---
_id: '8075'
abstract:
- lang: eng
text: Ion channel models are the building blocks of computational neuron models.
Their biological fidelity is therefore crucial for the interpretation of simulations.
However, the number of published models, and the lack of standardization, make
the comparison of ion channel models with one another and with experimental data
difficult. Here, we present a framework for the automated large-scale classification
of ion channel models. Using annotated metadata and responses to a set of voltage-clamp
protocols, we assigned 2378 models of voltage- and calcium-gated ion channels
coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface
provides an interactive resource for the categorization of new and existing models
and experimental recordings. It enables quantitative comparisons of simulated
and/or measured ion channel kinetics, and facilitates field-wide standardization
of experimentally-constrained modeling.
article_number: e22152
article_processing_charge: No
article_type: original
author:
- first_name: William F
full_name: Podlaski, William F
last_name: Podlaski
- first_name: Alexander
full_name: Seeholzer, Alexander
last_name: Seeholzer
- first_name: Lukas N
full_name: Groschner, Lukas N
last_name: Groschner
- first_name: Gero
full_name: Miesenböck, Gero
last_name: Miesenböck
- first_name: Rajnish
full_name: Ranjan, Rajnish
last_name: Ranjan
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
Mapping the function of neuronal ion channels in model and experiment. eLife.
2017;6. doi:10.7554/elife.22152
apa: Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R.,
& Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model
and experiment. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.22152
chicago: Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck,
Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels
in Model and Experiment.” ELife. eLife Sciences Publications, Ltd, 2017.
https://doi.org/10.7554/elife.22152.
ieee: W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and
T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,”
eLife, vol. 6. eLife Sciences Publications, Ltd, 2017.
ista: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
2017. Mapping the function of neuronal ion channels in model and experiment. eLife.
6, e22152.
mla: Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels
in Model and Experiment.” ELife, vol. 6, e22152, eLife Sciences Publications,
Ltd, 2017, doi:10.7554/elife.22152.
short: W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P.
Vogels, ELife 6 (2017).
date_created: 2020-06-30T13:32:18Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:16:46Z
day: '06'
ddc:
- '570'
doi: 10.7554/elife.22152
extern: '1'
external_id:
pmid:
- '28267430'
file:
- access_level: open_access
checksum: e5c5a33bcb3ac38ad62df1010ab29040
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T12:08:40Z
date_updated: 2020-07-16T12:08:40Z
file_id: '8124'
file_name: 2017_elife_Podlaski.pdf
file_size: 16034505
relation: main_file
success: 1
file_date_updated: 2020-07-16T12:08:40Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications, Ltd
quality_controlled: '1'
status: public
title: Mapping the function of neuronal ion channels in model and experiment
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 6
year: '2017'
...
---
_id: '8129'
abstract:
- lang: eng
text: "Cortical circuits exhibit intricate recurrent architectures that are remarkably
similar across different brain areas. Such stereotyped structure suggests the
existence of common computational principles. However, such principles have remained
largely elusive. Inspired by gated-memory networks, namely long short-term memory
networks (LSTMs), we introduce a recurrent neural network in which information
is gated through inhibitory cells that are subtractive (subLSTM). We propose a
natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical
microcircuits. Our empirical evaluation across sequential image classification
and language modelling tasks shows that subLSTM units can achieve similar performance
to LSTM units. These results suggest that cortical circuits can be optimised to
solve complex contextual problems and proposes a novel view on their computational
function.\r\nOverall our work provides a step towards unifying recurrent networks
as used in machine learning with their biological counterparts."
article_processing_charge: No
arxiv: 1
author:
- first_name: Rui Ponte
full_name: Costa, Rui Ponte
last_name: Costa
- first_name: Yannis M.
full_name: Assael, Yannis M.
last_name: Assael
- first_name: Brendan
full_name: Shillingford, Brendan
last_name: Shillingford
- first_name: Nando de
full_name: Freitas, Nando de
last_name: Freitas
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits
as gated-recurrent neural networks. In: Advances in Neural Information Processing
Systems. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.'
apa: 'Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, & Vogels,
T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In Advances
in Neural Information Processing Systems (Vol. 30, pp. 272–283). Long Beach,
CA, United States: Neural Information Processing Systems Foundation.'
chicago: Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas,
and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.”
In Advances in Neural Information Processing Systems, 30:272–83. Neural
Information Processing Systems Foundation, 2017.
ieee: R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels,
“Cortical microcircuits as gated-recurrent neural networks,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017,
vol. 30, pp. 272–283.
ista: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical
microcircuits as gated-recurrent neural networks. Advances in Neural Information
Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.'
mla: Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural
Networks.” Advances in Neural Information Processing Systems, vol. 30,
Neural Information Processing Systems Foundation, 2017, pp. 272–83.
short: R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:,
Advances in Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2017, pp. 272–283.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NIPS: Neural Information Processing System'
start_date: 2017-12-04
date_created: 2020-07-16T19:13:10Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:17:03Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1711.02448'
intvolume: ' 30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.02448
month: '12'
oa: 1
oa_version: Preprint
page: 272-283
publication: Advances in Neural Information Processing Systems
publication_identifier:
issn:
- '10495258'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Cortical microcircuits as gated-recurrent neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2017'
...
---
_id: '817'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular
complexes to be imaged in three-dimensions in their native environments. Cryo-electron
tomograms are reconstructed from projection images taken at defined tilt-angles.
In order to recover high-resolution information from cryo-electron tomograms,
it is necessary to measure and correct for the contrast transfer function (CTF)
of the microscope. Most commonly, this is performed using protocols that approximate
the sample as a two-dimensional (2D) plane. This approximation accounts for differences
in defocus and therefore CTF across the tilted sample. It does not account for
differences in defocus of objects at different heights within the sample; instead,
a 3D approach is required. Currently available approaches for 3D-CTF correction
are computationally expensive and have not been widely implemented. Here we simulate
the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and
present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF,
that is compatible with standard tomogram reconstruction workflows in IMOD. We
validate the approach on synthetic data and test it using subtomogram averaging
of real data. Consistent with our simulations, we find that 3D-CTF correction
allows high-resolution structures to be obtained with much smaller subtomogram
averaging datasets than are required using 2D-CTF. We also show that using equivalent
dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures.
We present a 3.4. Å resolution structure determined by subtomogram averaging.
author:
- first_name: Beata
full_name: Turoňová, Beata
last_name: Turoňová
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron
tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal
of Structural Biology. 2017;199(3):187-195. doi:10.1016/j.jsb.2017.07.007
apa: Turoňová, B., Schur, F. K., Wan, W., & Briggs, J. (2017). Efficient 3D-CTF
correction for cryo-electron tomography using NovaCTF improves subtomogram averaging
resolution to 3.4Å. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2017.07.007
chicago: Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient
3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram
Averaging Resolution to 3.4Å.” Journal of Structural Biology. Academic
Press, 2017. https://doi.org/10.1016/j.jsb.2017.07.007.
ieee: B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction
for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å,” Journal of Structural Biology, vol. 199, no. 3. Academic Press,
pp. 187–195, 2017.
ista: Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for
cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å. Journal of Structural Biology. 199(3), 187–195.
mla: Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography
Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of
Structural Biology, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:10.1016/j.jsb.2017.07.007.
short: B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology
199 (2017) 187–195.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:16Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2017.07.007
extern: '1'
file:
- access_level: open_access
checksum: 7f2d4bbac767f9acc254d1a4114d181a
content_type: application/pdf
creator: kschuh
date_created: 2019-03-22T09:29:44Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6168'
file_name: 2017_Elsevier_Turonova.pdf
file_size: 1310009
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 199'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 187-195
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6832'
quality_controlled: '1'
status: public
title: Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves
subtomogram averaging resolution to 3.4Å
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2017'
...
---
_id: '818'
abstract:
- lang: eng
text: 'Antibiotics have diverse effects on bacteria, including massive changes in
bacterial gene expression. Whereas the gene expression changes under many antibiotics
have been measured, the temporal organization of these responses and their dependence
on the bacterial growth rate are unclear. As described in Chapter 1, we quantified
the temporal gene expression changes in the bacterium Escherichia coli in response
to the sudden exposure to antibiotics using a fluorescent reporter library and
a robotic system. Our data show temporally structured gene expression responses,
with response times for individual genes ranging from tens of minutes to several
hours. We observed that many stress response genes were activated in response
to antibiotics. As certain stress responses cross-protect bacteria from other
stressors, we then asked whether cellular responses to antibiotics have a similar
protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid
stress response protects bacteria from subsequent acid stress. We combined microfluidics
with time-lapse imaging to monitor survival, intracellular pH, and acid stress
response in single cells. This approach revealed that the variable expression
of the acid resistance operon gadBC strongly correlates with single-cell survival
time. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. Overall, we provide a way
to identify single-cell cross-protection between antibiotics and environmental
stressors from temporal gene expression data, and show how antibiotics can increase
bacterial fitness in changing environments. While gene expression changes to antibiotics
show a clear temporal structure at the population-level, it is unclear whether
this clear temporal order is followed by every single cell. Using dual-reporter
strains described in Chapter 3, we measured gene expression dynamics of promoter
pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that
the oxidative stress response and the DNA stress response showed little timing
variability and a clear temporal order under the antibiotic nitrofurantoin. In
contrast, the acid stress response under trimethoprim ran independently from all
other activated response programs including the DNA stress response, which showed
particularly high timing variability in this stress condition. In summary, this
approach provides insight into the temporal organization of gene expression programs
at the single-cell level and suggests dependencies between response programs and
the underlying variability-introducing mechanisms. Altogether, this work advances
our understanding of the diverse effects that antibiotics have on bacteria. These
results were obtained by taking into account gene expression dynamics, which allowed
us to identify general principles, molecular mechanisms, and dependencies between
genes. Our findings may have implications for infectious disease treatments, and
microbial communities in the human body and in nature. '
acknowledgement: 'First of all, I would like to express great gratitude to my PhD
supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom
to explore different scientific directions during this project, and follow the research
lines of my interest. I am thankful for constructive and often extensive discussions
and his support and commitment during the different stages of my PhD. I want to
thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest
and their valuable input to this project. Special thanks to Nassos for career guidance,
and for accepting me in his lab. A big thank you goes to the past, present and affiliated
members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová,
Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr,
Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed
working and discussing with you very much and I will miss our lengthy group meetings,
our inspiring journal clubs, and our common lunches. Special thanks to Bor for great
mental and professional support during the hard months of thesis writing, and to
Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial
Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and
collaborator Georg Rieckh for his enthusiasm and for getting so involved in these
projects, for his endurance and for his company throughout the years. Thanks to
the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular
I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange,
and enjoyable time together. Thanks to everybody who contributed to the cover for
Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh,
Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by
the graphic designer Martina Markus from the University of Cologne. Thanks to all
my office mates in the first floor Bertalanffy building throughout the years: for
ensuring a pleasant working atmosphere, and for your company! In general, I want
to thank all the people that make IST such a great environment, with the many possibilities
to shape our own social and research environment. I want to thank my family for
all kind of practical support during the years, and my second family in Argentina
for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being
great siblings, and to Helena and Valentin for the joy you brought to my life. My
deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and
for believing in me. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
citation:
ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862
apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria
– insights from dynamic gene expression responses to antibiotics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862
chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria –
Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of
Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.
ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics,” Institute of Science and
Technology Austria, 2017.
ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. Institute of Science and
Technology Austria.
mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.
short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and
Technology Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2023-09-07T12:00:26Z
day: '27'
ddc:
- '571'
- '579'
degree_awarded: PhD
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:th_862
file:
- access_level: closed
checksum: da3993c5f90f59a8e8623cc31ad501dd
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:48:51Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6210'
file_name: Thesis_KarinMitosch.docx
file_size: 6331071
relation: source_file
- access_level: open_access
checksum: 24c3d9e51992f1b721f3df55aa13fcb8
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:48:51Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6211'
file_name: Thesis_KarinMitosch.pdf
file_size: 9289852
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '113'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6831'
pubrep_id: '862'
related_material:
record:
- id: '2001'
relation: part_of_dissertation
status: public
- id: '666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Timing, variability and cross-protection in bacteria – insights from dynamic
gene expression responses to antibiotics
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '819'
abstract:
- lang: eng
text: 'Contagious diseases must transmit from infectious to susceptible hosts in
order to reproduce. Whilst vectored pathogens can rely on intermediaries to find
new hosts for them, many infectious pathogens require close contact or direct
interaction between hosts for transmission. Hence, this means that conspecifics
are often the main source of infection for most animals and so, in theory, animals
should avoid conspecifics to reduce their risk of infection. Of course, in reality
animals must interact with one another, as a bare minimum, to mate. However, being
social provides many additional benefits and group living has become a taxonomically
diverse and widespread trait. How then do social animals overcome the issue of
increased disease? Over the last few decades, the social insects (ants, termites
and some bees and wasps) have become a model system for studying disease in social
animals. On paper, a social insect colony should be particularly susceptible to
disease, given that they often contain thousands of potential hosts that are closely
related and frequently interact, as well as exhibiting stable environmental conditions
that encourage microbial growth. Yet, disease outbreaks appear to be rare and
attempts to eradicate pest species using pathogens have failed time and again.
Evolutionary biologists investigating this observation have discovered that the
reduced disease susceptibility in social insects is, in part, due to collectively
performed disease defences of the workers. These defences act like a “social immune
system” for the colony, resulting in a per capita decrease in disease, termed
social immunity. Our understanding of social immunity, and its importance in relation
to the immunological defences of each insect, continues to grow, but there remain
many open questions. In this thesis I have studied disease defence in garden ants.
In the first data chapter, I use the invasive garden ant, Lasius neglectus, to
investigate how colonies mitigate lethal infections and prevent them from spreading
systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour
that uses endogenously produced acidic poison to kill diseased brood and to prevent
the pathogen from replicating. In the second experimental chapter, I continue
to study the use of poison in invasive garden ant colonies, finding that it is
sprayed prophylactically within the nest. However, this spraying has negative
effects on developing pupae when they have had their cocoons artificially removed.
Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon
spinning in this species. In the next experimental chapter, I investigated how
colony founding black garden ant queens (Lasius niger) prevent disease when a
co-foundress dies. I show that ant queens prophylactically perform undertaking
behaviours, similar to those performed by the workers in mature nests. When a
co-foundress was infected, these undertaking behaviours improved the survival
of the healthy queen. In the final data chapter, I explored how immunocompetence
(measured as antifungal activity) changes as incipient black garden ant colonies
grow and mature, from the solitary queen phase to colonies with several hundred
workers. Queen and worker antifungal activity varied throughout this time period,
but despite social immunity, did not decrease as colonies matured. In addition
to the above data chapters, this thesis includes two co-authored reviews. In the
first, we examine the state of the art in the field of social immunity and how
it might develop in the future. In the second, we identify several challenges
and open questions in the study of disease defence in animals. We highlight how
social insects offer a unique model to tackle some of these problems, as disease
defence can be studied from the cell to the society. '
acknowledgement: "ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely
spoilt to work in a lab with such good resources and I must thank the wonderful
Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help
and keeping the lab up and running. You guys will probably be the most missed once
I realise just how much work you have been saving me! For the same reason, I must
say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding
my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you
will be sorely missed now that I will have to take this task on myself. Of course,
I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing
and being a constant source of guidance and inspiration. You have given me the perfect
balance of independence and supervision. I cannot thank you enough for creating
such a great working environment and allowing me the freedom to follow my own research
questions. I have had so many exceptional opportunities – attending and presenting
at conferences all over the world, inviting me to write the ARE with you, going
to workshops in Panama and Switzerland, and even organising our own PhD course –
that I often think I must have had the best PhD in the world. You have taught me
so much and made me a scientist. I sincerely hope we get the chance to work together
again in the future. Thank you for everything. I must also thank my PhD Committee,
Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout
the duration of my PhD. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
citation:
ama: Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861
apa: Pull, C. (2017). Disease defence in garden ants. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861
chicago: Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science
and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861.
ieee: C. Pull, “Disease defence in garden ants,” Institute of Science and Technology
Austria, 2017.
ista: Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology
Austria.
mla: Pull, Christopher. Disease Defence in Garden Ants. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.
short: C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-28T11:31:32Z
day: '26'
ddc:
- '576'
- '577'
- '578'
- '579'
- '590'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:th_861
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publist_id: '6830'
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- id: '616'
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- id: '806'
relation: part_of_dissertation
status: public
- id: '734'
relation: part_of_dissertation
status: public
- id: '732'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Disease defence in garden ants
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '820'
abstract:
- lang: eng
text: "The lac operon is a classic model system for bacterial gene regulation, and
has been studied extensively in E. coli, a classic model organism. However, not
much is known about E. coli’s ecology and life outside the laboratory, in particular
in soil and water environments. The natural diversity of the lac operon outside
the laboratory, its role in the ecology of E. coli and the selection pressures
it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore
the genetic diversity, phylogenetic history and signatures of selection of the
lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia.
I found that complete lac operons were present in all isolates examined, which
in all but one case were functional. The lac operon phylogeny conformed to the
whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal
gene transfer as an explanation for the presence of functional lac operons in
these clades. All lac operon genes showed a signature of purifying selection;
this signature was strongest for the lacY gene. Lac operon genes of human and
environmental isolates showed similar signatures of selection, except the lacZ
gene, which showed a stronger signature of selection in environmental isolates.\r\nIn
Chapter Three, I try to identify the natural genetic variation relevant for phenotype
and fitness in the lac operon, comparing growth rate on lactose and LacZ activity
of the lac operons of these wild isolates in a common genetic background. Sequence
variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase
binding motif, predicted variation in LacZ activity at full induction, using a
thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation
in LacZ activity, nor RNA polymerase binding predicted by the model correlated
with variation in growth rate. Lac operons of human and environmental isolates
did not differ systematically in either growth rate on lactose or LacZ protein
activity, suggesting that these lac operons have been exposed to similar selection
pressures. We thus have no evidence that the phenotypic variation we measured
is relevant for fitness.\r\nTo start assessing the effect of genomic background
on the growth phenotype conferred by the lac operon, I compared growth on minimal
medium with lactose between lac operon constructs and the corresponding original
isolates, I found that maximal growth rate was determined by genomic background,
with almost all backgrounds conferring higher growth rates than lab strain K12
MG1655. However, I found no evidence that the lactose concentration at which growth
was half maximal depended on genomic background."
acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon
Bollback for giving me the chance to do this work, for sharing the ideas that lay
at the basis of this work, for his honesty and openness, showing himself to me as
a person and not just as a boss. Thanks to Nick Barton for his guidance at the last
stage, reading and commenting extensively on several versions of this manuscript,
and for his encouragement; thanks to both Jon and Nick for their kindness and patience.
Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be
in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter
my thesis committee at the last moment, and for his very sharp, helpful and relevant
comments during and after the defense. Thanks to my collaborators and discussion
partners: Anne Kupczok, for her guidance, ideas and discussions during the construction
of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh
for making me aware of the issue of parameter identifiability, suggesting how to
solve it, and for his unfortunate idea to start the plasmid enterprise in the first
place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments
on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting,
fast forwarding the analysis to turbo speed and making beautiful figures, and making
the discussion fun on top of it all; Vanessa Barone for her last minute comments,
especially on Chapter Three, providing a sharp and very helpful experimentalist
perspective at the last moment; Maros Pleska and Marjon de Vos for their comments
on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation
between growth rate and lactose concentration; Bor Kavcic for his input on growth
rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton,
Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific
environment to work in, as well as a lot of warmth and colour to everyday life.
And thanks to the friends I found here, to the people who were there for me and
to the people who changed my life, making it stranger and more beautiful than I
could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof,
Karin, Irene, Misha, Mato, Guillaume and Zanin. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Fabienne
full_name: Jesse, Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
citation:
ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857
apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857
chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and
Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.
ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology
Austria, 2017.
ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology
Austria.
mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and
Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.
short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-25T00:00:00Z
date_updated: 2023-09-07T12:01:21Z
day: '25'
ddc:
- '576'
- '577'
- '579'
degree_awarded: PhD
department:
- _id: JoBo
doi: 10.15479/AT:ISTA:th_857
ec_funded: 1
file:
- access_level: open_access
checksum: c62257a7bff0c5f39e1abffc6bfcca5c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:00Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5252'
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content_type: application/x-tex
creator: dernst
date_created: 2019-04-05T08:51:59Z
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file_name: 2017_thesis_Jesse_source.tex
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '87'
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6829'
pubrep_id: '857'
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
title: The lac operon in the wild
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '821'
abstract:
- lang: eng
text: "This dissertation focuses on algorithmic aspects of program verification,
and presents modeling and complexity advances on several problems related to the\r\nstatic
analysis of programs, the stateless model checking of concurrent programs, and
the competitive analysis of real-time scheduling algorithms.\r\nOur contributions
can be broadly grouped into five categories.\r\n\r\nOur first contribution is
a set of new algorithms and data structures for the quantitative and data-flow
analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt
has been observed that the control-flow graphs of typical programs have special
structure, and are characterized as graphs of small treewidth.\r\nWe utilize this
structural property to provide faster algorithms for the quantitative and data-flow
analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic
treatment of the considered problem,\r\nwhere several interesting analyses, such
as the reachability, shortest path, and certain kind of data-flow analysis problems
follow as special cases. \r\nWe exploit the constant-treewidth property to obtain
algorithmic improvements for on-demand versions of the problems, \r\nand provide
data structures with various tradeoffs between the resources spent in the preprocessing
and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative
problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff,
minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur
second contribution is a set of algorithms for Dyck reachability with applications
to data-dependence analysis and alias analysis.\r\nIn particular, we develop an
optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous
in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we
develop an efficient algorithm for context-sensitive data-dependence analysis
via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library
code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in
almost linear time, after which the contribution of the library in the complexity
of the client analysis is (i)~linear in the number of call sites and (ii)~only
logarithmic in the size of the whole library, as opposed to linear in the size
of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix
Multiplication-hard in general, and the hardness also holds for graphs of constant
treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial
algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur
third contribution is the formalization and algorithmic treatment of the Quantitative
Interprocedural Analysis framework.\r\nIn this framework, the transitions of a
recursive program are annotated as good, bad or neutral, and receive a weight
which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative
Interprocedural Analysis problem asks to determine whether there exists an infinite
run of the program where the long-run ratio of the bad weights over the good weights
is above a given threshold.\r\nWe illustrate how several quantitative problems
related to static analysis of recursive programs can be instantiated in this framework,\r\nand
present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution
is a new dynamic partial-order reduction for the stateless model checking of concurrent
programs. Traditional approaches rely on the standard Mazurkiewicz equivalence
between traces, by means of partitioning the trace space into equivalence classes,
and attempting to explore a few representatives from each class.\r\nWe present
a new dynamic partial-order reduction method called the Data-centric Partial
Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between
traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning
of the trace space than any exploration method based on the standard Mazurkiewicz
equivalence.\r\nDepending on the program, the new partitioning can be even exponentially
coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored
class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic
verification techniques in the competitive analysis and synthesis of real-time
scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage
automata on infinite words to compute the competitive ratio of real-time schedulers
subject to various environmental constraints.\r\nOn the synthesis side, we introduce
a new instance of two-player mean-payoff partial-information games, and show\r\nhow
the synthesis of an optimal real-time scheduler can be reduced to computing winning
strategies in this new type of games."
acknowledgement: "First, I am thankful to my advisor, Krishnendu Chatterjee, for offering
me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide
range of interesting topics, as well as for his constant availability and continuous
support throughout my doctoral studies. I have had the privilege of collaborating
with, discussing and getting inspired by all members of my committee: Thomas A.
Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people
has been very instrumental both to the research carried out for this dissertation,
and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my
numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to
results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions
on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration
on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our
initial discussions on partial order reduction techniques in stateless model checking.
I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful
collaborations on\r\ntopics outside the scope of this dissertation, as well as the
interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary
and Marek Chalupa, with whom I have shared my excitement on various research topics.
Together with my collaborators, I thank officemates and members of the Chatterjee
and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha
Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna,
\ Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi,
Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei
Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong,
Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and
office spaces, with many of the above people I have been fortunate to share numerous
whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied
by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her
continuous assistance in matters\r\nthat often exceeded her official duties, and
who made my integration in Austria a smooth process."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Pavlogiannis A. Algorithmic advances in program analysis and their applications.
2017. doi:10.15479/AT:ISTA:th_854
apa: Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their
applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854
chicago: Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their
Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.
ieee: A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,”
Institute of Science and Technology Austria, 2017.
ista: Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications.
Institute of Science and Technology Austria.
mla: Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their
Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.
short: A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications,
Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '09'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrCh
doi: 10.15479/AT:ISTA:th_854
ec_funded: 1
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language:
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month: '08'
oa: 1
oa_version: Published Version
page: '418'
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6828'
pubrep_id: '854'
related_material:
record:
- id: '1071'
relation: part_of_dissertation
status: public
- id: '1437'
relation: part_of_dissertation
status: public
- id: '1602'
relation: part_of_dissertation
status: public
- id: '1604'
relation: part_of_dissertation
status: public
- id: '1607'
relation: part_of_dissertation
status: public
- id: '1714'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Algorithmic advances in program analysis and their applications
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '822'
abstract:
- lang: eng
text: 'Polymicrobial infections constitute small ecosystems that accommodate several
bacterial species. Commonly, these bacteria are investigated in isolation. However,
it is unknown to what extent the isolates interact and whether their interactions
alter bacterial growth and ecosystem resilience in the presence and absence of
antibiotics. We quantified the complete ecological interaction network for 72
bacterial isolates collected from 23 individuals diagnosed with polymicrobial
urinary tract infections and found that most interactions cluster based on evolutionary
relatedness. Statistical network analysis revealed that competitive and cooperative
reciprocal interactions are enriched in the global network, while cooperative
interactions are depleted in the individual host community networks. A population
dynamics model parameterized by our measurements suggests that interactions restrict
community stability, explaining the observed species diversity of these communities.
We further show that the clinical isolates frequently protect each other from
clinically relevant antibiotics. Together, these results highlight that ecological
interactions are crucial for the growth and survival of bacteria in polymicrobial
infection communities and affect their assembly and resilience. '
article_processing_charge: No
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Alan
full_name: Mcnally, Alan
last_name: Mcnally
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological
stability, and collective antibiotic tolerance in polymicrobial infections. PNAS.
2017;114(40):10666-10671. doi:10.1073/pnas.1713372114
apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114
chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach.
“Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance
in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1713372114.
ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp.
10666–10671, 2017.
ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks,
ecological stability, and collective antibiotic tolerance in polymicrobial infections.
PNAS. 114(40), 10666–10671.
mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective
Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no.
40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.
short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-10-03T00:00:00Z
date_updated: 2023-09-26T16:18:48Z
day: '03'
department:
- _id: ToBo
doi: 10.1073/pnas.1713372114
ec_funded: 1
external_id:
isi:
- '000412130500061'
pmid:
- '28923953'
intvolume: ' 114'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/
month: '10'
oa: 1
oa_version: Submitted Version
page: 10666 - 10671
pmid: 1
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6827'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interaction networks, ecological stability, and collective antibiotic tolerance
in polymicrobial infections
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2017'
...
---
_id: '823'
abstract:
- lang: eng
text: The resolution of a linear system with positive integer variables is a basic
yet difficult computational problem with many applications. We consider sparse
uncorrelated random systems parametrised by the density c and the ratio α=N/M
between number of variables N and number of constraints M. By means of ensemble
calculations we show that the space of feasible solutions endows a Van-Der-Waals
phase diagram in the plane (c, α). We give numerical evidence that the associated
computational problems become more difficult across the critical point and in
particular in the coexistence region.
article_number: '093404'
article_processing_charge: No
author:
- first_name: Simona
full_name: Colabrese, Simona
last_name: Colabrese
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Luca
full_name: Leuzzi, Luca
last_name: Leuzzi
- first_name: Enzo
full_name: Marinari, Enzo
last_name: Marinari
citation:
ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer
linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017;2017(9). doi:10.1088/1742-5468/aa85c3'
apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase
transitions in integer linear problems. Journal of Statistical Mechanics:
Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3'
chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari.
“Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics:
Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.'
ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions
in integer linear problems,” Journal of Statistical Mechanics: Theory and
Experiment, vol. 2017, no. 9. IOPscience, 2017.'
ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions
in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017(9), 093404.'
mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.”
Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no.
9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.'
short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical
Mechanics: Theory and Experiment 2017 (2017).'
date_created: 2018-12-11T11:48:41Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-26T16:18:12Z
day: '26'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa85c3
ec_funded: 1
external_id:
isi:
- '000411842900001'
intvolume: ' 2017'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.06303
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOPscience
publist_id: '6826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transitions in integer linear problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '8235'
abstract:
- lang: eng
text: Due to large homology of human and canine EGFR, dogs suffering from spontaneous
EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic
compounds can be developed for both human and veterinary patients. This study
describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with
potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG
was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc.
Successful coupling of 10 DTPA molecules per antibody on average was proven by
significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots.
Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained
its binding capacity towards human and canine EGFR in flow cytometry, immuno-
and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was
determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma
cells by a competition binding technique. Stability tests of the radiolabeled
compound identified TRIS buffered saline as the ideal formulation for short-term
storage with 87.11 ±6.04% intact compound being still detected 60 minutes post
radiolabeling. High stability, specificity and EGFR binding affinity pinpoint
towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the
first proof-of-concept diagnostic and therapeutic applications in canine cancer
patients.
article_processing_charge: No
article_type: original
author:
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Neydher
full_name: Berroterán-Infante, Neydher
last_name: Berroterán-Infante
- first_name: Christina
full_name: Rami-Mark, Christina
last_name: Rami-Mark
- first_name: Monika
full_name: Dumanic, Monika
last_name: Dumanic
- first_name: Miroslawa
full_name: Matz, Miroslawa
last_name: Matz
- first_name: Michael
full_name: Willmann, Michael
last_name: Willmann
- first_name: Fritz
full_name: Andreae, Fritz
last_name: Andreae
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Wolfgang
full_name: Wadsak, Wolfgang
last_name: Wadsak
- first_name: Markus
full_name: Mitterhauser, Markus
last_name: Mitterhauser
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled
caninized anti-EGFR antibody for comparative oncology trials. Oncotarget.
2017;8:83128-83141. doi:10.18632/oncotarget.20914
apa: Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann,
M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR
antibody for comparative oncology trials. Oncotarget. Impact Journals.
https://doi.org/10.18632/oncotarget.20914
chicago: Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika
Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development
of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.”
Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20914.
ieee: J. Singer et al., “Development of a radiolabeled caninized anti-EGFR
antibody for comparative oncology trials,” Oncotarget, vol. 8. Impact Journals,
pp. 83128–83141, 2017.
ista: Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M,
Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development
of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials.
Oncotarget. 8, 83128–83141.
mla: Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody
for Comparative Oncology Trials.” Oncotarget, vol. 8, Impact Journals,
2017, pp. 83128–41, doi:10.18632/oncotarget.20914.
short: J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann,
F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget
8 (2017) 83128–83141.
date_created: 2020-08-10T11:53:18Z
date_published: 2017-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '15'
doi: 10.18632/oncotarget.20914
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.20914
month: '09'
oa: 1
oa_version: Published Version
page: 83128-83141
publication: Oncotarget
publication_identifier:
issn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Development of a radiolabeled caninized anti-EGFR antibody for comparative
oncology trials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8236'
abstract:
- lang: eng
text: Th2 immunity and allergic immune surveillance play critical roles in host
responses to pathogens, parasites and allergens. Numerous studies have reported
significant links between Th2 responses and cancer, including insights into the
functions of IgE antibodies and associated effector cells in both antitumour immune
surveillance and therapy. The interdisciplinary field of AllergoOncology was given
Task Force status by the European Academy of Allergy and Clinical Immunology in
2014. Affiliated expert groups focus on the interface between allergic responses
and cancer, applied to immune surveillance, immunomodulation and the functions
of IgE‐mediated immune responses against cancer, to derive novel insights into
more effective treatments. Coincident with rapid expansion in clinical application
of cancer immunotherapies, here we review the current state‐of‐the‐art and future
translational opportunities, as well as challenges in this relatively new field.
Recent developments include improved understanding of Th2 antibodies, intratumoral
innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation
by dendritic cells, as well as immunotherapeutic strategies such as vaccines and
recombinant antibodies, and finally, the management of allergy in daily clinical
oncology. Shedding light on the crosstalk between allergic response and cancer
is paving the way for new avenues of treatment.
article_processing_charge: No
article_type: original
author:
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
orcid: 0000-0003-4019-5765
- first_name: H. J.
full_name: Bax, H. J.
last_name: Bax
- first_name: R.
full_name: Bianchini, R.
last_name: Bianchini
- first_name: M.
full_name: Capron, M.
last_name: Capron
- first_name: C.
full_name: Corrigan, C.
last_name: Corrigan
- first_name: M.
full_name: Castells, M.
last_name: Castells
- first_name: D.
full_name: Dombrowicz, D.
last_name: Dombrowicz
- first_name: T. R.
full_name: Daniels-Wells, T. R.
last_name: Daniels-Wells
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: E.
full_name: Fiebiger, E.
last_name: Fiebiger
- first_name: S.
full_name: Gatault, S.
last_name: Gatault
- first_name: H. J.
full_name: Gould, H. J.
last_name: Gould
- first_name: J.
full_name: Janda, J.
last_name: Janda
- first_name: D. H.
full_name: Josephs, D. H.
last_name: Josephs
- first_name: P.
full_name: Karagiannis, P.
last_name: Karagiannis
- first_name: F.
full_name: Levi-Schaffer, F.
last_name: Levi-Schaffer
- first_name: A.
full_name: Meshcheryakova, A.
last_name: Meshcheryakova
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Mekori, Y.
last_name: Mekori
- first_name: F.
full_name: Mungenast, F.
last_name: Mungenast
- first_name: E. A.
full_name: Nigro, E. A.
last_name: Nigro
- first_name: M. L.
full_name: Penichet, M. L.
last_name: Penichet
- first_name: F.
full_name: Redegeld, F.
last_name: Redegeld
- first_name: L.
full_name: Saul, L.
last_name: Saul
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: J. F.
full_name: Spicer, J. F.
last_name: Spicer
- first_name: A. G.
full_name: Siccardi, A. G.
last_name: Siccardi
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: M. C.
full_name: Turner, M. C.
last_name: Turner
- first_name: E.
full_name: Untersmayr, E.
last_name: Untersmayr
- first_name: L.
full_name: Vangelista, L.
last_name: Vangelista
- first_name: S. N.
full_name: Karagiannis, S. N.
last_name: Karagiannis
citation:
ama: 'Jensen-Jarolim E, Bax HJ, Bianchini R, et al. AllergoOncology - the impact
of allergy in oncology: EAACI position paper. Allergy. 2017;72(6):866-887.
doi:10.1111/all.13119'
apa: 'Jensen-Jarolim, E., Bax, H. J., Bianchini, R., Capron, M., Corrigan, C., Castells,
M., … Karagiannis, S. N. (2017). AllergoOncology - the impact of allergy in oncology:
EAACI position paper. Allergy. Wiley. https://doi.org/10.1111/all.13119'
chicago: 'Jensen-Jarolim, E., H. J. Bax, R. Bianchini, M. Capron, C. Corrigan, M.
Castells, D. Dombrowicz, et al. “AllergoOncology - the Impact of Allergy in Oncology:
EAACI Position Paper.” Allergy. Wiley, 2017. https://doi.org/10.1111/all.13119.'
ieee: 'E. Jensen-Jarolim et al., “AllergoOncology - the impact of allergy
in oncology: EAACI position paper,” Allergy, vol. 72, no. 6. Wiley, pp.
866–887, 2017.'
ista: 'Jensen-Jarolim E, Bax HJ, Bianchini R, Capron M, Corrigan C, Castells M,
Dombrowicz D, Daniels-Wells TR, Singer J, Fiebiger E, Gatault S, Gould HJ, Janda
J, Josephs DH, Karagiannis P, Levi-Schaffer F, Meshcheryakova A, Mechtcheriakova
D, Mekori Y, Mungenast F, Nigro EA, Penichet ML, Redegeld F, Saul L, Singer J,
Spicer JF, Siccardi AG, Spillner E, Turner MC, Untersmayr E, Vangelista L, Karagiannis
SN. 2017. AllergoOncology - the impact of allergy in oncology: EAACI position
paper. Allergy. 72(6), 866–887.'
mla: 'Jensen-Jarolim, E., et al. “AllergoOncology - the Impact of Allergy in Oncology:
EAACI Position Paper.” Allergy, vol. 72, no. 6, Wiley, 2017, pp. 866–87,
doi:10.1111/all.13119.'
short: E. Jensen-Jarolim, H.J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells,
D. Dombrowicz, T.R. Daniels-Wells, J. Singer, E. Fiebiger, S. Gatault, H.J. Gould,
J. Janda, D.H. Josephs, P. Karagiannis, F. Levi-Schaffer, A. Meshcheryakova, D.
Mechtcheriakova, Y. Mekori, F. Mungenast, E.A. Nigro, M.L. Penichet, F. Redegeld,
L. Saul, J. Singer, J.F. Spicer, A.G. Siccardi, E. Spillner, M.C. Turner, E. Untersmayr,
L. Vangelista, S.N. Karagiannis, Allergy 72 (2017) 866–887.
date_created: 2020-08-10T11:53:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '01'
doi: 10.1111/all.13119
extern: '1'
intvolume: ' 72'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/all.13119
month: '06'
oa: 1
oa_version: Published Version
page: 866-887
publication: Allergy
publication_identifier:
issn:
- 0105-4538
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'AllergoOncology - the impact of allergy in oncology: EAACI position paper'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2017'
...
---
_id: '8237'
abstract:
- lang: eng
text: Monoclonal antibodies find broad application as therapy for various types
of cancer by employing multiple mechanisms of action against tumors. Manipulating
the Fc-mediated functions of antibodies that engage immune effector cells, such
as NK cells, represents a strategy to influence effector cell activation and to
enhance antibody potency and potentially efficacy. We developed a novel approach
to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies.
This entailed coupling single expression vector (pVitro1) antibody cloning, using
polymerase incomplete primer extension (PIPE) polymerase chain reaction, together
with simultaneous Fc region point mutagenesis and high yield transient expression
in human mammalian cells. Employing this, we engineered wild type, low (N297Q,
NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels
recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan
4. Antibodies were generated with universal mutagenic primers applicable to any
IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in
small culture volumes, at high yields and within 12 days from design to purified
material. Antibody variants conserved their Fab-mediated recognition of target
antigens and their direct anti-proliferative effects against cancer cells. Fc
mutations had a significant impact on antibody interactions with Fc receptors
(FcRs) on human NK cells, and consequently on the potency of NK cell activation,
quantified by immune complex-mediated calcium mobilization and by antibody-dependent
cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and
testing of Fc region engagement with cognate FcRs can facilitate the design of
antibodies with defined effector functions and potentially enhanced efficacy against
tumor cells.
article_number: '1112'
article_processing_charge: No
article_type: original
author:
- first_name: Kristina M.
full_name: Ilieva, Kristina M.
last_name: Ilieva
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Daniela Y.
full_name: Achkova, Daniela Y.
last_name: Achkova
- first_name: Tihomir S.
full_name: Dodev, Tihomir S.
last_name: Dodev
- first_name: Silvia
full_name: Mele, Silvia
last_name: Mele
- first_name: Silvia
full_name: Crescioli, Silvia
last_name: Crescioli
- first_name: Heather J.
full_name: Bax, Heather J.
last_name: Bax
- first_name: Anthony
full_name: Cheung, Anthony
last_name: Cheung
- first_name: Panagiotis
full_name: Karagiannis, Panagiotis
last_name: Karagiannis
- first_name: Isabel
full_name: Correa, Isabel
last_name: Correa
- first_name: Mariangela
full_name: Figini, Mariangela
last_name: Figini
- first_name: Rebecca
full_name: Marlow, Rebecca
last_name: Marlow
- first_name: Debra H.
full_name: Josephs, Debra H.
last_name: Josephs
- first_name: Andrew J.
full_name: Beavil, Andrew J.
last_name: Beavil
- first_name: John
full_name: Maher, John
last_name: Maher
- first_name: James F.
full_name: Spicer, James F.
last_name: Spicer
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Andrew N.
full_name: Tutt, Andrew N.
last_name: Tutt
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
citation:
ama: Ilieva KM, Singer J, Achkova DY, et al. Functionally active Fc mutant antibodies
recognizing cancer antigens generated rapidly at high yields. Frontiers in
Immunology. 2017;8. doi:10.3389/fimmu.2017.01112
apa: Ilieva, K. M., Singer, J., Achkova, D. Y., Dodev, T. S., Mele, S., Crescioli,
S., … Karagiannis, S. N. (2017). Functionally active Fc mutant antibodies recognizing
cancer antigens generated rapidly at high yields. Frontiers in Immunology.
Frontiers. https://doi.org/10.3389/fimmu.2017.01112
chicago: Ilieva, Kristina M., Judit Singer, Daniela Y. Achkova, Tihomir S. Dodev,
Silvia Mele, Silvia Crescioli, Heather J. Bax, et al. “Functionally Active Fc
Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.”
Frontiers in Immunology. Frontiers, 2017. https://doi.org/10.3389/fimmu.2017.01112.
ieee: K. M. Ilieva et al., “Functionally active Fc mutant antibodies recognizing
cancer antigens generated rapidly at high yields,” Frontiers in Immunology,
vol. 8. Frontiers, 2017.
ista: Ilieva KM, Singer J, Achkova DY, Dodev TS, Mele S, Crescioli S, Bax HJ, Cheung
A, Karagiannis P, Correa I, Figini M, Marlow R, Josephs DH, Beavil AJ, Maher J,
Spicer JF, Jensen-Jarolim E, Tutt AN, Karagiannis SN. 2017. Functionally active
Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields.
Frontiers in Immunology. 8, 1112.
mla: Ilieva, Kristina M., et al. “Functionally Active Fc Mutant Antibodies Recognizing
Cancer Antigens Generated Rapidly at High Yields.” Frontiers in Immunology,
vol. 8, 1112, Frontiers, 2017, doi:10.3389/fimmu.2017.01112.
short: K.M. Ilieva, J. Singer, D.Y. Achkova, T.S. Dodev, S. Mele, S. Crescioli,
H.J. Bax, A. Cheung, P. Karagiannis, I. Correa, M. Figini, R. Marlow, D.H. Josephs,
A.J. Beavil, J. Maher, J.F. Spicer, E. Jensen-Jarolim, A.N. Tutt, S.N. Karagiannis,
Frontiers in Immunology 8 (2017).
date_created: 2020-08-10T11:53:32Z
date_published: 2017-09-11T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '11'
doi: 10.3389/fimmu.2017.01112
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3389/fimmu.2017.01112
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
status: public
title: Functionally active Fc mutant antibodies recognizing cancer antigens generated
rapidly at high yields
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8239'
abstract:
- lang: eng
text: Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts
during smoking and is best known for its genotoxic capacity. Here, we aimed to
assess whether acrolein at concentrations relevant for smokers may also exert
immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c
allergy model repeated nasal exposure to acrolein abrogated allergen-specific
antibody and cytokine formation, and led to a relative accumulation of regulatory
T cells in the lungs. Only the acrolein-treated mice were protected from bronchial
hyperreactivity as well as from anaphylactic reactions upon challenge with the
specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral
Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls.
Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon
receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone
Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which
could be antagonized by resveratrol. Our mouse and human data thus revealed that
acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells.
This provides a novel explanation why smokers have a lower allergy, but higher
cancer risk.
article_number: '45067'
article_processing_charge: No
article_type: original
author:
- first_name: Franziska
full_name: Roth-Walter, Franziska
last_name: Roth-Walter
- first_name: Cornelia
full_name: Bergmayr, Cornelia
last_name: Bergmayr
- first_name: Sarah
full_name: Meitz, Sarah
last_name: Meitz
- first_name: Stefan
full_name: Buchleitner, Stefan
last_name: Buchleitner
- first_name: Caroline
full_name: Stremnitzer, Caroline
last_name: Stremnitzer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Anna
full_name: Moskovskich, Anna
last_name: Moskovskich
- first_name: Mario A.
full_name: Müller, Mario A.
last_name: Müller
- first_name: Georg A.
full_name: Roth, Georg A.
last_name: Roth
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Zdenek
full_name: Dvorak, Zdenek
last_name: Dvorak
- first_name: Alina
full_name: Neunkirchner, Alina
last_name: Neunkirchner
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Roth-Walter F, Bergmayr C, Meitz S, et al. Janus-faced Acrolein prevents allergy
but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse
model for passive respiratory exposure. Scientific Reports. 2017;7. doi:10.1038/srep45067'
apa: 'Roth-Walter, F., Bergmayr, C., Meitz, S., Buchleitner, S., Stremnitzer, C.,
Singer, J., … Jensen-Jarolim, E. (2017). Janus-faced Acrolein prevents allergy
but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse
model for passive respiratory exposure. Scientific Reports. Springer Nature.
https://doi.org/10.1038/srep45067'
chicago: 'Roth-Walter, Franziska, Cornelia Bergmayr, Sarah Meitz, Stefan Buchleitner,
Caroline Stremnitzer, Judit Singer, Anna Moskovskich, et al. “Janus-Faced Acrolein
Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+
Cells: Mouse Model for Passive Respiratory Exposure.” Scientific Reports.
Springer Nature, 2017. https://doi.org/10.1038/srep45067.'
ieee: 'F. Roth-Walter et al., “Janus-faced Acrolein prevents allergy but
accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model
for passive respiratory exposure,” Scientific Reports, vol. 7. Springer
Nature, 2017.'
ista: 'Roth-Walter F, Bergmayr C, Meitz S, Buchleitner S, Stremnitzer C, Singer
J, Moskovskich A, Müller MA, Roth GA, Manzano-Szalai K, Dvorak Z, Neunkirchner
A, Jensen-Jarolim E. 2017. Janus-faced Acrolein prevents allergy but accelerates
tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive
respiratory exposure. Scientific Reports. 7, 45067.'
mla: 'Roth-Walter, Franziska, et al. “Janus-Faced Acrolein Prevents Allergy but
Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model
for Passive Respiratory Exposure.” Scientific Reports, vol. 7, 45067, Springer
Nature, 2017, doi:10.1038/srep45067.'
short: F. Roth-Walter, C. Bergmayr, S. Meitz, S. Buchleitner, C. Stremnitzer, J.
Singer, A. Moskovskich, M.A. Müller, G.A. Roth, K. Manzano-Szalai, Z. Dvorak,
A. Neunkirchner, E. Jensen-Jarolim, Scientific Reports 7 (2017).
date_created: 2020-08-10T11:53:46Z
date_published: 2017-03-23T00:00:00Z
date_updated: 2021-01-12T08:17:40Z
day: '23'
doi: 10.1038/srep45067
extern: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/srep45067
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting
immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2017'
...
---
_id: '824'
abstract:
- lang: eng
text: 'In shear flows at transitional Reynolds numbers, localized patches of turbulence,
known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev.
Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic
solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds
number. Combining slicing methods for continuous symmetry reduction with Poincaré
sections for the first time in a shear flow setting, we compute and visualize
the unstable manifold of the lower-branch solution and show that it extends towards
the neighbourhood of the upper-branch solution. Surprisingly, this connection
even persists far above the bifurcation point and appears to mediate the first
stage of the puff generation: amplification of streamwise localized fluctuations.
When the state-space trajectories on the unstable manifold reach the vicinity
of the upper branch, corresponding fluctuations expand in space and eventually
take the usual shape of a puff.'
article_number: R1
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow.
Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516
apa: Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized
chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2017.516
chicago: Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press,
2017. https://doi.org/10.1017/jfm.2017.516.
ieee: N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos
in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University
Press, 2017.
ista: Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in
pipe flow. Journal of Fluid Mechanics. 827, R1.
mla: Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge
University Press, 2017, doi:10.1017/jfm.2017.516.
short: N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-18T00:00:00Z
date_updated: 2023-09-26T16:17:43Z
day: '18'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.516
external_id:
isi:
- '000408326300001'
intvolume: ' 827'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.10484
month: '08'
oa: 1
oa_version: Submitted Version
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6824'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic path to spatially localized chaos in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 827
year: '2017'
...
---
_id: '8240'
abstract:
- lang: eng
text: "Background/Aim: Cancer cell lines are indispensible surrogate models in cancer
research, as they can be used off-the-shelf, expanded to the desired extent, easily
modified and exchanged between research groups for affirmation, reproduction or
follow-up experiments.\r\nAs malignant cells are prone to genomic instability,
phenotypical changes may occur after certain passages in culture. Thus, cell lines
have to be regularly authenticated to ensure data quality. In between experiments
these cell lines are often stored in liquid nitrogen for extended time periods.\r\nAlthough
freezing of cells is a necessary evil, little research is performed on how long-term
storage affects cancer cell lines. Therefore, this study investigated the effects
of a 28-year long liquid nitrogen storage period on BT474 cells with regard to
phenotypical changes, differences in cell-surface receptor expression as well
as cytokine and gene expressional variations.\r\nMethods: Two batches of BT474
cells, one frozen in 1986, the other directly purchased from ATCC were investigated
by light microscopy, cell growth analysis, flow cytometry and cytokine as well
as whole-transcriptome expression profiling.\r\nResults: The cell lines were morphologically
indifferent and showed similar growth rates and similar cell-surface receptor
expression. Transcriptome analysis revealed significant differences in only 26
of 40,716 investigated RefSeq transcripts with 4 of them being up-regulated and
22 down-regulated.\r\nConclusion: This study demonstrates that even after very
long periods of storage in liquid nitrogen, cancer cell lines display only minimal
changes in their gene expression profiles. However, also such minor changes should
be carefully assessed before continuation of experiments, especially if phenotypic
alterations can be additionally observed."
article_processing_charge: No
article_type: original
author:
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Thomas W.
full_name: Grunt, Thomas W.
last_name: Grunt
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
citation:
ama: Singer J, Grunt TW, Jensen-Jarolim E, Singer J. Long term storage in liquid
nitrogen leads to only minor phenotypic and gene expression changes in the mammary
carcinoma model cell line BT474. Oncotarget. 2017;8:35076-35087. doi:10.18632/oncotarget.16623
apa: Singer, J., Grunt, T. W., Jensen-Jarolim, E., & Singer, J. (2017). Long
term storage in liquid nitrogen leads to only minor phenotypic and gene expression
changes in the mammary carcinoma model cell line BT474. Oncotarget. Impact
Journals. https://doi.org/10.18632/oncotarget.16623
chicago: Singer, Judit, Thomas W. Grunt, Erika Jensen-Jarolim, and Josef Singer.
“Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene
Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” Oncotarget.
Impact Journals, 2017. https://doi.org/10.18632/oncotarget.16623.
ieee: J. Singer, T. W. Grunt, E. Jensen-Jarolim, and J. Singer, “Long term storage
in liquid nitrogen leads to only minor phenotypic and gene expression changes
in the mammary carcinoma model cell line BT474,” Oncotarget, vol. 8. Impact
Journals, pp. 35076–35087, 2017.
ista: Singer J, Grunt TW, Jensen-Jarolim E, Singer J. 2017. Long term storage in
liquid nitrogen leads to only minor phenotypic and gene expression changes in
the mammary carcinoma model cell line BT474. Oncotarget. 8, 35076–35087.
mla: Singer, Judit, et al. “Long Term Storage in Liquid Nitrogen Leads to Only Minor
Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line
BT474.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 35076–87, doi:10.18632/oncotarget.16623.
short: J. Singer, T.W. Grunt, E. Jensen-Jarolim, J. Singer, Oncotarget 8 (2017)
35076–35087.
date_created: 2020-08-10T11:53:53Z
date_published: 2017-03-28T00:00:00Z
date_updated: 2021-01-12T08:17:41Z
day: '28'
doi: 10.18632/oncotarget.16623
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.16623
month: '03'
oa: 1
oa_version: Published Version
page: 35076-35087
publication: Oncotarget
publication_identifier:
issn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Long term storage in liquid nitrogen leads to only minor phenotypic and gene
expression changes in the mammary carcinoma model cell line BT474
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '825'
abstract:
- lang: eng
text: What data is needed about data? Describing the process to answer this question
for the institutional data repository IST DataRep.
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. Metadata for research data in practice. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207.
doi:10.31263/voebm.v70i2.1678
apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.
https://doi.org/10.31263/voebm.v70i2.1678
chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1678.
ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70,
no. 2. VÖB, pp. 200–207, 2017.
ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.
mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol.
70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.
short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
& Bibliothekare 70 (2017) 200–207.
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:44Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1678
file:
- access_level: open_access
checksum: 7c4544d07efa2c2add8612b489abb4e2
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:32:17Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5850'
file_name: 2017_VOEB_Petritsch.pdf
file_size: 7843975
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 200 - 207
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6823'
scopus_import: 1
status: public
title: Metadata for research data in practice
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: 70
year: '2017'
...
---
_id: '8299'
abstract:
- lang: eng
text: 'Permissionless blockchain-based cryptocurrencies commonly use proof-of-work
(PoW) or proof-of-stake (PoS) to ensure their security, e.g. to prevent double
spending attacks. However, both approaches have disadvantages: PoW leads to massive
amounts of wasted electricity and re-centralization, whereas major stakeholders
in PoS might be able to create a monopoly. In this work, we propose proof-of-personhood
(PoP), a mechanism that binds physical entities to virtual identities in a way
that enables accountability while preserving anonymity. Afterwards we introduce
PoPCoin, a new cryptocurrency, whose consensus mechanism leverages PoP to eliminate
the dis-advantages of PoW and PoS while ensuring security. PoPCoin leads to a
continuously fair and democratic wealth creation process which paves the way for
an experimental basic income infrastructure.'
article_number: '7966966'
article_processing_charge: No
author:
- first_name: Maria
full_name: Borge, Maria
last_name: Borge
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. Proof-of-personhood:
Redemocratizing permissionless cryptocurrencies. In: 2017 IEEE European Symposium
on Security and Privacy Workshops. IEEE; 2017. doi:10.1109/eurospw.2017.46'
apa: 'Borge, M., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., &
Ford, B. (2017). Proof-of-personhood: Redemocratizing permissionless cryptocurrencies.
In 2017 IEEE European Symposium on Security and Privacy Workshops. Paris,
France: IEEE. https://doi.org/10.1109/eurospw.2017.46'
chicago: 'Borge, Maria, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser,
Nicolas Gailly, and Bryan Ford. “Proof-of-Personhood: Redemocratizing Permissionless
Cryptocurrencies.” In 2017 IEEE European Symposium on Security and Privacy
Workshops. IEEE, 2017. https://doi.org/10.1109/eurospw.2017.46.'
ieee: 'M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, and B. Ford,
“Proof-of-personhood: Redemocratizing permissionless cryptocurrencies,” in 2017
IEEE European Symposium on Security and Privacy Workshops, Paris, France,
2017.'
ista: 'Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. 2017.
Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. 2017 IEEE
European Symposium on Security and Privacy Workshops. EuroS&PW: European Symposium
on Security and Privacy Workshops, 7966966.'
mla: 'Borge, Maria, et al. “Proof-of-Personhood: Redemocratizing Permissionless
Cryptocurrencies.” 2017 IEEE European Symposium on Security and Privacy Workshops,
7966966, IEEE, 2017, doi:10.1109/eurospw.2017.46.'
short: M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, B. Ford,
in:, 2017 IEEE European Symposium on Security and Privacy Workshops, IEEE, 2017.
conference:
end_date: 2017-04-28
location: Paris, France
name: 'EuroS&PW: European Symposium on Security and Privacy Workshops'
start_date: 2017-04-26
date_created: 2020-08-26T11:48:11Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2021-01-12T08:17:57Z
day: '30'
doi: 10.1109/eurospw.2017.46
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
publication: 2017 IEEE European Symposium on Security and Privacy Workshops
publication_identifier:
eisbn:
- '9781538622445'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'Proof-of-personhood: Redemocratizing permissionless cryptocurrencies'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '8301'
abstract:
- lang: eng
text: Software-update mechanisms are critical to the security of modern systems,
but their typically centralized design presents a lucrative and frequently attacked
target. In this work, we propose CHAINIAC, a decentralized software-update framework
that eliminates single points of failure, enforces transparency, and provides
efficient verifiability of integrity and authenticity for software-release processes.
Independent witness servers collectively verify conformance of software updates
to release policies, build verifiers validate the source-to-binary correspondence,
and a tamper-proof release log stores collectively signed updates, thus ensuring
that no release is accepted by clients before being widely disclosed and validated.
The release log embodies a skipchain, a novel data structure, enabling arbitrarily
out-of-date clients to efficiently validate updates and signing keys. Evaluation
of our CHAINIAC prototype on reproducible Debian packages shows that the automated
update process takes the average of 5 minutes per release for individual packages,
and only 20 seconds for the aggregate timeline. We further evaluate the framework
using real-world data from the PyPI package repository and show that it offers
clients security comparable to verifying every single update themselves while
consuming only one-fifth of the bandwidth and having a minimal computational overhead.
article_processing_charge: No
author:
- first_name: Kirill
full_name: Nikitin, Kirill
last_name: Nikitin
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ismail
full_name: Khoffi, Ismail
last_name: Khoffi
- first_name: Justin
full_name: Cappos, Justin
last_name: Cappos
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Nikitin K, Kokoris Kogias E, Jovanovic P, et al. CHAINIAC: Proactive software-update
transparency via collectively signed skipchains and verified builds. In: Proceedings
of the 26th USENIX Conference on Security Symposium. USENIX Association; 2017:1271–1287.'
apa: 'Nikitin, K., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Khoffi,
I., … Ford, B. (2017). CHAINIAC: Proactive software-update transparency via collectively
signed skipchains and verified builds. In Proceedings of the 26th USENIX Conference
on Security Symposium (pp. 1271–1287). Vancouver, Canada: USENIX Association.'
chicago: 'Nikitin, Kirill, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus
Gasser, Nicolas Gailly, Ismail Khoffi, Justin Cappos, and Bryan Ford. “CHAINIAC:
Proactive Software-Update Transparency via Collectively Signed Skipchains and
Verified Builds.” In Proceedings of the 26th USENIX Conference on Security
Symposium, 1271–1287. USENIX Association, 2017.'
ieee: 'K. Nikitin et al., “CHAINIAC: Proactive software-update transparency
via collectively signed skipchains and verified builds,” in Proceedings of
the 26th USENIX Conference on Security Symposium, Vancouver, Canada, 2017,
pp. 1271–1287.'
ista: 'Nikitin K, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Khoffi I, Cappos
J, Ford B. 2017. CHAINIAC: Proactive software-update transparency via collectively
signed skipchains and verified builds. Proceedings of the 26th USENIX Conference
on Security Symposium. SEC: Security Symposium, 1271–1287.'
mla: 'Nikitin, Kirill, et al. “CHAINIAC: Proactive Software-Update Transparency
via Collectively Signed Skipchains and Verified Builds.” Proceedings of the
26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp.
1271–1287.'
short: K. Nikitin, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, I. Khoffi,
J. Cappos, B. Ford, in:, Proceedings of the 26th USENIX Conference on Security
Symposium, USENIX Association, 2017, pp. 1271–1287.
conference:
end_date: 2017-08-18
location: Vancouver, Canada
name: 'SEC: Security Symposium'
start_date: 2017-08-16
date_created: 2020-08-26T12:04:44Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:18:00Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-nikitin.pdf
month: '09'
oa: 1
oa_version: Published Version
page: 1271–1287
publication: Proceedings of the 26th USENIX Conference on Security Symposium
publication_identifier:
isbn:
- '9781931971409'
publication_status: published
publisher: USENIX Association
quality_controlled: '1'
status: public
title: 'CHAINIAC: Proactive software-update transparency via collectively signed skipchains
and verified builds'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '8306'
abstract:
- lang: eng
text: Bias-resistant public randomness is a critical component in many (distributed)
protocols. Generating public randomness is hard, however, because active adversaries
may behave dishonestly to bias public random choices toward their advantage. Existing
solutions do not scale to hundreds or thousands of participants, as is needed
in many decentralized systems. We propose two large-scale distributed protocols,
RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and
unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted
client to divide a set of randomness servers into groups for scalability, and
it depends on the pigeonhole principle to ensure output integrity, even for non-random,
adversarial group choices. RandHerd implements an efficient, decentralized randomness
beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound
in a one-time setup to arrange participants into verifiably unbiased random secret-sharing
groups, which then repeatedly produce random output at predefined intervals. Our
prototype demonstrates that RandHound and RandHerd achieve good performance across
hundreds of participants while retaining a low failure probability by properly
selecting protocol parameters, such as a group size and secret-sharing threshold.
For example, when sharding 512 nodes into groups of 32, our experiments show that
RandHound can produce fresh random output after 240 seconds. RandHerd, after a
setup phase of 260 seconds, is able to generate fresh random output in intervals
of approximately 6 seconds. For this configuration, both protocols operate at
a failure probability of at most 0.08% against a Byzantine adversary.
article_processing_charge: No
author:
- first_name: E.
full_name: Syta, E.
last_name: Syta
- first_name: P.
full_name: Jovanovic, P.
last_name: Jovanovic
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: N.
full_name: Gailly, N.
last_name: Gailly
- first_name: L.
full_name: Gasser, L.
last_name: Gasser
- first_name: I.
full_name: Khoffi, I.
last_name: Khoffi
- first_name: M. J.
full_name: Fischer, M. J.
last_name: Fischer
- first_name: B.
full_name: Ford, B.
last_name: Ford
citation:
ama: 'Syta E, Jovanovic P, Kokoris Kogias E, et al. Scalable bias-resistant distributed
randomness. In: 2017 IEEE Symposium on Security and Privacy. IEEE; 2017:444-460.
doi:10.1109/SP.2017.45'
apa: 'Syta, E., Jovanovic, P., Kokoris Kogias, E., Gailly, N., Gasser, L., Khoffi,
I., … Ford, B. (2017). Scalable bias-resistant distributed randomness. In 2017
IEEE Symposium on Security and Privacy (pp. 444–460). San Jose, CA, United
States: IEEE. https://doi.org/10.1109/SP.2017.45'
chicago: Syta, E., P. Jovanovic, Eleftherios Kokoris Kogias, N. Gailly, L. Gasser,
I. Khoffi, M. J. Fischer, and B. Ford. “Scalable Bias-Resistant Distributed Randomness.”
In 2017 IEEE Symposium on Security and Privacy, 444–60. IEEE, 2017. https://doi.org/10.1109/SP.2017.45.
ieee: E. Syta et al., “Scalable bias-resistant distributed randomness,” in
2017 IEEE Symposium on Security and Privacy, San Jose, CA, United States,
2017, pp. 444–460.
ista: 'Syta E, Jovanovic P, Kokoris Kogias E, Gailly N, Gasser L, Khoffi I, Fischer
MJ, Ford B. 2017. Scalable bias-resistant distributed randomness. 2017 IEEE Symposium
on Security and Privacy. SP: Symposium on Security and Privacy, 444–460.'
mla: Syta, E., et al. “Scalable Bias-Resistant Distributed Randomness.” 2017
IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–60, doi:10.1109/SP.2017.45.
short: E. Syta, P. Jovanovic, E. Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi,
M.J. Fischer, B. Ford, in:, 2017 IEEE Symposium on Security and Privacy, IEEE,
2017, pp. 444–460.
conference:
end_date: 2017-05-26
location: San Jose, CA, United States
name: 'SP: Symposium on Security and Privacy'
start_date: 2017-05-22
date_created: 2020-08-26T12:26:08Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:18:02Z
day: '01'
doi: 10.1109/SP.2017.45
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/1067
month: '06'
oa: 1
oa_version: Preprint
page: 444-460
publication: 2017 IEEE Symposium on Security and Privacy
publication_identifier:
isbn:
- '9781509055340'
issn:
- 2375-1207
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Scalable bias-resistant distributed randomness
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '833'
abstract:
- lang: eng
text: We present an efficient algorithm to compute Euler characteristic curves of
gray scale images of arbitrary dimension. In various applications the Euler characteristic
curve is used as a descriptor of an image. Our algorithm is the first streaming
algorithm for Euler characteristic curves. The usage of streaming removes the
necessity to store the entire image in RAM. Experiments show that our implementation
handles terabyte scale images on commodity hardware. Due to lock-free parallelism,
it scales well with the number of processor cores. Additionally, we put the concept
of the Euler characteristic curve in the wider context of computational topology.
In particular, we explain the connection with persistence diagrams.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of
multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer;
2017:397-409. doi:10.1007/978-3-319-64689-3_32'
apa: 'Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic
curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger
(Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of
Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32'
chicago: Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden,
and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32.
ieee: 'T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves
of multidimensional images,” presented at the CAIP: Computer Analysis of Images
and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.'
ista: 'Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves
of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS,
vol. 10424, 397–409.'
mla: Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol.
10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.
short: T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer,
2017, pp. 397–409.
conference:
end_date: 2017-08-24
location: Ystad, Sweden
name: 'CAIP: Computer Analysis of Images and Patterns'
start_date: 2017-08-22
date_created: 2018-12-11T11:48:45Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2023-09-26T16:10:03Z
day: '28'
department:
- _id: HeEd
doi: 10.1007/978-3-319-64689-3_32
editor:
- first_name: Michael
full_name: Felsberg, Michael
last_name: Felsberg
- first_name: Anders
full_name: Heyden, Anders
last_name: Heyden
- first_name: Norbert
full_name: Krüger, Norbert
last_name: Krüger
external_id:
isi:
- '000432085900032'
intvolume: ' 10424'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02045
month: '07'
oa: 1
oa_version: Submitted Version
page: 397 - 409
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6815'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Streaming algorithm for Euler characteristic curves of multidimensional images
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10424
year: '2017'
...