: 1
oa_version: Published Version
page: 1604 - 1633
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6957'
pubrep_id: '1014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to escape local optima in black box optimisation when non elitism outperforms
elitism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 80
year: '2018'
...
---
_id: '321'
abstract:
- lang: eng
text: The twelve papers in this special section focus on learning systems with shared
information for computer vision and multimedia communication analysis. In the
real world, a realistic setting for computer vision or multimedia recognition
problems is that we have some classes containing lots of training data and many
classes containing a small amount of training data. Therefore, how to use frequent
classes to help learning rare classes for which it is harder to collect the training
data is an open question. Learning with shared information is an emerging topic
in machine learning, computer vision and multimedia analysis. There are different
levels of components that can be shared during concept modeling and machine learning
stages, such as sharing generic object parts, sharing attributes, sharing transformations,
sharing regularization parameters and sharing training examples, etc. Regarding
the specific methods, multi-task learning, transfer learning and deep learning
can be seen as using different strategies to share information. These learning
with shared information methods are very effective in solving real-world large-scale
problems.
article_processing_charge: No
article_type: original
author:
- first_name: Trevor
full_name: Darrell, Trevor
last_name: Darrell
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Nico
full_name: Sebe, Nico
last_name: Sebe
- first_name: Ying
full_name: Wu, Ying
last_name: Wu
- first_name: Yan
full_name: Yan, Yan
last_name: Yan
citation:
ama: Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the
special section on learning with Shared information for computer vision and multimedia
analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence.
2018;40(5):1029-1031. doi:10.1109/TPAMI.2018.2804998
apa: Darrell, T., Lampert, C., Sebe, N., Wu, Y., & Yan, Y. (2018). Guest editors’
introduction to the special section on learning with Shared information for computer
vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine
Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2018.2804998
chicago: Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest
Editors’ Introduction to the Special Section on Learning with Shared Information
for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2018.2804998.
ieee: T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction
to the special section on learning with Shared information for computer vision
and multimedia analysis,” IEEE Transactions on Pattern Analysis and Machine
Intelligence, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.
ista: Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction
to the special section on learning with Shared information for computer vision
and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence.
40(5), 1029–1031.
mla: Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section
on Learning with Shared Information for Computer Vision and Multimedia Analysis.”
IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40,
no. 5, IEEE, 2018, pp. 1029–31, doi:10.1109/TPAMI.2018.2804998.
short: T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern
Analysis and Machine Intelligence 40 (2018) 1029–1031.
date_created: 2018-12-11T11:45:48Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:07:54Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1109/TPAMI.2018.2804998
external_id:
isi:
- '000428901200001'
file:
- access_level: open_access
checksum: b19c75da06faf3291a3ca47dfa50ef63
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:50:48Z
date_updated: 2020-07-14T12:46:03Z
file_id: '7835'
file_name: 2018_IEEE_Darrell.pdf
file_size: 141724
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has_accepted_license: '1'
intvolume: ' 40'
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language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1029 - 1031
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '7544'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guest editors' introduction to the special section on learning with Shared
information for computer vision and multimedia analysis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '9841'
abstract:
- lang: eng
text: Around 150 million years ago, eusocial termites evolved from within the cockroaches,
50 million years before eusocial Hymenoptera, such as bees and ants, appeared.
Here, we report the 2-Gb genome of the German cockroach, Blattella germanica,
and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary
signatures of termite eusociality by comparing the genomes and transcriptomes
of three termites and the cockroach against the background of 16 other eusocial
and non-eusocial insects. Dramatic adaptive changes in genes underlying the production
and perception of pheromones confirm the importance of chemical communication
in the termites. These are accompanied by major changes in gene regulation and
the molecular evolution of caste determination. Many of these results parallel
molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific
solutions are remarkably different, thus revealing a striking case of convergence
in one of the major evolutionary transitions in biological complexity.
article_processing_charge: No
author:
- first_name: Mark C.
full_name: Harrison, Mark C.
last_name: Harrison
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Hugh M.
full_name: Robertson, Hugh M.
last_name: Robertson
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Tristan
full_name: Bitard-Feildel, Tristan
last_name: Bitard-Feildel
- first_name: Hsu
full_name: Chao, Hsu
last_name: Chao
- first_name: Christopher P.
full_name: Childers, Christopher P.
last_name: Childers
- first_name: Huyen
full_name: Dinh, Huyen
last_name: Dinh
- first_name: Harshavardhan
full_name: Doddapaneni, Harshavardhan
last_name: Doddapaneni
- first_name: Shannon
full_name: Dugan, Shannon
last_name: Dugan
- first_name: Johannes
full_name: Gowin, Johannes
last_name: Gowin
- first_name: Carolin
full_name: Greiner, Carolin
last_name: Greiner
- first_name: Yi
full_name: Han, Yi
last_name: Han
- first_name: Haofu
full_name: Hu, Haofu
last_name: Hu
- first_name: Daniel S. T.
full_name: Hughes, Daniel S. T.
last_name: Hughes
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Lukas P. M.
full_name: Kremer, Lukas P. M.
last_name: Kremer
- first_name: Sandra L.
full_name: Lee, Sandra L.
last_name: Lee
- first_name: Alberto
full_name: Lopez-Ezquerra, Alberto
last_name: Lopez-Ezquerra
- first_name: Ludovic
full_name: Mallet, Ludovic
last_name: Mallet
- first_name: Jose M.
full_name: Monroy-Kuhn, Jose M.
last_name: Monroy-Kuhn
- first_name: Annabell
full_name: Moser, Annabell
last_name: Moser
- first_name: Shwetha C.
full_name: Murali, Shwetha C.
last_name: Murali
- first_name: Donna M.
full_name: Muzny, Donna M.
last_name: Muzny
- first_name: Saria
full_name: Otani, Saria
last_name: Otani
- first_name: Maria-Dolors
full_name: Piulachs, Maria-Dolors
last_name: Piulachs
- first_name: Monica
full_name: Poelchau, Monica
last_name: Poelchau
- first_name: Jiaxin
full_name: Qu, Jiaxin
last_name: Qu
- first_name: Florentine
full_name: Schaub, Florentine
last_name: Schaub
- first_name: Ayako
full_name: Wada-Katsumata, Ayako
last_name: Wada-Katsumata
- first_name: Kim C.
full_name: Worley, Kim C.
last_name: Worley
- first_name: Qiaolin
full_name: Xie, Qiaolin
last_name: Xie
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Michael
full_name: Poulsen, Michael
last_name: Poulsen
- first_name: Richard A.
full_name: Gibbs, Richard A.
last_name: Gibbs
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Erich
full_name: Bornberg-Bauer, Erich
last_name: Bornberg-Bauer
citation:
ama: 'Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes
reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r'
apa: 'Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel,
T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal
molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r'
chicago: 'Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning,
Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from:
Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad,
2018. https://doi.org/10.5061/dryad.51d4r.'
ieee: 'M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular
basis of termite eusociality.” Dryad, 2018.'
ista: 'Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao
H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu
H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet
L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau
M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs
RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from:
Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.'
mla: 'Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular
Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r.'
short: M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel,
H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner,
Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee,
A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny,
S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C.
Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles,
J. Korb, E. Bornberg-Bauer, (2018).
date_created: 2021-08-09T13:13:48Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-11T14:10:56Z
day: '12'
department:
- _id: BeVi
doi: 10.5061/dryad.51d4r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.51d4r
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '448'
relation: used_in_publication
status: public
status: public
title: 'Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '397'
abstract:
- lang: eng
text: 'Concurrent sets with range query operations are highly desirable in applications
such as in-memory databases. However, few set implementations offer range queries.
Known techniques for augmenting data structures with range queries (or operations
that can be used to build range queries) have numerous problems that limit their
usefulness. For example, they impose high overhead or rely heavily on garbage
collection. In this work, we show how to augment data structures with highly efficient
range queries, without relying on garbage collection. We identify a property of
epoch-based memory reclamation algorithms that makes them ideal for implementing
range queries, and produce three algorithms, which use locks, transactional memory
and lock-free techniques, respectively. Our algorithms are applicable to more
data structures than previous work, and are shown to be highly efficient on a
large scale Intel system. '
alternative_title:
- PPoPP
article_processing_charge: No
author:
- first_name: Maya
full_name: Arbel Raviv, Maya
last_name: Arbel Raviv
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
citation:
ama: 'Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient
range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489'
apa: 'Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation
for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles
and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489'
chicago: Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation
for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.
ieee: 'M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient
range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming,
Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.'
ista: 'Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient
range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP,
vol. 53, 14–27.'
mla: Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation
for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489.
short: M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.
conference:
end_date: 2018-02-28
location: Vienna, Austria
name: 'PPoPP: Principles and Practice of Parallel Programming'
start_date: 2018-02-24
date_created: 2018-12-11T11:46:14Z
date_published: 2018-02-10T00:00:00Z
date_updated: 2023-09-11T14:10:25Z
day: '10'
department:
- _id: DaAl
doi: 10.1145/3178487.3178489
external_id:
isi:
- '000446161100002'
intvolume: ' 53'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 14 - 27
publication_identifier:
isbn:
- 978-1-4503-4982-6
publication_status: published
publisher: ACM
publist_id: '7430'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Harnessing epoch-based reclamation for efficient range queries
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 53
year: '2018'
...
---
_id: '32'
abstract:
- lang: eng
text: The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between
neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified
the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in
vivo during the peak of myelination by targeting the GluA2 subunit. Expression
of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered
proliferation of OPCs and reduced their differentiation into oligodendrocytes.
Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit
(C-tail), a modification designed to affect the interaction between GluA2 and
AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs,
decreased the differentiation of OPCs without affecting their proliferation. These
findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs,
as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in
the mouse corpus callosum, are important for balancing the response of OPCs to
proliferation and differentiation cues. In the brain, oligodendrocyte precursor
cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from
neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC
synapses alters proliferation and differentiation of OPCs. This expands the traditional
view of synaptic transmission by suggesting neurons also use synapses to modulate
behavior of glia.
acknowledgement: This work was supported by Deutsche Forschungsgemeinschaft (DFG)
grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience
(CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the
Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the
DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported
by the Tistou & Charlotte Kerstan Foundation.
article_processing_charge: No
author:
- first_name: Ting
full_name: Chen, Ting
last_name: Chen
- first_name: Bartosz
full_name: Kula, Bartosz
last_name: Kula
- first_name: Balint
full_name: Nagy, Balint
id: 30F830CE-02D1-11E9-9BAA-DAF4881429F2
last_name: Nagy
orcid: 0000-0002-4002-4686
- first_name: Ruxandra
full_name: Barzan, Ruxandra
last_name: Barzan
- first_name: Andrea
full_name: Gall, Andrea
last_name: Gall
- first_name: Ingrid
full_name: Ehrlich, Ingrid
last_name: Ehrlich
- first_name: Maria
full_name: Kukley, Maria
last_name: Kukley
citation:
ama: Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor
cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell
Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066
apa: Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., & Kukley,
M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation
and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2018.09.066
chicago: Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid
Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell
Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell
Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.
ieee: T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell
proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell
Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.
ista: Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo
regulation of Oligodendrocyte processor cell proliferation and differentiation
by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.
mla: Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation
and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports,
vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.
short: T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell
Reports 25 (2018) 852–861.e7.
date_created: 2018-12-11T11:44:16Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-09-11T14:13:32Z
day: '23'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2018.09.066
external_id:
isi:
- '000448219500005'
file:
- access_level: open_access
checksum: d9f74277fd57176e04732707d575cf08
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:42:57Z
date_updated: 2020-07-14T12:46:03Z
file_id: '5703'
file_name: 2018_CellReports_Chen.pdf
file_size: 4461997
relation: main_file
file_date_updated: 2020-07-14T12:46:03Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 852 - 861.e7
publication: Cell Reports
publication_status: published
publisher: Elsevier
publist_id: '8023'
quality_controlled: '1'
scopus_import: '1'
status: public
title: In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation
by the AMPA-receptor Subunit GluA2
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 25
year: '2018'
...
---
_id: '5672'
abstract:
- lang: eng
text: The release of IgM is the first line of an antibody response and precedes
the generation of high affinity IgG in germinal centers. Once secreted by freshly
activated plasmablasts, IgM is released into the efferent lymph of reactive lymph
nodes as early as 3 d after immunization. As pentameric IgM has an enormous size
of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through
the densely lymphocyte-packed environment of a lymph node parenchyma in order
to reach its exit. In this issue of JEM, Thierry et al. show that, in order to
reach the blood stream, IgM molecules take a specific micro-anatomical route via
lymph node conduits.
article_processing_charge: No
author:
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine.
2018;215(12):2959-2961. doi:10.1084/jem.20181934
apa: Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental
Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934
chicago: Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental
Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934.
ieee: A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental
Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.
ista: Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine.
215(12), 2959–2961.
mla: Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental
Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61,
doi:10.1084/jem.20181934.
short: A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.
date_created: 2018-12-16T22:59:18Z
date_published: 2018-11-20T00:00:00Z
date_updated: 2023-09-11T14:12:06Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1084/jem.20181934
external_id:
isi:
- '000451920600002'
file:
- access_level: open_access
checksum: 687beea1d64c213f4cb9e3c29ec11a14
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T08:49:52Z
date_updated: 2020-07-14T12:47:09Z
file_id: '5931'
file_name: 2018_JournalExperMed_Reversat.pdf
file_size: 1216437
relation: main_file
file_date_updated: 2020-07-14T12:47:09Z
has_accepted_license: '1'
intvolume: ' 215'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2959-2961
publication: Journal of Experimental Medicine
publication_identifier:
issn:
- '00221007'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: IgM's exit route
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 215
year: '2018'
...
---
_id: '398'
abstract:
- lang: eng
text: 'Objective: To report long-term results after Pipeline Embolization Device
(PED) implantation, characterize complex and standard aneurysms comprehensively,
and introduce a modified flow disruption scale. Methods: We retrospectively reviewed
a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs.
Aneurysm complexity was assessed using our proposed classification. Immediate
angiographic results were analyzed using previously published grading scales and
our novel flow disruption scale. Results: According to our new definition, 46
(78%) aneurysms were classified as complex. Most PED interventions were performed
in the paraophthalmic and cavernous internal carotid artery segments. Excellent
neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients.
Our data showed low permanent procedure-related mortality (0%) and morbidity (3%)
rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total
obliteration in a further 14%. Complete obliteration after deployment of a single
PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale
was an independent predictor of aneurysm occlusion in a multivariable analysis.
All aneurysms with a high flow disruption grade showed complete occlusion at follow-up
regardless of PED number or aneurysm complexity. Conclusions: Treatment with the
PED should be recognized as a primary management strategy for a highly selected
cohort with predominantly complex intracranial aneurysms. We further show that
a priori assessment of aneurysm complexity and our new postinterventional angiographic
flow disruption scale predict occlusion probability and may help to determine
the adequate number of per-aneurysm devices.'
article_processing_charge: No
author:
- first_name: Philippe
full_name: Dodier, Philippe
last_name: Dodier
- first_name: Josa
full_name: Frischer, Josa
last_name: Frischer
- first_name: Wei
full_name: Wang, Wei
last_name: Wang
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Ammar
full_name: Mallouhi, Ammar
last_name: Mallouhi
- first_name: Wolfgang
full_name: Serles, Wolfgang
last_name: Serles
- first_name: Andreas
full_name: Gruber, Andreas
last_name: Gruber
- first_name: Engelbert
full_name: Knosp, Engelbert
last_name: Knosp
- first_name: Gerhard
full_name: Bavinzski, Gerhard
last_name: Bavinzski
citation:
ama: Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic
factor after flow diverter treatment long term experience with the pipeline embolization
device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096
apa: Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W.,
… Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after
flow diverter treatment long term experience with the pipeline embolization device.
World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096
chicago: Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi,
Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate
Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term
Experience with the Pipeline Embolization Device.” World Neurosurgery.
Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.
ieee: P. Dodier et al., “Immediate flow disruption as a prognostic factor
after flow diverter treatment long term experience with the pipeline embolization
device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.
ista: Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A,
Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after
flow diverter treatment long term experience with the pipeline embolization device.
World Neurosurgery. 13, e568–e578.
mla: Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor
after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization
Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.
short: P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A.
Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.
date_created: 2018-12-11T11:46:15Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:12:33Z
day: '01'
department:
- _id: BeBi
doi: 10.1016/j.wneu.2018.02.096
external_id:
isi:
- '000432942700070'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: e568-e578
publication: World Neurosurgery
publication_status: published
publisher: Elsevier
publist_id: '7431'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Immediate flow disruption as a prognostic factor after flow diverter treatment
long term experience with the pipeline embolization device
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '458'
abstract:
- lang: eng
text: We consider congruences of straight lines in a plane with the combinatorics
of the square grid, with all elementary quadrilaterals possessing an incircle.
It is shown that all the vertices of such nets (we call them incircular or IC-nets)
lie on confocal conics. Our main new results are on checkerboard IC-nets in the
plane. These are congruences of straight lines in the plane with the combinatorics
of the square grid, combinatorially colored as a checkerboard, such that all black
coordinate quadrilaterals possess inscribed circles. We show how this larger class
of IC-nets appears quite naturally in Laguerre geometry of oriented planes and
spheres and leads to new remarkable incidence theorems. Most of our results are
valid in hyperbolic and spherical geometries as well. We present also generalizations
in spaces of higher dimension, called checkerboard IS-nets. The construction of
these nets is based on a new 9 inspheres incidence theorem.
acknowledgement: DFG Collaborative Research Center TRR 109 “Discretization in Geometry
and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexander
full_name: Bobenko, Alexander
last_name: Bobenko
citation:
ama: Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions
of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292
apa: Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/7292
chicago: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal
Conics.” Transactions of the American Mathematical Society. American Mathematical
Society, 2018. https://doi.org/10.1090/tran/7292.
ieee: A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions
of the American Mathematical Society, vol. 370, no. 4. American Mathematical
Society, pp. 2825–2854, 2018.
ista: Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions
of the American Mathematical Society. 370(4), 2825–2854.
mla: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.”
Transactions of the American Mathematical Society, vol. 370, no. 4, American
Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292.
short: A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society
370 (2018) 2825–2854.
date_created: 2018-12-11T11:46:35Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-11T14:19:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/7292
ec_funded: 1
external_id:
isi:
- '000423197800019'
intvolume: ' 370'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.04637
month: '04'
oa: 1
oa_version: Preprint
page: 2825 - 2854
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '7363'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incircular nets and confocal conics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 370
year: '2018'
...
---
_id: '426'
abstract:
- lang: eng
text: Sperm cells are the most morphologically diverse cells across animal taxa.
Within species, sperm and ejaculate traits have been suggested to vary with the
male's competitive environment, e.g., level of sperm competition, female mating
status and quality, and also with male age, body mass, physiological condition,
and resource availability. Most previous studies have based their conclusions
on the analysis of only one or a few ejaculates per male without investigating
differences among the ejaculates of the same individual. This masks potential
ejaculate-specific traits. Here, we provide data on the length, quantity, and
viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior.
Males of this ant species are relatively long-lived and can mate with large numbers
of female sexuals throughout their lives. We analyzed all ejaculates across the
individuals' lifespan and manipulated the availability of mating partners. Our
study shows that both the number and size of sperm cells transferred during copulations
differ among individuals and also among ejaculates of the same male. Sperm quality
does not decrease with male age, but the variation in sperm number between ejaculates
indicates that males need considerable time to replenish their sperm supplies.
Producing many ejaculates in a short time appears to be traded-off against male
longevity rather than sperm quality.
acknowledgement: "Research with C. obscurior from Brazil was permitted by Instituto
Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no.
20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1
), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice
concerning graphs. One referee made helpful comments on the manuscript.\r\n"
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits
in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003
apa: Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific
sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003
chicago: Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and
Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology.
Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003.
ieee: S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific
sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier,
pp. 284–290, 2018.
ista: Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific
sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.
mla: Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant
Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90,
doi:10.1016/j.jinsphys.2017.12.003.
short: S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018)
284–290.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-12T07:43:26Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.jinsphys.2017.12.003
external_id:
isi:
- '000434751100034'
intvolume: ' 107'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 284-290
publication: Journal of Insect Physiology
publication_status: published
publisher: Elsevier
publist_id: '7397'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Individual- and ejaculate-specific sperm traits in ant males
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 107
year: '2018'
...
---
_id: '5788'
abstract:
- lang: eng
text: In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner or payoff of the game. Such
games are central in formal verification since they model the interaction between
a non-terminating system and its environment. We study bidding games in which
the players bid for the right to move the token. Two bidding rules have been defined.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the “bank” rather than the
other player. While poorman reachability games have been studied before, we present,
for the first time, results on infinite-duration poorman games. A central quantity
in these games is the ratio between the two players’ initial budgets. The questions
we study concern a necessary and sufficient ratio with which a player can achieve
a goal. For reachability objectives, such threshold ratios are known to exist
for both bidding rules. We show that the properties of poorman reachability games
extend to complex qualitative objectives such as parity, similarly to the Richman
case. Our most interesting results concern quantitative poorman games, namely
poorman mean-payoff games, where we construct optimal strategies depending on
the initial ratio, by showing a connection with random-turn based games. The connection
in itself is interesting, because it does not hold for reachability poorman games.
We also solve the complexity problems that arise in poorman bidding games.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games.
In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2'
apa: 'Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration
poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International
Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2'
chicago: Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration
Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.
ieee: G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding
games,” presented at the 14th International Conference on Web and Internet Economics,
WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.
ista: Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding
games. 14th International Conference on Web and Internet Economics, WINE, LNCS,
vol. 11316, 21–36.
mla: Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316,
Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.
short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.
conference:
end_date: 2018-12-17
location: Oxford, UK
name: 14th International Conference on Web and Internet Economics, WINE
start_date: 2018-12-15
date_created: 2018-12-30T22:59:14Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-12T07:44:01Z
day: '21'
department:
- _id: ToHe
doi: 10.1007/978-3-030-04612-5_2
external_id:
arxiv:
- '1804.04372'
isi:
- '000865933000002'
intvolume: ' 11316'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04372
month: '11'
oa: 1
oa_version: Preprint
page: 21-36
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
isbn:
- '9783030046118'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Infinite-duration poorman-bidding games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11316
year: '2018'
...