---
_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
file:
- access_level: open_access
checksum: 3a3ec003f6ee73f41f82a544d63dfc77
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:44Z
date_updated: 2020-07-14T12:48:10Z
file_id: '4900'
file_name: IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf
file_size: 4103115
relation: main_file
- access_level: closed
checksum: bd2facc45ff8a2e20c5ed313c2ccaa83
content_type: application/zip
creator: dernst
date_created: 2019-04-05T07:59:31Z
date_updated: 2020-07-14T12:48:10Z
file_id: '6201'
file_name: 2017_thesis_Pavlogiannis.zip
file_size: 14744374
relation: source_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
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: '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'
...
---
_id: '834'
abstract:
- lang: eng
text: 'Thermal and many-body localized phases are separated by a dynamical phase
transition of a new kind. We analyze the distribution of off-diagonal matrix elements
of local operators across this transition in two different models of disordered
spin chains. We show that the behavior of matrix elements can be used to characterize
the breakdown of thermalization and to extract the many-body Thouless energy.
We find that upon increasing the disorder strength the system enters a critical
region around the many-body localization transition. The properties of the system
in this region are: (i) the Thouless energy becomes smaller than the level spacing,
(ii) the matrix elements show critical dependence on the energy difference, and
(iii) the matrix elements, viewed as amplitudes of a fictitious wave function,
exhibit strong multifractality. This critical region decreases with the system
size, which we interpret as evidence for a diverging correlation length at the
many-body localization transition. Our findings show that the correlation length
becomes larger than the accessible system sizes in a broad range of disorder strength
values and shed light on the critical behavior near the many-body localization
transition.'
acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover,
and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS
Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of
this work were completed (supported in part by the National Science Foundation under
Grant No. NSF PHY11-25915)
article_number: '104201'
article_processing_charge: No
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Papic
full_name: Zlatko, Papic
last_name: Zlatko
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
citation:
ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the
many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201
apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality
across the many-body localization transition. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201
chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality
across the Many-Body Localization Transition.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.
ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality
across the many-body localization transition,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 10. American Physical Society,
2017.
ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across
the many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 96(10), 104201.
mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body
Localization Transition.” Physical Review B - Condensed Matter and Materials
Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.
short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 96 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-09-06T00:00:00Z
date_updated: 2023-09-26T15:51:54Z
day: '06'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104201
external_id:
isi:
- '000409429300004'
intvolume: ' 96'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02389
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6814'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thouless energy and multifractality across the many-body localization transition
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '835'
abstract:
- lang: eng
text: An outstanding question in animal development, tissue homeostasis and disease
is how cell populations adapt to sensory inputs. During Drosophila larval development,
hematopoietic sites are in direct contact with sensory neuron clusters of the
peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for
their survival and recruitment to these microenvironments, known as Hematopoietic
Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by
sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes.
These hemocyte responses depend on PNS activity, as shown by agonist treatment
and transient silencing of sensory neurons. Activin-β has a key role in this regulation,
which is apparent from reporter expression and mutant analyses. This mechanism
of local sensory neurons controlling blood cell adaptation invites evolutionary
parallels with vertebrate hematopoietic progenitors and the independent myeloid
system of tissue macrophages, whose regulation by local microenvironments remain
undefined.
article_number: '15990'
article_processing_charge: No
author:
- first_name: Kalpana
full_name: Makhijani, Kalpana
last_name: Makhijani
- first_name: Brandy
full_name: Alexander, Brandy
last_name: Alexander
- first_name: Deepti
full_name: Rao, Deepti
last_name: Rao
- first_name: Sophia
full_name: Petraki, Sophia
last_name: Petraki
- first_name: Leire
full_name: Herboso, Leire
last_name: Herboso
- first_name: Katelyn
full_name: Kukar, Katelyn
last_name: Kukar
- first_name: Itrat
full_name: Batool, Itrat
last_name: Batool
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Katrina
full_name: Gold, Katrina
last_name: Gold
- first_name: Corinna
full_name: Wong, Corinna
last_name: Wong
- first_name: Michael
full_name: O'Connor, Michael
last_name: O'Connor
- first_name: Katja
full_name: Brückner, Katja
last_name: Brückner
citation:
ama: Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic
sites by Activin-β from active sensory neurons. Nature Communications.
2017;8. doi:10.1038/ncomms15990
apa: Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K.,
… Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β
from active sensory neurons. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/ncomms15990
chicago: Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire
Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic
Sites by Activin-β from Active Sensory Neurons.” Nature Communications.
Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15990.
ieee: K. Makhijani et al., “Regulation of Drosophila hematopoietic sites
by Activin-β from active sensory neurons,” Nature Communications, vol.
8. Nature Publishing Group, 2017.
ista: Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I,
Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila
hematopoietic sites by Activin-β from active sensory neurons. Nature Communications.
8, 15990.
mla: Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by
Activin-β from Active Sensory Neurons.” Nature Communications, vol. 8,
15990, Nature Publishing Group, 2017, doi:10.1038/ncomms15990.
short: K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I.
Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications
8 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2023-09-26T15:51:28Z
day: '27'
ddc:
- '570'
- '576'
- '616'
doi: 10.1038/ncomms15990
extern: '1'
external_id:
isi:
- '000406360100001'
file:
- access_level: open_access
checksum: 99a3d63308d4250eda0a35341171f80e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:32Z
date_updated: 2020-07-14T12:48:12Z
file_id: '5153'
file_name: IST-2017-859-v1+1_ncomms15990.pdf
file_size: 3027104
relation: main_file
file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6813'
pubrep_id: '859'
quality_controlled: '1'
status: public
title: Regulation of Drosophila hematopoietic sites by Activin-β from active sensory
neurons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '837'
abstract:
- lang: eng
text: 'The hippocampus is a key brain region for memory and notably for spatial
memory, and is needed for both spatial working and reference memories. Hippocampal
place cells selectively discharge in specific locations of the environment to
form mnemonic represen tations of space. Several behavioral protocols have been
designed to test spatial memory which requires the experimental subject to utilize
working memory and reference memory. However, less is known about how these memory
traces are presented in the hippo campus, especially considering tasks that require
both spatial working and long -term reference memory demand. The aim of my thesis
was to elucidate how spatial working memory, reference memory, and the combination
of both are represented in the hippocampus. In this thesis, using a radial eight
-arm maze, I examined how the combined demand on these memories influenced place
cell assemblies while reference memories were partially updated by changing some
of the reward- arms. This was contrasted with task varian ts requiring working
or reference memories only. Reference memory update led to gradual place field
shifts towards the rewards on the switched arms. Cells developed enhanced firing
in passes between newly -rewarded arms as compared to those containing an unchanged
reward. The working memory task did not show such gradual changes. Place assemblies
on occasions replayed trajectories of the maze; at decision points the next arm
choice was preferentially replayed in tasks needing reference memory while in
the pure working memory task the previously visited arm was replayed. Hence trajectory
replay only reflected the decision of the animal in tasks needing reference memory
update. At the reward locations, in all three tasks outbound trajectories of the
current arm were preferentially replayed, showing the animals’ next path to the
center. At reward locations trajectories were replayed preferentially in reverse
temporal order. Moreover, in the center reverse replay was seen in the working
memory task but in the other tasks forward replay was seen. Hence, the direction
of reactivation was determined by the goal locations so that part of the trajectory
which was closer to the goal was reactivated later in an HSE while places further
away from the goal were reactivated earlier. Altogether my work demonstrated that
reference memory update triggers several levels of reorganization of the hippocampal
cognitive map which are not seen in simpler working memory demand s. Moreover,
hippocampus is likely to be involved in spatial decisions through reactivating
planned trajectories when reference memory recall is required for such a decision. '
acknowledgement: 'I am very grateful for the opportunity I have had as a graduate
student to explore and incredibly interesting branch of neuroscience, and for the
people who made it possible. Firstly, I would like to offer my thanks to my supervisor
Professor Jozsef Csicsvari for his great support, guidance and patience offered
over the years. The door to his office was always open whenever I had questions.
I have learned a lot from him about carefully designing experiments, asking interesting
questions and how to integrate results into a broader picture. I also express my
gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific
role model who is always willing to teach , and advice and talk through problems
with his full attention. Many thanks to my wonderful “office mates” over the years
and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree
Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián
Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in
the lab for the many useful discussions about science and for making the laboratory
such a nice and friendly place to work in. A special thank goes to Michael LoBianco
and Jago Wallenschus for wonderful technical support. I would also like to thank
Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam
and thesi s committee members despite their busy schedule. I am also very thankful
to IST Austria for their support all throughout my PhD. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
citation:
ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks. 2017. doi:10.15479/AT:ISTA:th_858
apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858
chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.
ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks,” Institute of Science and Technology Austria, 2017.
ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria.
mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.
short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial
Tasks, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-08-23T00:00:00Z
date_updated: 2023-09-07T12:06:38Z
day: '23'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:th_858
file:
- access_level: closed
checksum: f11925fbbce31e495124b6bc4f10573c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:59:51Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6213'
file_name: 2017_Xu_Haibing_Thesis_Source.docx
file_size: 3589490
relation: source_file
- access_level: open_access
checksum: ffb10749a537d615fab1ef0937ccb157
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:59:51Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6214'
file_name: 2017_Xu_Thesis_IST.pdf
file_size: 11668613
relation: main_file
file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6811'
pubrep_id: '858'
related_material:
record:
- id: '5828'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks
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: '838'
abstract:
- lang: eng
text: 'In this thesis we discuss the exact security of message authentications codes
HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length
keyed hash function f into a variable input-length function. A practical single-key
variant of NMAC called HMAC is a very popular and widely deployed message authentication
code (MAC). PMAC is a block-cipher based mode of operation, which also happens
to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti
and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF),
and thus also a MAC, under two assumptions. Unfortunately, for many instantiations
of HMAC one of them has been found to be wrong. To restore the provable guarantees
for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC
was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a
pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure
variable input-length PRF. For adversaries making q queries, each of length at
most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves
an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently
best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by
giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one
initially XORs a mask to every message block, where the mask for the i th block
is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is
the i -th codeword of the Gray code. Our attack applies more generally to any
sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As
for NMAC , our first contribution is a simpler and uniform proof: If f is an ε
-secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q
queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length
at most ` blocks each. We also show that this ε + `qδ bound is basically tight
by constructing an f for which an attack with advantage `qδ exists. Moreover,
we analyze the PRF-security of a modification of NMAC called NI by An and Bellare
that avoids the constant rekeying on multi-block messages in NMAC and allows for
an information-theoretic analysis. We carry out such an analysis, obtaining a
tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2
q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved
by using τ i ’s that are k -wise independent, for k > 1 (the original has k
= 1). We observe that the security of PMAC will not increase in general if k =
2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4.
Due to simple extension attacks, this is the best bound one can hope for, using
any distribution on the masks. Whether k = 3 is already sufficient to get this
level of security is left as an open problem. Keywords: Message authentication
codes, Pseudorandom functions, HMAC, PMAC. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828
apa: Rybar, M. (2017). (The exact security of) Message authentication codes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828
chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.
ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute
of Science and Technology Austria, 2017.
ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute
of Science and Technology Austria.
mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.
short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute
of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2023-09-07T12:02:28Z
day: '26'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:th_828
file:
- access_level: open_access
checksum: ff8639ec4bded6186f44c7bd3ee26804
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:13Z
date_updated: 2020-07-14T12:48:12Z
file_id: '4799'
file_name: IST-2017-828-v1+3_2017_Rybar_thesis.pdf
file_size: 847400
relation: main_file
- access_level: closed
checksum: 3462101745ce8ad199c2d0f75dae4a7e
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:24:11Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6202'
file_name: 2017_Thesis_Rybar_source.zip
file_size: 26054879
relation: source_file
file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6810'
pubrep_id: '828'
related_material:
record:
- id: '2082'
relation: part_of_dissertation
status: public
- id: '6196'
relation: part_of_dissertation
status: public
status: public
title: (The exact security of) Message authentication codes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '839'
abstract:
- lang: eng
text: 'This thesis describes a brittle fracture simulation method for visual effects
applications. Building upon a symmetric Galerkin boundary element method, we first
compute stress intensity factors following the theory of linear elastic fracture
mechanics. We then use these stress intensities to simulate the motion of a propagating
crack front at a significantly higher resolution than the overall deformation
of the breaking object. Allowing for spatial variations of the material''s toughness
during crack propagation produces visually realistic, highly-detailed fracture
surfaces. Furthermore, we introduce approximations for stress intensities and
crack opening displacements, resulting in both practical speed-up and theoretically
superior runtime complexity compared to previous methods. While we choose a quasi-static
approach to fracture mechanics, ignoring dynamic deformations, we also couple
our fracture simulation framework to a standard rigid-body dynamics solver, enabling
visual effects artists to simulate both large scale motion, as well as fracturing
due to collision forces in a combined system. As fractures inside of an object
grow, their geometry must be represented both in the coarse boundary element mesh,
as well as at the desired fine output resolution. Using a boundary element method,
we avoid complicated volumetric meshing operations. Instead we describe a simple
set of surface meshing operations that allow us to progressively add cracks to
the mesh of an object and still re-use all previously computed entries of the
linear boundary element system matrix. On the high resolution level, we opt for
an implicit surface representation. We then describe how to capture fracture surfaces
during crack propagation, as well as separate the individual fragments resulting
from the fracture process, based on this implicit representation. We show results
obtained with our method, either solving the full boundary element system in every
time step, or alternatively using our fast approximations. These results demonstrate
that both of these methods perform well in basic test cases and produce realistic
fracture surfaces. Furthermore we show that our fast approximations substantially
out-perform the standard approach in more demanding scenarios. Finally, these
two methods naturally combine, using the full solution while the problem size
is manageably small and switching to the fast approximations later on. The resulting
hybrid method gives the user a direct way to choose between speed and accuracy
of the simulation. '
acknowledgement: "ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all,
let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for
supporting me throughout my PhD. Obviously, none of this work would\r\nhave been
possible without you.\r\nFurthermore, Thank You to all the people who have contributed
to this work in various\r\nways, in particular Martin Schanz and his group for providing
and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and
Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions
during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel,
and all the members – past and present – of his\r\nand Chris’ research groups at
IST Austria for always providing honest and insightful\r\nfeedback throughout many
joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang
Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs
only virtual objects have been harmed in the process of creating this work, I would\r\nlike
to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo”
models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg
for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different
ways.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
citation:
ama: Hahn D. Brittle fracture simulation with boundary elements for computer graphics.
2017. doi:10.15479/AT:ISTA:th_855
apa: Hahn, D. (2017). Brittle fracture simulation with boundary elements for
computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855
chicago: Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer
Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855.
ieee: D. Hahn, “Brittle fracture simulation with boundary elements for computer
graphics,” Institute of Science and Technology Austria, 2017.
ista: Hahn D. 2017. Brittle fracture simulation with boundary elements for computer
graphics. Institute of Science and Technology Austria.
mla: Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer
Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855.
short: D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer
Graphics, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-14T00:00:00Z
date_updated: 2024-02-21T13:48:02Z
day: '14'
ddc:
- '004'
- '005'
- '006'
- '531'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_855
ec_funded: 1
file:
- access_level: open_access
checksum: 6c1ae8c90bfaba5e089417fefbc4a272
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:46Z
date_updated: 2020-07-14T12:48:13Z
file_id: '5100'
file_name: IST-2017-855-v1+1_thesis_online_pdfA.pdf
file_size: 14596191
relation: main_file
- access_level: closed
checksum: 421672f68d563b029869c5cf1713f919
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:40:30Z
date_updated: 2020-07-14T12:48:13Z
file_id: '6207'
file_name: 2017_thesis_Hahn_source.zip
file_size: 15060566
relation: source_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6809'
pubrep_id: '855'
related_material:
record:
- id: '1362'
relation: part_of_dissertation
status: public
- id: '1633'
relation: part_of_dissertation
status: public
- id: '5568'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Brittle fracture simulation with boundary elements for computer graphics
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '840'
abstract:
- lang: eng
text: Heavy holes confined in quantum dots are predicted to be promising candidates
for the realization of spin qubits with long coherence times. Here we focus on
such heavy-hole states confined in germanium hut wires. By tuning the growth density
of the latter we can realize a T-like structure between two neighboring wires.
Such a structure allows the realization of a charge sensor, which is electrostatically
and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3
e. By integrating the T-like structure into a radiofrequency reflectometry setup,
single-shot measurements allowing the extraction of hole tunneling times are performed.
The extracted tunneling times of less than 10 μs are attributed to the small effective
mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.
acknowledged_ssus:
- _id: M-Shop
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in
germanium hut wires probed by single-shot reflectometry. Nano Letters.
2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627
apa: Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole
tunneling times in germanium hut wires probed by single-shot reflectometry. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627
chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros.
“Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.
ieee: L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling
times in germanium hut wires probed by single-shot reflectometry,” Nano Letters,
vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.
ista: Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times
in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9),
5706–5710.
mla: Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed
by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical
Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.
short: L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017)
5706–5710.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-10T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '10'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.7b02627
ec_funded: 1
external_id:
isi:
- '000411043500078'
file:
- access_level: open_access
checksum: 761371a0129b2aa442424b9561450ece
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:33Z
date_updated: 2020-07-14T12:48:13Z
file_id: '4951'
file_name: IST-2017-865-v1+1_acs.nanolett.7b02627.pdf
file_size: 2449546
relation: main_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 5706 - 5710
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6808'
pubrep_id: '865'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '69'
relation: dissertation_contains
status: public
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2017'
...
---
_id: '8423'
abstract:
- lang: eng
text: In this paper we show that for a generic strictly convex domain, one can recover
the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard
map from the (maximal) marked length spectrum of the domain.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Guan
full_name: Huang, Guan
last_name: Huang
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Alfonso
full_name: Sorrentino, Alfonso
last_name: Sorrentino
citation:
ama: Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic
strictly convex billiard tables. Duke Mathematical Journal. 2017;167(1):175-209.
doi:10.1215/00127094-2017-0038
apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2017). On the marked length
spectrum of generic strictly convex billiard tables. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-2017-0038
chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length
Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal.
Duke University Press, 2017. https://doi.org/10.1215/00127094-2017-0038.
ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of
generic strictly convex billiard tables,” Duke Mathematical Journal, vol.
167, no. 1. Duke University Press, pp. 175–209, 2017.
ista: Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of
generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209.
mla: Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex
Billiard Tables.” Duke Mathematical Journal, vol. 167, no. 1, Duke University
Press, 2017, pp. 175–209, doi:10.1215/00127094-2017-0038.
short: G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017)
175–209.
date_created: 2020-09-17T10:42:42Z
date_published: 2017-12-08T00:00:00Z
date_updated: 2021-01-12T08:19:11Z
day: '08'
doi: 10.1215/00127094-2017-0038
extern: '1'
external_id:
arxiv:
- '1603.08838'
intvolume: ' 167'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.08838
month: '12'
oa: 1
oa_version: Preprint
page: 175-209
publication: Duke Mathematical Journal
publication_identifier:
issn:
- 0012-7094
publication_status: published
publisher: Duke University Press
quality_controlled: '1'
status: public
title: On the marked length spectrum of generic strictly convex billiard tables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2017'
...