---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
fulldoi: https://doi.org/10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113'
apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113'
chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.'
ieee: 'R. Faria et al., “Data from: Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes, Dryad, 10.5061/dryad.72cg113.'
mla: 'Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a
Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.'
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
(2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
fulldoi: https://doi.org/10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6095'
relation: used_in_publication
status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here we reveal
that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
capsule, whereas the formation of a capsule roof is controlled by signals from
the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
out to be important for shaping membranous facial bones during development. This
suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria Eleni
full_name: Kastriti, Maria Eleni
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
2018. doi:10.5061/dryad.f1s76f2'
apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2'
chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.'
ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
Dryad, 10.5061/dryad.f1s76f2.'
mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad,
2018, doi:10.5061/dryad.f1s76f2.'
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-04-14T13:02:22Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
fulldoi: https://doi.org/10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '162'
relation: used_in_publication
status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9840'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- 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: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44'
apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data
from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
Dryad. https://doi.org/10.5061/dryad.42n44'
chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
Dryad, 2018. https://doi.org/10.5061/dryad.42n44.'
ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.'
mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage
Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.'
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2025-04-15T08:17:50Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
fulldoi: https://doi.org/10.5061/dryad.42n44
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.42n44
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '423'
relation: used_in_publication
status: public
status: public
title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
populations'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
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
fulldoi: https://doi.org/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: '6459'
article_processing_charge: No
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018.
doi:10.5281/zenodo.1410279
apa: 'Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented
at the OAT: Open Access Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279'
chicago: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria,
2018. https://doi.org/10.5281/zenodo.1410279.
ieee: B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.
ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.
mla: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria,
2018, doi:10.5281/zenodo.1410279.
short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.
conference:
end_date: 2018-09-26
location: Graz, Austria
name: 'OAT: Open Access Tage'
start_date: 2018-09-24
date_created: 2019-05-16T07:27:14Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2026-03-31T12:35:03Z
day: '24'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.1410279
file:
- access_level: open_access
checksum: 9063ab4d10ea93353c3a03bbf53fbcf1
content_type: application/pdf
creator: dernst
date_created: 2019-05-16T07:26:25Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6460'
file_name: Poster_Beitrag_125_Petritsch.pdf
file_size: 1967778
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
fulldoi: https://doi.org/10.5281/zenodo.1410279
has_accepted_license: '1'
keyword:
- Open Access
- Publication Analysis
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
status: public
title: Open Access at IST Austria 2009-2017
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6497'
abstract:
- lang: eng
text: T cells are actively scanning pMHC-presenting cells in lymphoid organs and
nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the
T cell actomyosin cytoskeleton facilitates this task in distinct environments
is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative
regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface
stiffness in primary T cells. Nonetheless, intravital imaging revealed robust
motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and
differentiation during immune responses. In contrast, accumulation of Myo9b−/−
CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for
T cell crossing of basement membranes, such as those which are present between
dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control
of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell
adaptation from lymphoid to NLT surveillance and the establishment of protective
tissue–resident T cell populations.
article_processing_charge: No
author:
- first_name: Federica
full_name: Moalli, Federica
last_name: Moalli
- first_name: Xenia
full_name: Ficht, Xenia
last_name: Ficht
- first_name: Philipp
full_name: Germann, Philipp
last_name: Germann
- first_name: Mykhailo
full_name: Vladymyrov, Mykhailo
last_name: Vladymyrov
- first_name: Bettina
full_name: Stolp, Bettina
last_name: Stolp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Ruth
full_name: Lyck, Ruth
last_name: Lyck
- first_name: Jasmin
full_name: Balmer, Jasmin
last_name: Balmer
- first_name: Amleto
full_name: Fiocchi, Amleto
last_name: Fiocchi
- first_name: Mario
full_name: Kreutzfeldt, Mario
last_name: Kreutzfeldt
- first_name: Doron
full_name: Merkler, Doron
last_name: Merkler
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Akitaka
full_name: Ariga, Akitaka
last_name: Ariga
- first_name: Michael H.
full_name: Stoffel, Michael H.
last_name: Stoffel
- first_name: James
full_name: Sharpe, James
last_name: Sharpe
- first_name: Martin
full_name: Bähler, Martin
last_name: Bähler
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Alba
full_name: Diz-Muñoz, Alba
last_name: Diz-Muñoz
- first_name: Jens V.
full_name: Stein, Jens V.
last_name: Stein
citation:
ama: Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid
tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine.
2018;2015(7):1869–1890. doi:10.1084/jem.20170896
apa: Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I.,
… Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue
seeding of protective CD8+T cells. The Journal of Experimental Medicine.
Rockefeller University Press. https://doi.org/10.1084/jem.20170896
chicago: Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina
Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables
Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental
Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896.
ieee: F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid
tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine,
vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.
ista: Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer
J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe
J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb
enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental
Medicine. 2015(7), 1869–1890.
mla: Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid
Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine,
vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896.
short: F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R.
Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga,
M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal
of Experimental Medicine 2015 (2018) 1869–1890.
date_created: 2019-05-28T12:36:47Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-19T14:52:08Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1084/jem.20170896
external_id:
isi:
- '000440822900011'
file:
- access_level: open_access
checksum: 86ae5331f9bfced9a6358a790a04bef4
content_type: application/pdf
creator: kschuh
date_created: 2019-05-28T12:40:05Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6498'
file_name: 2018_rupress_Moalli.pdf
file_size: 3841660
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
fulldoi: https://doi.org/10.1084/jem.20170896
has_accepted_license: '1'
intvolume: ' 2015'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1869–1890
publication: The Journal of Experimental Medicine
publication_identifier:
eissn:
- 1540-9538
issn:
- 0022-1007
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective
CD8+T cells
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: 2015
year: '2018'
...
---
_id: '6499'
abstract:
- lang: eng
text: Expansion microscopy is a recently introduced imaging technique that achieves
super‐resolution through physically expanding the specimen by ~4×, after embedding
into a swellable gel. The resolution attained is, correspondingly, approximately
fourfold better than the diffraction limit, or ~70 nm. This is a major improvement
over conventional microscopy, but still lags behind modern STED or STORM setups,
whose resolution can reach 20–30 nm. We addressed this issue here by introducing
an improved gel recipe that enables an expansion factor of ~10× in each dimension,
which corresponds to an expansion of the sample volume by more than 1,000‐fold.
Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm
on conventional epifluorescence microscopes. X10 provides multi‐color images similar
or even superior to those produced with more challenging methods, such as STED,
STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest
and easiest option for high‐quality super‐resolution imaging currently available.
X10 should be usable in any laboratory, irrespective of the machinery owned or
of the technical knowledge.
article_number: e45836
article_processing_charge: No
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Manuel
full_name: Maidorn, Manuel
last_name: Maidorn
- first_name: Dagmar
full_name: Crzan, Dagmar
last_name: Crzan
- first_name: Hanna
full_name: Wildhagen, Hanna
last_name: Wildhagen
- first_name: Selda
full_name: Kabatas, Selda
last_name: Kabatas
- first_name: Silvio O
full_name: Rizzoli, Silvio O
last_name: Rizzoli
citation:
ama: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10
expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO
reports. 2018;19(9). doi:10.15252/embr.201845836
apa: Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &
Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional
microscopes. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.201845836
chicago: Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda
Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution
on Conventional Microscopes.” EMBO Reports. Embo Press, 2018. https://doi.org/10.15252/embr.201845836.
ieee: S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S.
O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional
microscopes,” EMBO reports, vol. 19, no. 9. Embo Press, 2018.
ista: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018.
X10 expansion microscopy enables 25‐nm resolution on conventional microscopes.
EMBO reports. 19(9), e45836.
mla: Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution
on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, Embo
Press, 2018, doi:10.15252/embr.201845836.
short: S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli,
EMBO Reports 19 (2018).
date_created: 2019-05-28T13:16:08Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-12-11T11:48:40Z
day: '01'
ddc:
- '580'
department:
- _id: JoDa
doi: 10.15252/embr.201845836
external_id:
isi:
- '000443682200009'
file:
- access_level: open_access
checksum: 6ec90abc637f09cca3a7b6424d7e7a26
content_type: application/pdf
creator: kschuh
date_created: 2019-05-28T13:17:19Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6500'
file_name: 2018_embo_Truckenbrodt.pdf
file_size: 2005572
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
fulldoi: https://doi.org/10.15252/embr.201845836
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: EMBO reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: X10 expansion microscopy enables 25‐nm resolution on conventional microscopes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2018'
...
---
_id: '6525'
abstract:
- lang: eng
text: This chapter finds an agreement of equivariant indices of semi-classical homomorphisms
between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface.
On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs
bundles, whose mirror was proposed by Hitchin to be certain even exterior powers
of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present.
The agreement arises from a mysterious functional equation. This gives strong
computational evidence for Hitchin’s proposal.
article_processing_charge: No
author:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
- first_name: Anton
full_name: Mellit, Anton
id: 388D3134-F248-11E8-B48F-1D18A9856A87
last_name: Mellit
- first_name: Du
full_name: Pei, Du
last_name: Pei
citation:
ama: 'Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde
formulas. In: Geometry and Physics: Volume I. Oxford University Press;
2018:189-218. doi:10.1093/oso/9780198802013.003.0009'
apa: 'Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes
by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp.
189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009'
chicago: 'Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes
by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218.
Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.'
ieee: 'T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant
verlinde formulas,” in Geometry and Physics: Volume I, Oxford University
Press, 2018, pp. 189–218.'
ista: 'Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant
verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.'
mla: 'Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde
Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018,
pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.'
short: 'T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford
University Press, 2018, pp. 189–218.'
date_created: 2019-06-06T12:42:01Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2026-04-16T10:30:22Z
day: '01'
department:
- _id: TaHa
doi: 10.1093/oso/9780198802013.003.0009
fulldoi: https://doi.org/10.1093/oso/9780198802013.003.0009
language:
- iso: eng
month: '01'
oa_version: None
page: 189-218
publication: 'Geometry and Physics: Volume I'
publication_identifier:
eisbn:
- '9780191840500'
isbn:
- '9780198802013'
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mirror symmetry with branes by equivariant verlinde formulas
type: book_chapter
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2018'
...
---
_id: '6558'
abstract:
- lang: eng
text: This paper studies the problem of distributed stochastic optimization in an
adversarial setting where, out of m machines which allegedly compute stochastic
gradients every iteration, an α-fraction are Byzantine, and may behave adversarially.
Our main result is a variant of stochastic gradient descent (SGD) which finds
ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations.
In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot
tolerate Byzantine failures. Further, we provide a lower bound showing that, up
to logarithmic factors, our algorithm is information-theoretically optimal both
in terms of sample complexity and time complexity.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Zeyuan
full_name: Allen-Zhu, Zeyuan
last_name: Allen-Zhu
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
citation:
ama: 'Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In:
Advances in Neural Information Processing Systems. Vol 2018. Neural Information
Processing Systems Foundation; 2018:4613-4623.'
apa: 'Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic
gradient descent. In Advances in Neural Information Processing Systems
(Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems
Foundation.'
chicago: Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic
Gradient Descent.” In Advances in Neural Information Processing Systems,
2018:4613–23. Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,”
in Advances in Neural Information Processing Systems, Montreal, Canada,
2018, vol. 2018, pp. 4613–4623.
ista: 'Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent.
Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural
Information Processing Systems vol. 2018, 4613–4623.'
mla: Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances
in Neural Information Processing Systems, vol. 2018, Neural Information Processing
Systems Foundation, 2018, pp. 4613–23.
short: D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2018, pp.
4613–4623.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
date_created: 2019-06-13T08:22:37Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2026-06-18T19:08:25Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '1803.08917'
isi:
- '000461823304061'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08917
month: '12'
oa: 1
oa_version: Published Version
page: 4613-4623
publication: Advances in Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Byzantine stochastic gradient descent
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '6664'
abstract:
- lang: eng
text: Reed-Muller (RM) and polar codes are a class of capacity-achieving channel
coding schemes with the same factor graph representation. Low-complexity decoding
algorithms fall short in providing a good error-correction performance for RM
and polar codes. Using the symmetric group of RM and polar codes, the specific
decoding algorithm can be carried out on multiple permutations of the factor graph
to boost the error-correction performance. However, this approach results in high
decoding complexity. In this paper, we first derive the total number of factor
graph permutations on which the decoding can be performed. We further propose
a successive permutation (SP) scheme which finds the permutations on the fly,
thus the decoding always progresses on a single factor graph permutation. We show
that SP can be used to improve the error-correction performance of RM and polar
codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping
the memory requirements of the decoders unaltered. Our results for RM and polar
codes of length 128 and rate 0.5 show that when SP is used and at a target frame
error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for
RM and polar codes respectively.
arxiv: 1
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Nghia
full_name: Doan, Nghia
last_name: Doan
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: 'Warren '
full_name: 'Gross, Warren '
last_name: Gross
citation:
ama: 'Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes
by successive factor graph permutations. In: 2018 IEEE 10th International Symposium
on Turbo Codes & Iterative Information Processing. IEEE; 2018:1-5. doi:10.1109/istc.2018.8625281'
apa: 'Hashemi, S. A., Doan, N., Mondelli, M., & Gross, W. (2018). Decoding Reed-Muller
and polar codes by successive factor graph permutations. In 2018 IEEE 10th
International Symposium on Turbo Codes & Iterative Information Processing
(pp. 1–5). Hong Kong, China: IEEE. https://doi.org/10.1109/istc.2018.8625281'
chicago: Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren Gross. “Decoding
Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In 2018
IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing,
1–5. IEEE, 2018. https://doi.org/10.1109/istc.2018.8625281.
ieee: S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and
polar codes by successive factor graph permutations,” in 2018 IEEE 10th International
Symposium on Turbo Codes & Iterative Information Processing, Hong Kong,
China, 2018, pp. 1–5.
ista: 'Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar
codes by successive factor graph permutations. 2018 IEEE 10th International Symposium
on Turbo Codes & Iterative Information Processing. ISTC: Symposium on Turbo
Codes & Iterative Information Processing, 1–5.'
mla: Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive
Factor Graph Permutations.” 2018 IEEE 10th International Symposium on Turbo
Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5, doi:10.1109/istc.2018.8625281.
short: S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International
Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp.
1–5.
conference:
end_date: 2018-12-07
location: Hong Kong, China
name: 'ISTC: Symposium on Turbo Codes & Iterative Information Processing'
start_date: 2018-12-03
date_created: 2019-07-23T09:12:43Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2021-01-12T08:08:29Z
day: '01'
doi: 10.1109/istc.2018.8625281
extern: '1'
external_id:
arxiv:
- '1807.03912'
fulldoi: https://doi.org/10.1109/istc.2018.8625281
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.03912
month: '12'
oa: 1
oa_version: Preprint
page: 1-5
publication: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information
Processing
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Decoding Reed-Muller and polar codes by successive factor graph permutations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6665'
abstract:
- lang: eng
text: We prove that, at least for the binary erasure channel, the polar-coding paradigm
gives rise to codes that not only approach the Shannon limit but, in fact, do
so under the best possible scaling of their block length as a function of the
gap to capacity. This result exhibits the first known family of binary codes that
attain both optimal scaling and quasi-linear complexity of encoding and decoding.
Specifically, for any fixed δ > 0, we exhibit binary linear codes that ensure
reliable communication at rates within ε > 0 of capacity with block length n =
O(1/ε 2+δ ), construction complexity Θ(n), and encoding/decoding complexity Θ(n
log n).
arxiv: 1
author:
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
citation:
ama: 'Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal
scaling: Polar codes with large kernels. In: 2018 IEEE Information Theory Workshop.
IEEE; 2018:1-5. doi:10.1109/itw.2018.8613428'
apa: 'Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2018). Binary linear
codes with optimal scaling: Polar codes with large kernels. In 2018 IEEE Information
Theory Workshop (pp. 1–5). Guangzhou, China: IEEE. https://doi.org/10.1109/itw.2018.8613428'
chicago: 'Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary
Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” In 2018
IEEE Information Theory Workshop, 1–5. IEEE, 2018. https://doi.org/10.1109/itw.2018.8613428.'
ieee: 'A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with
optimal scaling: Polar codes with large kernels,” in 2018 IEEE Information
Theory Workshop, Guangzhou, China, 2018, pp. 1–5.'
ista: 'Fazeli A, Hassani H, Mondelli M, Vardy A. 2018. Binary linear codes with
optimal scaling: Polar codes with large kernels. 2018 IEEE Information Theory
Workshop. ITW: Information Theory Workshop, 1–5.'
mla: 'Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes
with Large Kernels.” 2018 IEEE Information Theory Workshop, IEEE, 2018,
pp. 1–5, doi:10.1109/itw.2018.8613428.'
short: A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, in:, 2018 IEEE Information
Theory Workshop, IEEE, 2018, pp. 1–5.
conference:
end_date: 2018-11-29
location: Guangzhou, China
name: 'ITW: Information Theory Workshop'
start_date: 2018-11-25
date_created: 2019-07-23T11:01:42Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2025-09-10T09:59:12Z
day: '01'
doi: 10.1109/itw.2018.8613428
extern: '1'
external_id:
arxiv:
- '1711.01339'
fulldoi: https://doi.org/10.1109/itw.2018.8613428
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.01339
month: '11'
oa: 1
oa_version: Preprint
page: 1-5
publication: 2018 IEEE Information Theory Workshop
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '9002'
relation: later_version
status: public
status: public
title: 'Binary linear codes with optimal scaling: Polar codes with large kernels'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6674'
abstract:
- lang: eng
text: Polar codes represent one of the major recent breakthroughs in coding theory
and, because of their attractive features, they have been selected for the incoming
5G standard. As such, a lot of attention has been devoted to the development of
decoding algorithms with good error performance and efficient hardware implementation.
One of the leading candidates in this regard is represented by successive-cancellation
list (SCL) decoding. However, its hardware implementation requires a large amount
of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly
reduce the memory consumption. In this paper, we consider the paradigm of PSCL
decoding from a practical standpoint, and we provide several improvements. First,
by changing the target signal-to-noise ratio and consequently modifying the construction
of the code, we are able to improve the performance at no additional computational,
latency, or memory cost. Second, we bridge the performance gap between SCL and
PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder.
In this way, we obtain almost the same performance of the SCL decoder with a significantly
lower memory requirement, as testified by hardware implementation results. Third,
we present an optimal scheme to allocate cyclic redundancy checks. Finally, we
provide a lower bound on the list size that guarantees optimal maximum a posteriori
performance for the binary erasure channel.
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: S. Hamed
full_name: Hassani, S. Hamed
last_name: Hassani
- first_name: Carlo
full_name: Condo, Carlo
last_name: Condo
- first_name: Rudiger L.
full_name: Urbanke, Rudiger L.
last_name: Urbanke
- first_name: Warren J.
full_name: Gross, Warren J.
last_name: Gross
citation:
ama: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder
partitioning: Towards practical list decoding of polar codes. IEEE Transactions
on Communications. 2018;66(9):3749-3759. doi:10.1109/tcomm.2018.2832207'
apa: 'Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., &
Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of
polar codes. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2018.2832207'
chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger
L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List
Decoding of Polar Codes.” IEEE Transactions on Communications. IEEE, 2018.
https://doi.org/10.1109/tcomm.2018.2832207.'
ieee: 'S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W.
J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,”
IEEE Transactions on Communications, vol. 66, no. 9. IEEE, pp. 3749–3759,
2018.'
ista: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018.
Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions
on Communications. 66(9), 3749–3759.'
mla: 'Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List
Decoding of Polar Codes.” IEEE Transactions on Communications, vol. 66,
no. 9, IEEE, 2018, pp. 3749–59, doi:10.1109/tcomm.2018.2832207.'
short: S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross,
IEEE Transactions on Communications 66 (2018) 3749–3759.
date_created: 2019-07-24T08:59:41Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2021-01-12T08:08:31Z
day: '01'
doi: 10.1109/tcomm.2018.2832207
extern: '1'
fulldoi: https://doi.org/10.1109/tcomm.2018.2832207
intvolume: ' 66'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 3749-3759
publication: IEEE Transactions on Communications
publication_identifier:
eissn:
- 1558-0857
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'Decoder partitioning: Towards practical list decoding of polar codes'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2018'
...
---
_id: '6675'
abstract:
- lang: eng
text: 'We present a coding paradigm that provides a new achievable rate for the
primitive relay channel by combining compress-and-forward and decode-and-forward
with a chaining construction. In the primitive relay channel model, the source
broadcasts a message to the relay and to the destination; and the relay facilitates
this communication by sending an additional message to the destination through
a separate channel. Two well-known coding approaches for this setting are decode-and-forward
and compress-and-forward: in the former, the relay decodes the message and sends
some of the information to the destination; in the latter, the relay does not
attempt to decode, but it sends a compressed description of the received sequence
to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs
of blocks and we use compress-and-forward for the first block and decode-and-forward
for the second. In particular, in the first block, the relay does not attempt
to decode and it sends only a part of the compressed description of the received
sequence; in the second block, the relay decodes the message and sends this information
plus the remaining part of the compressed sequence relative to the first block.
As a result, we strictly outperform both compress-and- forward and decode-and-forward.
Furthermore, this paradigm can be implemented with a low-complexity polar coding
scheme that has the typical attractive features of polar codes, i.e., quasi-linear
encoding/decoding complexity and super-polynomial decay of the error probability.
Throughout the paper we consider as a running example the special case of the
erasure relay channel and we compare the rates achievable by our proposed scheme
with the existing upper and lower bounds.'
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: 'Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive
relay channel. In: 2018 IEEE International Symposium on Information Theory.
IEEE; 2018:351-355. doi:10.1109/isit.2018.8437479'
apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2018). A new coding paradigm
for the primitive relay channel. In 2018 IEEE International Symposium on Information
Theory (pp. 351–355). Vail, CO, United States: IEEE. https://doi.org/10.1109/isit.2018.8437479'
chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm
for the Primitive Relay Channel.” In 2018 IEEE International Symposium on Information
Theory, 351–55. IEEE, 2018. https://doi.org/10.1109/isit.2018.8437479.
ieee: M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive
relay channel,” in 2018 IEEE International Symposium on Information Theory,
Vail, CO, United States, 2018, pp. 351–355.
ista: 'Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive
relay channel. 2018 IEEE International Symposium on Information Theory. ISIT:
International Symposium on Information Theory , 351–355.'
mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.”
2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp.
351–55, doi:10.1109/isit.2018.8437479.
short: M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium
on Information Theory, IEEE, 2018, pp. 351–355.
conference:
end_date: 2018-06-22
location: Vail, CO, United States
name: 'ISIT: International Symposium on Information Theory '
start_date: 2018-06-17
date_created: 2019-07-24T09:10:38Z
date_published: 2018-06-16T00:00:00Z
date_updated: 2024-10-09T20:59:04Z
day: '16'
doi: 10.1109/isit.2018.8437479
extern: '1'
external_id:
arxiv:
- '1801.03153'
fulldoi: https://doi.org/10.1109/isit.2018.8437479
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.03153
month: '06'
oa: 1
oa_version: Preprint
page: 351-355
publication: 2018 IEEE International Symposium on Information Theory
publication_identifier:
eissn:
- 2157-8117
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '7007'
relation: later_version
status: public
status: public
title: A new coding paradigm for the primitive relay channel
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6678'
abstract:
- lang: eng
text: We survey coding techniques that enable reliable transmission at rates that
approach the capacity of an arbitrary discrete memoryless channel. In particular,
we take the point of view of modern coding theory and discuss how recent advances
in coding for symmetric channels help provide more efficient solutions for the
asymmetric case. We consider, in more detail, three basic coding paradigms. The
first one is Gallager's scheme that consists of concatenating a linear code with
a non-linear mapping so that the input distribution can be appropriately shaped.
We explicitly show that both polar codes and spatially coupled codes can be employed
in this scenario. Furthermore, we derive a scaling law between the gap to capacity,
the cardinality of the input and output alphabets, and the required size of the
mapper. The second one is an integrated scheme in which the code is used both
for source coding, in order to create codewords distributed according to the capacity-achieving
input distribution, and for channel coding, in order to provide error protection.
Such a technique has been recently introduced by Honda and Yamamoto in the context
of polar codes, and we show how to apply it also to the design of sparse graph
codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates
the two tasks of source coding and channel coding by a chaining construction that
binds together several codewords. We present conditions for the source code and
the channel code, and we describe how to combine any source code with any channel
code that fulfill those conditions, in order to provide capacity-achieving schemes
for asymmetric channels. In particular, we show that polar codes, spatially coupled
codes, and homophonic codes are suitable as basic building blocks of the proposed
coding strategy. Rather than focusing on the exact details of the schemes, the
purpose of this tutorial is to present different coding techniques that can then
be implemented with many variants. There is no absolute winner and, in order to
understand the most suitable technique for a specific application scenario, we
provide a detailed comparison that takes into account several performance metrics.
article_type: original
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: 'Rudiger '
full_name: 'Urbanke, Rudiger '
last_name: Urbanke
citation:
ama: Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric
channels. IEEE Transactions on Information Theory. 2018;64(5):3371-3393.
doi:10.1109/tit.2018.2789885
apa: Mondelli, M., Hassani, H., & Urbanke, R. (2018). How to achieve the capacity
of asymmetric channels. IEEE Transactions on Information Theory. IEEE.
https://doi.org/10.1109/tit.2018.2789885
chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “How to Achieve the
Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory.
IEEE, 2018. https://doi.org/10.1109/tit.2018.2789885.
ieee: M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric
channels,” IEEE Transactions on Information Theory, vol. 64, no. 5. IEEE,
pp. 3371–3393, 2018.
ista: Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric
channels. IEEE Transactions on Information Theory. 64(5), 3371–3393.
mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.”
IEEE Transactions on Information Theory, vol. 64, no. 5, IEEE, 2018, pp.
3371–93, doi:10.1109/tit.2018.2789885.
short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory
64 (2018) 3371–3393.
date_created: 2019-07-24T12:38:49Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-23T12:50:46Z
day: '01'
doi: 10.1109/tit.2018.2789885
extern: '1'
external_id:
arxiv:
- '1406.7373'
fulldoi: https://doi.org/10.1109/tit.2018.2789885
intvolume: ' 64'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1406.7373
month: '05'
oa: 1
oa_version: Preprint
page: 3371-3393
publication: IEEE Transactions on Information Theory
publication_identifier:
issn:
- 0018-9448
- 1557-9654
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '6740'
relation: earlier_version
status: public
status: public
title: How to achieve the capacity of asymmetric channels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2018'
...
---
_id: '6728'
abstract:
- lang: eng
text: Polar codes are a channel coding scheme for the next generation of wireless
communications standard (5G). The belief propagation (BP) decoder allows for parallel
decoding of polar codes, making it suitable for high throughput applications.
However, the error-correction performance of polar codes under BP decoding is
far from the requirements of 5G. It has been shown that the error-correction performance
of BP can be improved if the decoding is performed on multiple permuted factor
graphs of polar codes. However, a different BP decoding scheduling is required
for each factor graph permutation which results in the design of a different decoder
for each permutation. Moreover, the selection of the different factor graph permutations
is at random, which prevents the decoder to achieve a desirable error correction
performance with a small number of permutations. In this paper, we first show
that the permutations on the factor graph can be mapped into suitable permutations
on the codeword positions. As a result, we can make use of a single decoder for
all the permutations. In addition, we introduce a method to construct a set of
predetermined permutations which can provide the correct codeword if the decoding
fails on the original permutation. We show that for the 5G polar code of length
1024, the error-correction performance of the proposed decoder is more than 0.25
dB better than that of the BP decoder with the same number of random permutations
at the frame error rate of 10 -4 .
arxiv: 1
author:
- first_name: Nghia
full_name: Doan, Nghia
last_name: Doan
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Warren J.
full_name: Gross, Warren J.
last_name: Gross
citation:
ama: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on
permuted factor graphs. In: 2018 IEEE Global Communications Conference .
IEEE; 2018. doi:10.1109/glocom.2018.8647308'
apa: 'Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2018). On the
decoding of polar codes on permuted factor graphs. In 2018 IEEE Global Communications
Conference . Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/glocom.2018.8647308'
chicago: Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On
the Decoding of Polar Codes on Permuted Factor Graphs.” In 2018 IEEE Global
Communications Conference . IEEE, 2018. https://doi.org/10.1109/glocom.2018.8647308.
ieee: N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of
polar codes on permuted factor graphs,” in 2018 IEEE Global Communications
Conference , Abu Dhabi, United Arab Emirates, 2018.
ista: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar
codes on permuted factor graphs. 2018 IEEE Global Communications Conference .
GLOBECOM: Global Communications Conference.'
mla: Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.”
2018 IEEE Global Communications Conference , IEEE, 2018, doi:10.1109/glocom.2018.8647308.
short: N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications
Conference , IEEE, 2018.
conference:
end_date: 2018-12-13
location: Abu Dhabi, United Arab Emirates
name: 'GLOBECOM: Global Communications Conference'
start_date: 2018-12-09
date_created: 2019-07-30T06:43:15Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2021-01-12T08:08:42Z
day: '01'
doi: 10.1109/glocom.2018.8647308
extern: '1'
external_id:
arxiv:
- '1806.11195'
fulldoi: https://doi.org/10.1109/glocom.2018.8647308
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.11195
month: '12'
oa: 1
oa_version: Preprint
publication: '2018 IEEE Global Communications Conference '
publication_identifier:
isbn:
- '9781538647271'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: On the decoding of polar codes on permuted factor graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6774'
abstract:
- lang: eng
text: "A central problem of algebraic topology is to understand the homotopy groups
\ \U0001D70B\U0001D451(\U0001D44B) of a topological space X. For the computational
version of the problem, it is well known that there is no algorithm to decide
whether the fundamental group \U0001D70B1(\U0001D44B) of a given finite simplicial
complex X is trivial. On the other hand, there are several algorithms that, given
a finite simplicial complex X that is simply connected (i.e., with \U0001D70B1(\U0001D44B)
\ trivial), compute the higher homotopy group \U0001D70B\U0001D451(\U0001D44B)
\ for any given \U0001D451≥2 . However, these algorithms come with a caveat:
They compute the isomorphism type of \U0001D70B\U0001D451(\U0001D44B) , \U0001D451≥2
\ as an abstract finitely generated abelian group given by generators and relations,
but they work with very implicit representations of the elements of \U0001D70B\U0001D451(\U0001D44B)
. Converting elements of this abstract group into explicit geometric maps from
the d-dimensional sphere \U0001D446\U0001D451 to X has been one of the main
unsolved problems in the emerging field of computational homotopy theory. Here
we present an algorithm that, given a simply connected space X, computes \U0001D70B\U0001D451(\U0001D44B)
\ and represents its elements as simplicial maps from a suitable triangulation
of the d-sphere \U0001D446\U0001D451 to X. For fixed d, the algorithm runs
in time exponential in size(\U0001D44B) , the number of simplices of X. Moreover,
we prove that this is optimal: For every fixed \U0001D451≥2 , we construct a
family of simply connected spaces X such that for any simplicial map representing
a generator of \U0001D70B\U0001D451(\U0001D44B) , the size of the triangulation
of \U0001D446\U0001D451 on which the map is defined, is exponential in size(\U0001D44B)
."
article_type: original
author:
- first_name: Marek
full_name: Filakovský, Marek
id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
last_name: Filakovský
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
orcid: 0000-0001-8878-8397
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Stephan Y
full_name: Zhechev, Stephan Y
id: 3AA52972-F248-11E8-B48F-1D18A9856A87
last_name: Zhechev
citation:
ama: Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives
of homotopy group elements. Journal of Applied and Computational Topology.
2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5
apa: Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing
simplicial representatives of homotopy group elements. Journal of Applied and
Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5
chicago: Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing
Simplicial Representatives of Homotopy Group Elements.” Journal of Applied
and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5.
ieee: M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial
representatives of homotopy group elements,” Journal of Applied and Computational
Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.
ista: Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives
of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4),
177–231.
mla: Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy
Group Elements.” Journal of Applied and Computational Topology, vol. 2,
no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5.
short: M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and
Computational Topology 2 (2018) 177–231.
corr_author: '1'
date_created: 2019-08-08T06:47:40Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2026-04-08T13:56:01Z
day: '01'
ddc:
- '514'
department:
- _id: UlWa
doi: 10.1007/s41468-018-0021-5
file:
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date_updated: 2020-07-14T12:47:40Z
file_id: '6775'
file_name: 2018_JourAppliedComputTopology_Filakovsky.pdf
file_size: 1056278
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
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intvolume: ' 2'
issue: 3-4
language:
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month: '12'
oa: 1
oa_version: Published Version
page: 177-231
project:
- _id: 25F8B9BC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M01980
name: Robust Invariants of Nonlinear Systems
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
record:
- id: '6681'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Computing simplicial representatives of homotopy group elements
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2018'
...
---
OA_place: publisher
_id: '69'
abstract:
- lang: eng
text: 'A qubit, a unit of quantum information, is essentially any quantum mechanical
two-level system which can be coherently controlled. Still, to be used for computation,
it has to fulfill criteria. Qubits, regardless of the system in which they are
realized, suffer from decoherence. This leads to loss of the information stored
in the qubit. The upper bound of the time scale on which decoherence happens is
set by the spin relaxation time. In this thesis I studied a two-level system consisting
of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire.
Such Ge hut wires have emerged as a promising material system for the realization
of spin qubits, due to the combination of two significant properties: long spin
coherence time as expected for group IV semiconductors due to the low hyperfine
interaction and a strong valence band spin-orbit coupling. Here, I present how
to fabricate quantum dot devices suitable for electrical transport measurements.
Coupled quantum dot devices allowed the realization of a charge sensor, which
is electrostatically and tunnel coupled to a quantum dot. By integrating the charge
sensor into a radio-frequency reflectometry setup, I performed for the first time
single-shot readout measurements of hole spins and extracted the hole spin relaxation
times in Ge hut wires.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
citation:
ama: Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires.
2018. doi:10.15479/AT:ISTA:TH_1047
apa: Vukušić, L. (2018). Charge sensing and spin relaxation times of holes in
Ge hut wires. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1047
chicago: Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge
Hut Wires.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1047.
ieee: L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,”
Institute of Science and Technology Austria, 2018.
ista: Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut
wires. Institute of Science and Technology Austria.
mla: Vukušić, Lada. Charge Sensing and Spin Relaxation Times of Holes in Ge Hut
Wires. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1047.
short: L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires,
Institute of Science and Technology Austria, 2018.
corr_author: '1'
date_created: 2018-12-11T11:44:28Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2026-04-08T14:09:47Z
day: '01'
ddc:
- '530'
- '600'
degree_awarded: PhD
department:
- _id: GeKa
- _id: GradSch
doi: 10.15479/AT:ISTA:TH_1047
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date_created: 2019-04-09T07:00:40Z
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file_id: '6247'
file_name: 2018_Thesis_Vukusic.pdf
file_size: 28452385
relation: main_file
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checksum: 7856771d9cd401fe0b311191076db6e1
content_type: application/zip
creator: dernst
date_created: 2019-04-09T07:00:40Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6248'
file_name: 2018_Thesis_Vukusic_source.zip
file_size: 53058704
relation: source_file
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fulldoi: https://doi.org/10.15479/AT:ISTA:TH_1047
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '103'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7985'
pubrep_id: '1047'
related_material:
record:
- id: '23'
relation: part_of_dissertation
status: public
- id: '840'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Charge sensing and spin relaxation times of holes in Ge hut wires
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2018'
...
---
_id: '690'
abstract:
- lang: eng
text: We consider spectral properties and the edge universality of sparse random
matrices, the class of random matrices that includes the adjacency matrices of
the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density
up to the spectral edges. Under a suitable condition on the sparsity, we also
prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations
if a deterministic shift of the spectral edge due to the sparsity is included.
For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom
fluctuations of the second largest eigenvalue when p is much larger than N−2/3
with a deterministic shift of order (Np)−1.
article_number: 543-616
article_processing_charge: No
arxiv: 1
author:
- first_name: Jii
full_name: Lee, Jii
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices.
Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8
apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse
random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8
chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse
Random Matrices.” Probability Theory and Related Fields. Springer, 2018.
https://doi.org/10.1007/s00440-017-0787-8.
ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random
matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer,
2018.
ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random
matrices. Probability Theory and Related Fields. 171(1–2), 543–616.
mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random
Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616,
Springer, 2018, doi:10.1007/s00440-017-0787-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).
date_created: 2018-12-11T11:47:56Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-09-10T14:00:58Z
day: '14'
department:
- _id: LaEr
doi: 10.1007/s00440-017-0787-8
ec_funded: 1
external_id:
arxiv:
- '1605.08767'
isi:
- '000432129600012'
fulldoi: https://doi.org/10.1007/s00440-017-0787-8
intvolume: ' 171'
isi: 1
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.08767
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '7017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law and Tracy–Widom limit for sparse random matrices
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 171
year: '2018'
...
---
_id: '691'
abstract:
- lang: eng
text: "Background: Transport protein particle (TRAPP) is a multisubunit complex
that regulates membrane trafficking through the Golgi apparatus. The clinical
phenotype associated with mutations in various TRAPP subunits has allowed elucidation
of their functions in specific tissues. The role of some subunits in human disease,
however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective:
We aimed to expand the range of neurodevelopmental disorders associated with mutations
in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods:
Linkage and homozygosity mapping and candidate gene analysis were used to identify
homozygous mutations in families. Patient fibroblasts were used to study splicing
defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals
from three unrelated families with a founder homozygous splice mutation in TRAPPC6B,
encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental
disorder characterised by microcephaly, epilepsy and autistic features, and showed
splicing defect. Zebrafish trappc6b morphants replicated the human phenotype,
displaying decreased head size and neuronal hyperexcitability, leading to a lower
seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional
evidence of the role of TRAPPC6B in brain development and function."
article_processing_charge: No
article_type: original
author:
- first_name: Isaac
full_name: Marin Valencia, Isaac
last_name: Marin Valencia
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Gifty
full_name: Bhat, Gifty
last_name: Bhat
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Valentina
full_name: Stanley, Valentina
last_name: Stanley
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Jeremy
full_name: Gleeson, Jeremy
last_name: Gleeson
- first_name: Farhad
full_name: Imam, Farhad
last_name: Imam
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation
in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly
epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54.
doi:10.1136/jmedgenet-2017-104627
apa: Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev,
D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates
with a neurodevelopmental disorder characterised by microcephaly epilepsy and
autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627
chicago: Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud
Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B
Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy
and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group,
2018. https://doi.org/10.1136/jmedgenet-2017-104627.
ieee: I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B
associates with a neurodevelopmental disorder characterised by microcephaly epilepsy
and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ
Publishing Group, pp. 48–54, 2018.
ista: Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat
G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson
J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features. Journal
of Medical Genetics. 55(1), 48–54.
mla: Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates
with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and
Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing
Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.
short: I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev,
G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki,
J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-04-15T07:50:28Z
day: '01'
department:
- _id: GaNo
doi: 10.1136/jmedgenet-2017-104627
external_id:
isi:
- '000418199800007'
pmid:
- '28626029'
fulldoi: https://doi.org/10.1136/jmedgenet-2017-104627
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/
month: '01'
oa: 1
oa_version: Submitted Version
page: 48 - 54
pmid: 1
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
publication: Journal of Medical Genetics
publication_identifier:
issn:
- 0022-2593
publication_status: published
publisher: BMJ Publishing Group
publist_id: '7016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2018'
...