---
_id: '1186'
abstract:
- lang: eng
text: The human pathogen Streptococcus pneumoniae is decorated with a special class
of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine
(PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography,
NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies,
we provide structural information of choline-binding protein L (CbpL) and demonstrate
its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated
three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported
in this work for the very first time-, (ii) an unprecedented anchorage module
showing alternate disposition of canonical and non-canonical choline-binding sites
that allows vine-like binding of fully-PCho-substituted teichoic acids (with two
choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural
and infection assays indicate an important role of the whole multimodular protein
allowing both to locate CbpL at specific places on the cell wall and to interact
with host components in order to facilitate pneumococcal lung infection and transmigration
from nasopharynx to the lungs and blood. CbpL implication in both resistance against
killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein
as relevant among the pathogenic arsenal of the pneumococcus.
acknowledgement: We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann,
for technical assistance and Lothar Petruschka for in silico analysis (all Dept.
of Genetics, University of Greifswald). We are further grateful to the staff from
SLS synchrotron beamline for help in data collection. This work was supported by
grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish
Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P
to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to
JAH and FG).
article_number: '38094'
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Malek
full_name: Saleh, Malek
last_name: Saleh
- first_name: Martín
full_name: Alcorlo, Martín
last_name: Alcorlo
- first_name: Alejandro
full_name: Gómez Mejóa, Alejandro
last_name: Gómez Mejóa
- first_name: David
full_name: Pantoja Uceda, David
last_name: Pantoja Uceda
- first_name: Miguel
full_name: Treviño, Miguel
last_name: Treviño
- first_name: Franziska
full_name: Vob, Franziska
last_name: Vob
- first_name: Mohammed
full_name: Abdullah, Mohammed
last_name: Abdullah
- first_name: Sergio
full_name: Galán Bartual, Sergio
last_name: Galán Bartual
- first_name: Jolien
full_name: Seinen, Jolien
last_name: Seinen
- first_name: Pedro
full_name: Sánchez Murcia, Pedro
last_name: Sánchez Murcia
- first_name: Federico
full_name: Gago, Federico
last_name: Gago
- first_name: Marta
full_name: Bruix, Marta
last_name: Bruix
- first_name: Sven
full_name: Hammerschmidt, Sven
last_name: Hammerschmidt
- first_name: Juan
full_name: Hermoso, Juan
last_name: Hermoso
citation:
ama: Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and
unique teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094
apa: Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda,
D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094
chicago: Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez
Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture
and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL
Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature
Publishing Group, 2016. https://doi.org/10.1038/srep38094.
ieee: J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.
ista: Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D,
Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago
F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique
teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 6, 38094.
mla: Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic
Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal
Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group,
2016, doi:10.1038/srep38094.
short: J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja
Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez
Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6
(2016).
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-05T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '05'
ddc:
- '576'
- '610'
department:
- _id: LeSa
doi: 10.1038/srep38094
file:
- access_level: open_access
checksum: e007d78b483bc59bf5ab98e9d42a6ec1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:18Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4804'
file_name: IST-2017-735-v1+1_srep38094.pdf
file_size: 2716045
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6167'
pubrep_id: '735'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modular architecture and unique teichoic acid recognition features of choline-binding
protein L CbpL contributing to pneumococcal pathogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '11866'
abstract:
- lang: eng
text: "We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time
algorithm for solving the single-source shortest paths problem on distributed
weighted networks (the CONGEST model); here n is the number of nodes in the network
and D is its (hop) diameter. This is the first non-trivial deterministic algorithm
for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation
Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large
as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s
Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running
time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al.
STOC 2011] modulo some lower-order terms, thus essentially settling the status
of this problem which was raised at least a decade ago [Elkin SIGACT News 2004].
It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for
approximating a network’s weighted diameter which almost matches the lower bound
by Holzer et al. [PODC 2012].\r\n\r\nIn achieving this result, we develop two
techniques which might be of independent interest and useful in other settings:
(i) a deterministic process that replaces the “hitting set argument” commonly
used for shortest paths computation in various settings, and (ii) a simple, deterministic,
construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these
techniques with many distributed algorithmic techniques, some of which from problems
that are not directly related to shortest paths, e.g. ruling sets [Goldberg et
al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance
estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads
to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation
O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation
O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights
are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC
2014]. The second result partially answers an open problem raised by McGregor
in 2006 [sublinear.info
, Problem 14]."
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. A deterministic almost-tight distributed
algorithm for approximating single-source shortest paths. In: 48th Annual ACM
SIGACT Symposium on Theory of Computing. Association for Computing Machinery;
2016:489-498. doi:10.1145/2897518.2897638'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2016). A deterministic
almost-tight distributed algorithm for approximating single-source shortest paths.
In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 489–498).
Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897638'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic
Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.”
In 48th Annual ACM SIGACT Symposium on Theory of Computing, 489–98. Association
for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897638.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight
distributed algorithm for approximating single-source shortest paths,” in 48th
Annual ACM SIGACT Symposium on Theory of Computing, Cambridge, MA, United
States, 2016, pp. 489–498.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2016. A deterministic almost-tight
distributed algorithm for approximating single-source shortest paths. 48th Annual
ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing,
489–498.'
mla: Henzinger, Monika H., et al. “A Deterministic Almost-Tight Distributed Algorithm
for Approximating Single-Source Shortest Paths.” 48th Annual ACM SIGACT Symposium
on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–98,
doi:10.1145/2897518.2897638.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 48th Annual ACM SIGACT
Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp.
489–498.
conference:
end_date: 2016-06-21
location: Cambridge, MA, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2016-06-19
date_created: 2022-08-16T09:19:31Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-17T10:32:23Z
day: '01'
doi: 10.1145/2897518.2897638
extern: '1'
external_id:
arxiv:
- '1504.07056'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.07056
month: '06'
oa: 1
oa_version: Preprint
page: 489 - 498
publication: 48th Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145034132-5
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A deterministic almost-tight distributed algorithm for approximating single-source
shortest paths
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '11867'
abstract:
- lang: eng
text: We present two deterministic dynamic algorithms for the maximum matching problem.
(1) An algorithm that maintains a (2+є)-approximate maximum matching in general
graphs with O(poly(logn, 1/є)) update time. (2) An algorithm that maintains an
αK approximation of the value of the maximum matching with O(n2/K) update time
in bipartite graphs, for every sufficiently large constant positive integer K.
Here, 1≤ αK < 2 is a constant determined by the value of K. Result (1) is the
first deterministic algorithm that can maintain an o(logn)-approximate maximum
matching with polylogarithmic update time, improving the seminal result of Onak
et al. [STOC 2010]. Its approximation guarantee almost matches the guarantee of
the best randomized polylogarithmic update time algorithm [Baswana et al. FOCS
2011]. Result (2) achieves a better-than-two approximation with arbitrarily small
polynomial update time on bipartite graphs. Previously the best update time for
this problem was O(m1/4) [Bernstein et al. ICALP 2015], where m is the current
number of edges in the graph.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Bhattacharya S, Henzinger MH, Nanongkai D. New deterministic approximation
algorithms for fully dynamic matching. In: 48th Annual ACM SIGACT Symposium
on Theory of Computing. Association for Computing Machinery; 2016:398-411.
doi:10.1145/2897518.2897568'
apa: 'Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2016). New deterministic
approximation algorithms for fully dynamic matching. In 48th Annual ACM SIGACT
Symposium on Theory of Computing (pp. 398–411). Cambridge, MA, United States:
Association for Computing Machinery. https://doi.org/10.1145/2897518.2897568'
chicago: Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “New Deterministic
Approximation Algorithms for Fully Dynamic Matching.” In 48th Annual ACM SIGACT
Symposium on Theory of Computing, 398–411. Association for Computing Machinery,
2016. https://doi.org/10.1145/2897518.2897568.
ieee: S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “New deterministic approximation
algorithms for fully dynamic matching,” in 48th Annual ACM SIGACT Symposium
on Theory of Computing, Cambridge, MA, United States, 2016, pp. 398–411.
ista: 'Bhattacharya S, Henzinger MH, Nanongkai D. 2016. New deterministic approximation
algorithms for fully dynamic matching. 48th Annual ACM SIGACT Symposium on Theory
of Computing. STOC: Symposium on Theory of Computing, 398–411.'
mla: Bhattacharya, Sayan, et al. “New Deterministic Approximation Algorithms for
Fully Dynamic Matching.” 48th Annual ACM SIGACT Symposium on Theory of Computing,
Association for Computing Machinery, 2016, pp. 398–411, doi:10.1145/2897518.2897568.
short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 48th Annual ACM SIGACT
Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp.
398–411.
conference:
end_date: 2016-06-21
location: Cambridge, MA, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2016-06-19
date_created: 2022-08-16T09:27:35Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-17T11:08:19Z
day: '01'
doi: 10.1145/2897518.2897568
extern: '1'
external_id:
arxiv:
- '1604.05765'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05765
month: '06'
oa: 1
oa_version: Preprint
page: 398 - 411
publication: 48th Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145034132-5
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: New deterministic approximation algorithms for fully dynamic matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1188'
abstract:
- lang: eng
text: "We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic constraints-based
modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with
the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation
is solved for the steady state in the WKB\r\napproximation that maps it into the
ground state of a quantum particle in an\r\nAiry potential plus a centrifugal
term. We retrieve scaling laws for growth rate\r\nfluctuations and time response
with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal
populations can have a faster response\r\nto perturbations."
acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant
agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011.
D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa
for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano
and Vera Luz Masoero for useful discussions, also late at night.
article_number: '123502'
author:
- 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: Davide
full_name: Masoero, Davide
last_name: Masoero
citation:
ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics:
Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f'
apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness
maximization, applied to metabolism & growth. Journal of Statistical
Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f'
chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy
Fitness Maximization, Applied to Metabolism & Growth.” Journal of
Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.'
ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.'
ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics: Theory
and Experiment. 2016(12), 123502.'
mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness
Maximization, Applied to Metabolism & Growth.” Journal of Statistical
Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016,
doi:10.1088/1742-5468/aa4e8f.'
short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and
Experiment 2016 (2016).'
date_created: 2018-12-11T11:50:37Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '30'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa4e8f
ec_funded: 1
intvolume: ' 2016'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.09048
month: '12'
oa: 1
oa_version: Preprint
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_status: published
publisher: IOPscience
publist_id: '6165'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymptotic analysis of noisy fitness maximization, applied to metabolism &
growth
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1189'
abstract:
- lang: eng
text: "Within the scope of this thesis, we show that a driven-dissipative system
with\r\nfew ultracold atoms can exhibit dissipatively bound states, even if the
atom-atom\r\ninteraction is purely repulsive. This bond arises due to the dipole-dipole
inter-\r\naction, which is restricted to one of the lower electronic energy states,
resulting\r\nin the distance-dependent coherent population trapping. The quality
of this al-\r\nready established method of dissipative binding is improved and
the application\r\nis extended to higher dimensions and a larger number of atoms.
\ Here, we simu-\r\nlate two- and three-atom systems using an adapted approach
to the Monte Carlo\r\nwave-function method and analyse the results. Finally,
\ we examine the possi-\r\nbility of finding a setting allowing trimer
\ states but prohibiting dimer states.\r\nIn the context of open quantum systems,
such a three-body bound states corre-\r\nsponds to the driven-dissipative analogue
of a Borromean state. These states can\r\nbe detected in modern experiments with
dipolar and Rydberg-dressed ultracold\r\natomic gases.\r\n"
article_processing_charge: No
author:
- first_name: Clemens
full_name: Jochum, Clemens
last_name: Jochum
citation:
ama: Jochum C. Dissipative Few-Body Quantum Systems. 2016.
apa: Jochum, C. (2016). Dissipative Few-Body Quantum Systems. Technical University
Vienna.
chicago: Jochum, Clemens. “Dissipative Few-Body Quantum Systems.” Technical University
Vienna, 2016.
ieee: C. Jochum, “Dissipative Few-Body Quantum Systems,” Technical University Vienna,
2016.
ista: Jochum C. 2016. Dissipative Few-Body Quantum Systems. Technical University
Vienna.
mla: Jochum, Clemens. Dissipative Few-Body Quantum Systems. Technical University
Vienna, 2016.
short: C. Jochum, Dissipative Few-Body Quantum Systems, Technical University Vienna,
2016.
date_created: 2018-12-11T11:50:37Z
date_published: 2016-11-28T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '28'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repositum.tuwien.ac.at/obvutwhs/content/titleinfo/1517088
month: '11'
oa: 1
oa_version: Published Version
page: '94'
publication_status: published
publisher: Technical University Vienna
publist_id: '6164'
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Peter
full_name: Rabl, Peter
last_name: Rabl
title: Dissipative Few-Body Quantum Systems
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '11891'
abstract:
- lang: eng
text: "We study dynamic (1+\U0001D716)-approximation algorithms for the all-pairs
shortest paths problem in unweighted undirected \U0001D45B-node \U0001D45A-edge
graphs under edge deletions. The fastest algorithm for this problem is a randomized
algorithm with a total update time of \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716)
and constant query time by Roditty and Zwick [SIAM J. Comput., 41 (2012), pp.
670--683]. The fastest deterministic algorithm is from a 1981 paper by Even and
Shiloach [J. ACM, 28 (1981), pp. 1--4]; it has a total update time of \U0001D442(\U0001D45A\U0001D45B2)
and constant query time. We improve these results as follows: (1) We present an
algorithm with a total update time of \U0001D442̃ (\U0001D45B5/2/\U0001D716) and
constant query time that has an additive error of 2 in addition to the 1+\U0001D716
multiplicative error. This beats the previous \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716)
time when \U0001D45A=Ω(\U0001D45B3/2). Note that the additive error is unavoidable
since, even in the static case, an \U0001D442(\U0001D45B3−\U0001D6FF)-time (a
so-called truly subcubic) combinatorial algorithm with 1+\U0001D716 multiplicative
error cannot have an additive error less than 2−\U0001D716, unless we make a major
breakthrough for Boolean matrix multiplication [D. Dor, S. Halrepin, and U. Zwick,
SIAM J. Comput., 29 (2000), pp. 1740--1759] and many other long-standing problems
[V. Vassilevska Williams and R. Williams, Proceedings of the 2010 IEEE 51st Annual
Symposium on Foundations of Computer Science, 2010, pp. 645--654]. The algorithm
can also be turned into a (2+\U0001D716)-approximation algorithm (without an additive
error) with the same time guarantees, improving the recent (3+\U0001D716)-approximation
algorithm with \U0001D442̃ (\U0001D45B5/2+\U0001D442(log(1/\U0001D716)/log\U0001D45B√))
running time of Bernstein and Roditty [Proceedings of the Twenty-Second Annual
ACM-SIAM Symposium on Discrete Algorithms, 2011, pp. 1355--1365] in terms of both
approximation and time guarantees. (2) We present a deterministic algorithm with
a total update time of \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716) and a query
time of \U0001D442(loglog\U0001D45B). The algorithm has a multiplicative error
of 1+\U0001D716 and gives the first improved deterministic algorithm since 1981.
It also answers an open question raised by Bernstein in [Proceedings of the Forty-Fifth
Annual ACM Symposium on Theory of Computing, 2013, pp. 725--734]. The deterministic
algorithm can be turned into a deterministic fully dynamic (1+\U0001D716)-approximation
with an amortized update time of \U0001D442̃ (\U0001D45A\U0001D45B/(\U0001D716\U0001D461))
and a query time of \U0001D442̃ (\U0001D461) for every \U0001D461≤\U0001D45B√.
In order to achieve our results, we introduce two new techniques: (i) A monotone
Even--Shiloach tree algorithm which maintains a bounded-distance shortest-paths
tree on a certain type of emulator called a locally persevering emulator. (ii)
A derandomization technique based on moving Even--Shiloach trees as a way to derandomize
the standard random set argument. These techniques might be of independent interest."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest
paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing.
2016;45(3):947-1006. doi:10.1137/140957299'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2016). Dynamic approximate
all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM
Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140957299'
chicago: 'Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic
Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.”
SIAM Journal on Computing. Society for Industrial & Applied Mathematics,
2016. https://doi.org/10.1137/140957299.'
ieee: 'M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization,” SIAM Journal
on Computing, vol. 45, no. 3. Society for Industrial & Applied Mathematics,
pp. 947–1006, 2016.'
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2016. Dynamic approximate all-pairs
shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on
Computing. 45(3), 947–1006.'
mla: 'Henzinger, Monika H., et al. “Dynamic Approximate All-Pairs Shortest Paths:
Breaking the O(Mn) Barrier and Derandomization.” SIAM Journal on Computing,
vol. 45, no. 3, Society for Industrial & Applied Mathematics, 2016, pp. 947–1006,
doi:10.1137/140957299.'
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, SIAM Journal on Computing 45
(2016) 947–1006.
date_created: 2022-08-17T08:37:00Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-17T14:21:40Z
day: '01'
doi: 10.1137/140957299
extern: '1'
external_id:
arxiv:
- '1308.0776'
intvolume: ' 45'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1308.0776
month: '05'
oa: 1
oa_version: Preprint
page: 947-1006
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and
derandomization'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2016'
...
---
_id: '1193'
abstract:
- lang: eng
text: We consider the recent formulation of the Algorithmic Lovász Local Lemma [1],
[2] for finding objects that avoid "bad features", or "flaws".
It extends the Moser-Tardos resampling algorithm [3] to more general discrete
spaces. At each step the method picks a flaw present in the current state and
"resamples" it using a "resampling oracle" provided by the
user. However, it is less flexible than the Moser-Tardos method since [1], [2]
require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and
thus can potentially be implemented more efficiently). We formulate a new "commutativity"
condition, and prove that it is sufficient for an arbitrary rule to work. It also
enables an efficient parallelization under an additional assumption. We then show
that existing resampling oracles for perfect matchings and permutations do satisfy
this condition. Finally, we generalize the precondition in [2] (in the case of
symmetric potential causality graphs). This unifies special cases that previously
were treated separately.
acknowledgement: European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no 616160
article_number: '7782993'
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings
- Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December.
IEEE; 2016. doi:10.1109/FOCS.2016.88'
apa: 'Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma.
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science
(Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88'
chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88.
ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings
- Annual IEEE Symposium on Foundations of Computer Science, New Brunswick,
NJ, USA , 2016, vol. 2016–December.
ista: 'Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma.
Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS:
Foundations of Computer Science vol. 2016–December, 7782993.'
mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.
short: V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of
Computer Science, IEEE, 2016.
conference:
end_date: 2016-09-11
location: 'New Brunswick, NJ, USA '
name: 'FOCS: Foundations of Computer Science'
start_date: 2016-09-09
date_created: 2018-12-11T11:50:38Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2023-09-19T14:24:57Z
day: '15'
department:
- _id: VlKo
doi: 10.1109/FOCS.2016.88
ec_funded: 1
external_id:
arxiv:
- '1506.08547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.08547v7
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings - Annual IEEE Symposium on Foundations of Computer Science
publication_status: published
publisher: IEEE
publist_id: '6158'
quality_controlled: '1'
related_material:
record:
- id: '5975'
relation: later_version
status: public
scopus_import: 1
status: public
title: Commutativity in the algorithmic Lovasz local lemma
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-December
year: '2016'
...
---
_id: '1195'
abstract:
- lang: eng
text: 'The genetic analysis of experimentally evolving populations typically relies
on short reads from pooled individuals (Pool-Seq). While this method provides
reliable allele frequency estimates, the underlying haplotype structure remains
poorly characterized. With small population sizes and adaptive variants that start
from low frequencies, the interpretation of selection signatures in most Evolve
and Resequencing studies remains challenging. To facilitate the characterization
of selection targets, we propose a new approach that reconstructs selected haplotypes
from replicated time series, using Pool-Seq data. We identify selected haplotypes
through the correlated frequencies of alleles carried by them. Computer simulations
indicate that selected haplotype-blocks of several Mb can be reconstructed with
high confidence and low error rates, even when allele frequencies change only
by 20% across three replicates. Applying this method to real data from D. melanogaster
populations adapting to a hot environment, we identify a selected haplotype-block
of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations
by experimental haplotyping, demonstrating the power and accuracy of our haplotype
reconstruction from Pool-Seq data. We propose that the combination of allele frequency
estimates with haplotype information will provide the key to understanding the
dynamics of adaptive alleles. '
acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics
for discussion and support on the project and par-\r\nticularly N. Barghi for helpful
comments on earlier versions of\r\nthe manuscript. This work was supported
\ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”."
author:
- first_name: Susan
full_name: Franssen, Susan
last_name: Franssen
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
citation:
ama: Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected
during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184.
doi:10.1093/molbev/msw210
apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of
haplotype-blocks selected during experimental evolution. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210
chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction
of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology
and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.
ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks
selected during experimental evolution.,” Molecular Biology and Evolution,
vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.
ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks
selected during experimental evolution. Molecular Biology and Evolution. 34(1),
174–184.
mla: Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during
Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no.
1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.
short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution
34 (2016) 174–184.
date_created: 2018-12-11T11:50:39Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2021-01-12T06:49:00Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1093/molbev/msw210
ec_funded: 1
file:
- access_level: open_access
checksum: 1e78d3aaffcb40dc8b02b7b4666019e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:35Z
date_updated: 2020-07-14T12:44:38Z
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checksum: 63bc6e6e61f347594d8c00c37f874a0b
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creator: system
date_created: 2018-12-12T10:16:37Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5225'
file_name: IST-2017-770-v1+3_Fig2.pdf
file_size: 21437
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content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5226'
file_name: IST-2017-770-v1+4_Fig3.pdf
file_size: 1172194
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checksum: e47b2a0c32142f423b3100150c0294f8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5227'
file_name: IST-2017-770-v1+5_Fig4.pdf
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relation: main_file
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checksum: a5a7d6b32e7e17d35d337d7ec2a9f6c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:39Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5228'
file_name: IST-2017-770-v1+6_Fig5.pdf
file_size: 50705
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 174 - 184
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6155'
pubrep_id: '770'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reconstruction of haplotype-blocks selected during experimental evolution.
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2016'
...
---
_id: '1197'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation
(http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation
(https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National
Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science
Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler
for helpful comments on the manuscript.
article_number: e1005855
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes
of the retinal population code. PLoS Computational Biology. 2016;12(11).
doi:10.1371/journal.pcbi.1005148
apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2016). Error-robust modes of the retinal population code. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148
chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS
Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust
modes of the retinal population code,” PLoS Computational Biology, vol.
12, no. 11. Public Library of Science, 2016.
ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust
modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.”
PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of
Science, 2016, doi:10.1371/journal.pcbi.1005148.
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational
Biology 12 (2016).
date_created: 2018-12-11T11:50:40Z
date_published: 2016-11-17T00:00:00Z
date_updated: 2023-02-23T14:05:40Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005148
file:
- access_level: open_access
checksum: 47b08cbd4dbf32b25ba161f5f4b262cc
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T10:35:00Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5884'
file_name: 2016_PLOS_Prentice.pdf
file_size: 4492021
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6153'
quality_controlled: '1'
related_material:
record:
- id: '9709'
relation: research_data
status: public
scopus_import: 1
status: public
title: Error-robust modes of the retinal population code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '11983'
abstract:
- lang: eng
text: A continuous process for the synthesis and inline separation of anhydrous
trifluoromethyl diazomethane in a single continuous flow process is presented.
The diazo building block is generated from the corresponding amine and NaNO2 under
acidic, aqueous conditions and subsequently diffuses through a gas-permeable membrane
into an organic stream. To avoid storage and transportation of the hazardous compound,
a representative downstream process in a packed-bed reactor yielding highly functionalized
building blocks was developed.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: Pieber B, Kappe CO. Generation and synthetic application of trifluoromethyl
diazomethane utilizing continuous flow technologies. Organic Letters. 2016;18(5):1076-1079.
doi:10.1021/acs.orglett.6b00194
apa: Pieber, B., & Kappe, C. O. (2016). Generation and synthetic application
of trifluoromethyl diazomethane utilizing continuous flow technologies. Organic
Letters. American Chemical Society. https://doi.org/10.1021/acs.orglett.6b00194
chicago: Pieber, Bartholomäus, and C. Oliver Kappe. “Generation and Synthetic Application
of Trifluoromethyl Diazomethane Utilizing Continuous Flow Technologies.” Organic
Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.orglett.6b00194.
ieee: B. Pieber and C. O. Kappe, “Generation and synthetic application of trifluoromethyl
diazomethane utilizing continuous flow technologies,” Organic Letters,
vol. 18, no. 5. American Chemical Society, pp. 1076–1079, 2016.
ista: Pieber B, Kappe CO. 2016. Generation and synthetic application of trifluoromethyl
diazomethane utilizing continuous flow technologies. Organic Letters. 18(5), 1076–1079.
mla: Pieber, Bartholomäus, and C. Oliver Kappe. “Generation and Synthetic Application
of Trifluoromethyl Diazomethane Utilizing Continuous Flow Technologies.” Organic
Letters, vol. 18, no. 5, American Chemical Society, 2016, pp. 1076–79, doi:10.1021/acs.orglett.6b00194.
short: B. Pieber, C.O. Kappe, Organic Letters 18 (2016) 1076–1079.
date_created: 2022-08-25T11:22:20Z
date_published: 2016-03-04T00:00:00Z
date_updated: 2023-02-21T10:10:21Z
day: '04'
doi: 10.1021/acs.orglett.6b00194
extern: '1'
external_id:
pmid:
- '26902154'
intvolume: ' 18'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 1076-1079
pmid: 1
publication: Organic Letters
publication_identifier:
eissn:
- 1523-7052
issn:
- 1523-7060
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generation and synthetic application of trifluoromethyl diazomethane utilizing
continuous flow technologies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '11985'
abstract:
- lang: eng
text: Hydrocodone, a high value active pharmaceutical ingredient (API), is usually
produced in a semisynthetic pathway from morphine, codeine or thebaine. The latter
alkaloid is an attractive precursor as it is not used as a remedy itself. The
key step in this production route is a selective olefin reduction forming 8,14-dihydrothebaine
which can be subsequently hydrolyzed to yield hydrocodone. Unfortunately, standard
hydrogenation procedures cannot be applied due to severe selectivity problems.
A transfer hydrogenation using in situ generated diimide is the only known alternative
to achieve a selective transformation. The most (atom) economic generation of
this highly unstable reducing agent is by oxidizing hydrazine hydrate (N2H4·H2O)
with O2. In the past, this route was “forbidden” on an industrial scale due to
its enormous explosion potential in batch. A continuous high-temperature/high-pressure
methodology allows an efficient, safe, and scalable processing of the hazardous
reaction mixture. The industrially relevant reduction was achieved by using four
consecutive liquid feeds (of N2H4·H2O) and residence time units, resulting in
a highly selective reduction within less than 1 h.
article_processing_charge: No
article_type: original
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: D. Phillip
full_name: Cox, D. Phillip
last_name: Cox
- first_name: C. Oliver
full_name: Kappe, C. Oliver
last_name: Kappe
citation:
ama: Pieber B, Cox DP, Kappe CO. Selective olefin reduction in thebaine using hydrazine
hydrate and O₂ under intensified continuous flow conditions. Organic Process
Research and Development. 2016;20(2):376-385. doi:10.1021/acs.oprd.5b00370
apa: Pieber, B., Cox, D. P., & Kappe, C. O. (2016). Selective olefin reduction
in thebaine using hydrazine hydrate and O₂ under intensified continuous flow conditions.
Organic Process Research and Development. American Chemical Society. https://doi.org/10.1021/acs.oprd.5b00370
chicago: Pieber, Bartholomäus, D. Phillip Cox, and C. Oliver Kappe. “Selective Olefin
Reduction in Thebaine Using Hydrazine Hydrate and O₂ under Intensified Continuous
Flow Conditions.” Organic Process Research and Development. American Chemical
Society, 2016. https://doi.org/10.1021/acs.oprd.5b00370.
ieee: B. Pieber, D. P. Cox, and C. O. Kappe, “Selective olefin reduction in thebaine
using hydrazine hydrate and O₂ under intensified continuous flow conditions,”
Organic Process Research and Development, vol. 20, no. 2. American Chemical
Society, pp. 376–385, 2016.
ista: Pieber B, Cox DP, Kappe CO. 2016. Selective olefin reduction in thebaine using
hydrazine hydrate and O₂ under intensified continuous flow conditions. Organic
Process Research and Development. 20(2), 376–385.
mla: Pieber, Bartholomäus, et al. “Selective Olefin Reduction in Thebaine Using
Hydrazine Hydrate and O₂ under Intensified Continuous Flow Conditions.” Organic
Process Research and Development, vol. 20, no. 2, American Chemical Society,
2016, pp. 376–85, doi:10.1021/acs.oprd.5b00370.
short: B. Pieber, D.P. Cox, C.O. Kappe, Organic Process Research and Development
20 (2016) 376–385.
date_created: 2022-08-25T11:34:28Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2023-02-21T10:10:26Z
day: '19'
doi: 10.1021/acs.oprd.5b00370
extern: '1'
intvolume: ' 20'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 376-385
publication: Organic Process Research and Development
publication_identifier:
eissn:
- 1520-586X
issn:
- 1083-6160
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selective olefin reduction in thebaine using hydrazine hydrate and O₂ under
intensified continuous flow conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2016'
...
---
_id: '11988'
abstract:
- lang: eng
text: A continuous Bucherer–Bergs hydantoin synthesis utilizing intensified conditions
is reported. The methodology is characterized by a two-feed flow approach to independently
feed the organic substrate and the aqueous reagent solution. The increased interfacial
area of the biphasic reaction mixture and the lack of headspace enabled almost
quantitative conversions within ca. 30 minutes at 120 °C and 20 bar even for unpolar
starting materials. In addition, a selective N(3)-monoalkylation of the resulting
heterocycles under batch microwave conditions is reported yielding potential acetylcholinesterase
inhibitors.
article_processing_charge: No
article_type: letter_note
author:
- first_name: C.
full_name: Kappe, C.
last_name: Kappe
- first_name: Julia
full_name: Monteiro, Julia
last_name: Monteiro
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Arlene
full_name: Corrêa, Arlene
last_name: Corrêa
citation:
ama: 'Kappe C, Monteiro J, Pieber B, Corrêa A. Continuous synthesis of hydantoins:
Intensifying the Bucherer–Bergs reaction. Synlett. 2016;27(01):83-87. doi:10.1055/s-0035-1560317'
apa: 'Kappe, C., Monteiro, J., Pieber, B., & Corrêa, A. (2016). Continuous synthesis
of hydantoins: Intensifying the Bucherer–Bergs reaction. Synlett. Georg
Thieme Verlag. https://doi.org/10.1055/s-0035-1560317'
chicago: 'Kappe, C., Julia Monteiro, Bartholomäus Pieber, and Arlene Corrêa. “Continuous
Synthesis of Hydantoins: Intensifying the Bucherer–Bergs Reaction.” Synlett.
Georg Thieme Verlag, 2016. https://doi.org/10.1055/s-0035-1560317.'
ieee: 'C. Kappe, J. Monteiro, B. Pieber, and A. Corrêa, “Continuous synthesis of
hydantoins: Intensifying the Bucherer–Bergs reaction,” Synlett, vol. 27,
no. 01. Georg Thieme Verlag, pp. 83–87, 2016.'
ista: 'Kappe C, Monteiro J, Pieber B, Corrêa A. 2016. Continuous synthesis of hydantoins:
Intensifying the Bucherer–Bergs reaction. Synlett. 27(01), 83–87.'
mla: 'Kappe, C., et al. “Continuous Synthesis of Hydantoins: Intensifying the Bucherer–Bergs
Reaction.” Synlett, vol. 27, no. 01, Georg Thieme Verlag, 2016, pp. 83–87,
doi:10.1055/s-0035-1560317.'
short: C. Kappe, J. Monteiro, B. Pieber, A. Corrêa, Synlett 27 (2016) 83–87.
date_created: 2022-08-25T11:52:22Z
date_published: 2016-01-04T00:00:00Z
date_updated: 2023-02-21T10:10:33Z
day: '04'
doi: 10.1055/s-0035-1560317
extern: '1'
intvolume: ' 27'
issue: '01'
language:
- iso: eng
month: '01'
oa_version: None
page: 83-87
publication: Synlett
publication_identifier:
eissn:
- 1437-2096
issn:
- 0936-5214
publication_status: published
publisher: Georg Thieme Verlag
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Continuous synthesis of hydantoins: Intensifying the Bucherer–Bergs reaction'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2016'
...
---
_id: '1200'
acknowledgement: C.H. acknowledges generous support from the ISTFELLOW program.
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Arne
full_name: Traulsen, Arne
last_name: Traulsen
citation:
ama: 'Hilbe C, Traulsen A. Only the combination of mathematics and agent based simulations
can leverage the full potential of evolutionary modeling: Comment on “Evolutionary
game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze.
Physics of Life Reviews. 2016;19:29-31. doi:10.1016/j.plrev.2016.10.004'
apa: 'Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics
and agent based simulations can leverage the full potential of evolutionary modeling:
Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J.
Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004'
chicago: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics
and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling:
Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J.
Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004.'
ieee: 'C. Hilbe and A. Traulsen, “Only the combination of mathematics and agent
based simulations can leverage the full potential of evolutionary modeling: Comment
on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau
and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31,
2016.'
ista: 'Hilbe C, Traulsen A. 2016. Only the combination of mathematics and agent
based simulations can leverage the full potential of evolutionary modeling: Comment
on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau
and A. Hintze. Physics of Life Reviews. 19, 29–31.'
mla: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics
and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling:
Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J.
Schossau and A. Hintze.” Physics of Life Reviews, vol. 19, Elsevier, 2016,
pp. 29–31, doi:10.1016/j.plrev.2016.10.004.'
short: C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31.
date_created: 2018-12-11T11:50:40Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
ddc:
- '530'
department:
- _id: KrCh
doi: 10.1016/j.plrev.2016.10.004
ec_funded: 1
file:
- access_level: open_access
checksum: 95e6dc78278334b99dacbf8822509364
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:02Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4855'
file_name: IST-2017-798-v1+1_comment_adami.pdf
file_size: 171352
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Submitted Version
page: 29 - 31
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6150'
pubrep_id: '798'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Only the combination of mathematics and agent based simulations can leverage
the full potential of evolutionary modeling: Comment on “Evolutionary game theory
using agent-based methods” by C. Adami, J. Schossau and A. Hintze'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2016'
...
---
_id: '1201'
abstract:
- lang: eng
text: In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear
actin cytoskeleton that protects the nucleus and its genomic content of migrating
cells squeezing through small spaces.
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Renkawitz J, Sixt MK. Formin’ a nuclear protection. Cell. 2016;167(6):1448-1449.
doi:10.1016/j.cell.2016.11.024
apa: Renkawitz, J., & Sixt, M. K. (2016). Formin’ a nuclear protection. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2016.11.024
chicago: Renkawitz, Jörg, and Michael K Sixt. “Formin’ a Nuclear Protection.” Cell.
Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.024.
ieee: J. Renkawitz and M. K. Sixt, “Formin’ a nuclear protection,” Cell,
vol. 167, no. 6. Cell Press, pp. 1448–1449, 2016.
ista: Renkawitz J, Sixt MK. 2016. Formin’ a nuclear protection. Cell. 167(6), 1448–1449.
mla: Renkawitz, Jörg, and Michael K. Sixt. “Formin’ a Nuclear Protection.” Cell,
vol. 167, no. 6, Cell Press, 2016, pp. 1448–49, doi:10.1016/j.cell.2016.11.024.
short: J. Renkawitz, M.K. Sixt, Cell 167 (2016) 1448–1449.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.cell.2016.11.024
intvolume: ' 167'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 1448 - 1449
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '6149'
quality_controlled: '1'
scopus_import: 1
status: public
title: Formin’ a nuclear protection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2016'
...
---
_id: '1202'
acknowledgement: The authors thank Sophie A.O. Armitage and Jan N. Offenborn for helpful
comments on the figures, and two anonymous reviewers for their helpful comments.
The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2)
within the priority programme SPP 1399 “Host–Parasite Coevolution”.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Kevin
full_name: Ferro, Kevin
last_name: Ferro
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Milutinovic B, Peuß R, Ferro K, Kurtz J. Immune priming in arthropods: an
update focusing on the red flour beetle. Zoology . 2016;119(4):254-261.
doi:10.1016/j.zool.2016.03.006'
apa: 'Milutinovic, B., Peuß, R., Ferro, K., & Kurtz, J. (2016). Immune priming
in arthropods: an update focusing on the red flour beetle. Zoology . Elsevier.
https://doi.org/10.1016/j.zool.2016.03.006'
chicago: 'Milutinovic, Barbara, Robert Peuß, Kevin Ferro, and Joachim Kurtz. “Immune
Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology
. Elsevier, 2016. https://doi.org/10.1016/j.zool.2016.03.006.'
ieee: 'B. Milutinovic, R. Peuß, K. Ferro, and J. Kurtz, “Immune priming in arthropods:
an update focusing on the red flour beetle,” Zoology , vol. 119, no. 4.
Elsevier, pp. 254–261, 2016.'
ista: 'Milutinovic B, Peuß R, Ferro K, Kurtz J. 2016. Immune priming in arthropods:
an update focusing on the red flour beetle. Zoology . 119(4), 254–261.'
mla: 'Milutinovic, Barbara, et al. “Immune Priming in Arthropods: An Update Focusing
on the Red Flour Beetle.” Zoology , vol. 119, no. 4, Elsevier, 2016, pp.
254–61, doi:10.1016/j.zool.2016.03.006.'
short: B. Milutinovic, R. Peuß, K. Ferro, J. Kurtz, Zoology 119 (2016) 254–261.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1016/j.zool.2016.03.006
file:
- access_level: open_access
checksum: 8396d5bd95f9c4295857162f902afabf
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T13:00:20Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5885'
file_name: 2016_Elsevier_Milutinovic.pdf
file_size: 1473211
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 119'
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 254 - 261
project:
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: 'Zoology '
publication_status: published
publisher: Elsevier
publist_id: '6147'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Immune priming in arthropods: an update focusing on the red flour beetle'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2016'
...
---
_id: '1203'
abstract:
- lang: eng
text: Haemophilus haemolyticus has been recently discovered to have the potential
to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae
(NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified
because none of the existing tests targeting the known phenotypes of H. haemolyticus
are able to specifically identify H. haemolyticus. Through comparative genomic
analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to
H. haemolyticus that can be used as targets for the identification of H. haemolyticus.
A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase
2 in the purine synthesis pathway) was developed and evaluated. The lower limit
of detection was 40 genomes/PCR; the sensitivity and specificity in detecting
H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination
of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets
(H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was
also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification
of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification
of H. influenzae, respectively. The dual-target testing scheme can be used for
the diagnosis and surveillance of infection and disease caused by H. haemolyticus
and NT H. influenzae.
acknowledgement: We are grateful to ABCs for providing strains and the Bacterial Meningitis
Laboratory for technical support.
author:
- first_name: Fang
full_name: Hu, Fang
last_name: Hu
- first_name: Lavanya
full_name: Rishishwar, Lavanya
last_name: Rishishwar
- first_name: Ambily
full_name: Sivadas, Ambily
last_name: Sivadas
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Jordan
full_name: King, Jordan
last_name: King
- first_name: Timothy
full_name: Murphy, Timothy
last_name: Murphy
- first_name: Janet
full_name: Gilsdorf, Janet
last_name: Gilsdorf
- first_name: Leonard
full_name: Mayer, Leonard
last_name: Mayer
- first_name: Xin
full_name: Wang, Xin
last_name: Wang
citation:
ama: Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus
haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for
their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017.
doi:10.1128/JCM.01511-16
apa: Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., …
Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and
nontypeable Haemophilus influenzae and a new testing scheme for their discrimination.
Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16
chicago: Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan
King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative
Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae
and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology.
American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.
ieee: F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus
and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,”
Journal of Clinical Microbiology, vol. 54, no. 12. American Society for
Microbiology, pp. 3010–3017, 2016.
ista: Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer
L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and
nontypeable Haemophilus influenzae and a new testing scheme for their discrimination.
Journal of Clinical Microbiology. 54(12), 3010–3017.
mla: Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus
and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.”
Journal of Clinical Microbiology, vol. 54, no. 12, American Society for
Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16.
short: F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf,
L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:04Z
day: '01'
department:
- _id: GaTk
doi: 10.1128/JCM.01511-16
intvolume: ' 54'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/
month: '12'
oa: 1
oa_version: Submitted Version
page: 3010 - 3017
publication: Journal of Clinical Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '6146'
quality_controlled: '1'
scopus_import: 1
status: public
title: Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus
influenzae and a new testing scheme for their discrimination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2016'
...
---
_id: '1204'
abstract:
- lang: eng
text: In science, as in life, "surprises" can be adequately appreciated
only in the presence of a null model, what we expect a priori. In physics, theories
sometimes express the values of dimensionless physical constants as combinations
of mathematical constants like π or e. The inverse problem also arises, whereby
the measured value of a physical constant admits a "surprisingly" simple
approximation in terms of well-known mathematical constants. Can we estimate the
probability for this to be a mere coincidence, rather than an inkling of some
theory? We answer the question in the most naive form.
author:
- first_name: Ariel
full_name: Amir, Ariel
last_name: Amir
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Tadashi
full_name: Tokieda, Tadashi
last_name: Tokieda
citation:
ama: Amir A, Lemeshko M, Tokieda T. Surprises in numerical expressions of physical
constants. American Mathematical Monthly. 2016;123(6):609-612. doi:10.4169/amer.math.monthly.123.6.609
apa: Amir, A., Lemeshko, M., & Tokieda, T. (2016). Surprises in numerical expressions
of physical constants. American Mathematical Monthly. Mathematical Association
of America. https://doi.org/10.4169/amer.math.monthly.123.6.609
chicago: Amir, Ariel, Mikhail Lemeshko, and Tadashi Tokieda. “Surprises in Numerical
Expressions of Physical Constants.” American Mathematical Monthly. Mathematical
Association of America, 2016. https://doi.org/10.4169/amer.math.monthly.123.6.609.
ieee: A. Amir, M. Lemeshko, and T. Tokieda, “Surprises in numerical expressions
of physical constants,” American Mathematical Monthly, vol. 123, no. 6.
Mathematical Association of America, pp. 609–612, 2016.
ista: Amir A, Lemeshko M, Tokieda T. 2016. Surprises in numerical expressions of
physical constants. American Mathematical Monthly. 123(6), 609–612.
mla: Amir, Ariel, et al. “Surprises in Numerical Expressions of Physical Constants.”
American Mathematical Monthly, vol. 123, no. 6, Mathematical Association
of America, 2016, pp. 609–12, doi:10.4169/amer.math.monthly.123.6.609.
short: A. Amir, M. Lemeshko, T. Tokieda, American Mathematical Monthly 123 (2016)
609–612.
date_created: 2018-12-11T11:50:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:04Z
day: '01'
department:
- _id: MiLe
doi: 10.4169/amer.math.monthly.123.6.609
intvolume: ' 123'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.00299
month: '06'
oa: 1
oa_version: Preprint
page: 609 - 612
publication: American Mathematical Monthly
publication_status: published
publisher: Mathematical Association of America
publist_id: '6143'
quality_controlled: '1'
scopus_import: 1
status: public
title: Surprises in numerical expressions of physical constants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 123
year: '2016'
...
---
_id: '1205'
abstract:
- lang: eng
text: In this paper, we present a formal model-driven engineering approach to establishing
a safety-assured implementation of Multifunction vehicle bus controller (MVBC)
based on the generic reference models and requirements described in the International
Electrotechnical Commission (IEC) standard IEC-61375. First, the generic models
described in IEC-61375 are translated into a network of timed automata, and some
safety requirements tested in IEC-61375 are formalized as timed computation tree
logic (TCTL) formulas. With the help of Uppaal, we check and debug whether the
timed automata satisfy the formulas or not. Within this step, several logic inconsistencies
in the original standard are detected and corrected. Then, we apply the tool Times
to generate C code from the verified model, which was later synthesized into a
real MVBC chip. Finally, the runtime verification tool RMOR is applied to verify
some safety requirements at the implementation level. We set up a real platform
with worldwide mostly used MVBC D113, and verify the correctness and the scalability
of the synthesized MVBC chip more comprehensively. The errors in the standard
has been confirmed and the resulted MVBC has been deployed in real train communication
network.
acknowledgement: "This research is sponsored in part by NSFC Program (No. 91218302,
No. 61527812), National Science and Technology Major Project (No. 2016ZX01038101),
Tsinghua University Initiative Scientific Research Program (20131089331), MIIT IT
funds (Research and application of TCN key technologies) of China, and the National
Key Technology R&D Program (No. 2015BAG14B01-02), Austrian Science Fund (FWF) under
grants S11402-N23 (RiSE/SHiNE) and Z211-N23.\r\n"
alternative_title:
- LNCS
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Houbing
full_name: Song, Houbing
last_name: Song
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ming
full_name: Gu, Ming
last_name: Gu
- first_name: Jiaguang
full_name: Sun, Jiaguang
last_name: Sun
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: 'Jiang Y, Liu H, Song H, et al. Safety assured formal model driven design of
the multifunction vehicle bus controller. In: Vol 9995. Springer; 2016:757-763.
doi:10.1007/978-3-319-48989-6_47'
apa: 'Jiang, Y., Liu, H., Song, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016).
Safety assured formal model driven design of the multifunction vehicle bus controller
(Vol. 9995, pp. 757–763). Presented at the FM: International Symposium on Formal
Methods, Limassol, Cyprus: Springer. https://doi.org/10.1007/978-3-319-48989-6_47'
chicago: Jiang, Yu, Han Liu, Houbing Song, Hui Kong, Ming Gu, Jiaguang Sun, and
Lui Sha. “Safety Assured Formal Model Driven Design of the Multifunction Vehicle
Bus Controller,” 9995:757–63. Springer, 2016. https://doi.org/10.1007/978-3-319-48989-6_47.
ieee: 'Y. Jiang et al., “Safety assured formal model driven design of the
multifunction vehicle bus controller,” presented at the FM: International Symposium
on Formal Methods, Limassol, Cyprus, 2016, vol. 9995, pp. 757–763.'
ista: 'Jiang Y, Liu H, Song H, Kong H, Gu M, Sun J, Sha L. 2016. Safety assured
formal model driven design of the multifunction vehicle bus controller. FM: International
Symposium on Formal Methods, LNCS, vol. 9995, 757–763.'
mla: Jiang, Yu, et al. Safety Assured Formal Model Driven Design of the Multifunction
Vehicle Bus Controller. Vol. 9995, Springer, 2016, pp. 757–63, doi:10.1007/978-3-319-48989-6_47.
short: Y. Jiang, H. Liu, H. Song, H. Kong, M. Gu, J. Sun, L. Sha, in:, Springer,
2016, pp. 757–763.
conference:
end_date: 2016-11-11
location: Limassol, Cyprus
name: 'FM: International Symposium on Formal Methods'
start_date: 2016-11-09
date_created: 2018-12-11T11:50:42Z
date_published: 2016-11-08T00:00:00Z
date_updated: 2023-09-18T08:12:48Z
day: '08'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-319-48989-6_47
file:
- access_level: open_access
checksum: fea0b3fae9a2a42e8bfec59840e30d8c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:13Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4673'
file_name: IST-2017-783-v1+1_FM-Safety-Assured-Development-of-MVBC.pdf
file_size: 281501
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9995'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 757 - 763
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '6144'
pubrep_id: '783'
quality_controlled: '1'
related_material:
record:
- id: '434'
relation: later_version
status: public
scopus_import: 1
status: public
title: Safety assured formal model driven design of the multifunction vehicle bus
controller
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9995
year: '2016'
...
---
_id: '1206'
abstract:
- lang: eng
text: We study a polar molecule immersed in a superfluid environment, such as a
helium nanodroplet or a Bose–Einstein condensate, in the presence of a strong
electrostatic field. We show that coupling of the molecular pendular motion, induced
by the field, to the fluctuating bath leads to formation of pendulons—spherical
harmonic librators dressed by a field of many-particle excitations. We study the
behavior of the pendulon in a broad range of molecule–bath and molecule–field
interaction strengths, and reveal that its spectrum features a series of instabilities
which are absent in the field-free case of the angulon quasiparticle. Furthermore,
we show that an external field allows to fine-tune the positions of these instabilities
in the molecular rotational spectrum. This opens the door to detailed experimental
studies of redistribution of orbital angular momentum in many-particle systems.
© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Redchenko E, Lemeshko M. Libration of strongly oriented polar molecules inside
a superfluid. ChemPhysChem. 2016;17(22):3649-3654. doi:10.1002/cphc.201601042
apa: Redchenko, E., & Lemeshko, M. (2016). Libration of strongly oriented polar
molecules inside a superfluid. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201601042
chicago: Redchenko, Elena, and Mikhail Lemeshko. “Libration of Strongly Oriented
Polar Molecules inside a Superfluid.” ChemPhysChem. Wiley-Blackwell, 2016.
https://doi.org/10.1002/cphc.201601042.
ieee: E. Redchenko and M. Lemeshko, “Libration of strongly oriented polar molecules
inside a superfluid,” ChemPhysChem, vol. 17, no. 22. Wiley-Blackwell, pp.
3649–3654, 2016.
ista: Redchenko E, Lemeshko M. 2016. Libration of strongly oriented polar molecules
inside a superfluid. ChemPhysChem. 17(22), 3649–3654.
mla: Redchenko, Elena, and Mikhail Lemeshko. “Libration of Strongly Oriented Polar
Molecules inside a Superfluid.” ChemPhysChem, vol. 17, no. 22, Wiley-Blackwell,
2016, pp. 3649–54, doi:10.1002/cphc.201601042.
short: E. Redchenko, M. Lemeshko, ChemPhysChem 17 (2016) 3649–3654.
date_created: 2018-12-11T11:50:43Z
date_published: 2016-09-18T00:00:00Z
date_updated: 2021-01-12T06:49:05Z
day: '18'
department:
- _id: JoFi
- _id: MiLe
doi: 10.1002/cphc.201601042
ec_funded: 1
intvolume: ' 17'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08161
month: '09'
oa: 1
oa_version: Preprint
page: 3649 - 3654
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ChemPhysChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6140'
quality_controlled: '1'
scopus_import: 1
status: public
title: Libration of strongly oriented polar molecules inside a superfluid
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1209'
abstract:
- lang: eng
text: 'NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the
least characterized complex of the mitochondrial electron transport chain. Because
of the ease of sample availability, previous work has focused almost exclusively
on bovine complex I. However, only medium resolution structural analyses of this
complex have been reported. Working with other mammalian complex I homologues
is a potential approach for overcoming these limitations. Due to the inherent
difficulty of expressing large membrane protein complexes, screening of complex
I homologues is limited to large mammals reared for human consumption. The high
sequence identity among these available sources may preclude the benefits of screening.
Here, we report the characterization of complex I purified from Ovis aries (ovine)
heart mitochondria. All 44 unique subunits of the intact complex were identified
by mass spectrometry. We identified differences in the subunit composition of
subcomplexes of ovine complex I as compared with bovine, suggesting differential
stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa
subunit, which is easily lost from the bovine enzyme, remains tightly bound to
ovine complex I. Additionally, we developed a novel purification protocol for
highly active and stable mitochondrial complex I using the branched-chain detergent
lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related,
significant differences exist between the biochemical properties of complex I
prepared from ovine and bovine mitochondria and that ovine complex I represents
a suitable alternative target for further structural studies. '
acknowledgement: "J.A.S supported in part by a Medical Research D.G.Council UK Ph.D.
fellowship.\r\nThis work was supported in part by European Union's 2020 Research
and Innovation Program under Grant 701309. \r\n"
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Gianluca
full_name: Degliesposti, Gianluca
last_name: Degliesposti
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. Purification
of ovine respiratory complex i results in a highly active and stable preparation.
Journal of Biological Chemistry. 2016;291(47):24657-24675. doi:10.1074/jbc.M116.735142
apa: Letts, J. A., Degliesposti, G., Fiedorczuk, K., Skehel, M., & Sazanov,
L. A. (2016). Purification of ovine respiratory complex i results in a highly
active and stable preparation. Journal of Biological Chemistry. American
Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.735142
chicago: Letts, James A, Gianluca Degliesposti, Karol Fiedorczuk, Mark Skehel, and
Leonid A Sazanov. “Purification of Ovine Respiratory Complex i Results in a Highly
Active and Stable Preparation.” Journal of Biological Chemistry. American
Society for Biochemistry and Molecular Biology, 2016. https://doi.org/10.1074/jbc.M116.735142.
ieee: J. A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, and L. A. Sazanov,
“Purification of ovine respiratory complex i results in a highly active and stable
preparation,” Journal of Biological Chemistry, vol. 291, no. 47. American
Society for Biochemistry and Molecular Biology, pp. 24657–24675, 2016.
ista: Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. 2016. Purification
of ovine respiratory complex i results in a highly active and stable preparation.
Journal of Biological Chemistry. 291(47), 24657–24675.
mla: Letts, James A., et al. “Purification of Ovine Respiratory Complex i Results
in a Highly Active and Stable Preparation.” Journal of Biological Chemistry,
vol. 291, no. 47, American Society for Biochemistry and Molecular Biology, 2016,
pp. 24657–75, doi:10.1074/jbc.M116.735142.
short: J.A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, L.A. Sazanov, Journal
of Biological Chemistry 291 (2016) 24657–24675.
date_created: 2018-12-11T11:50:44Z
date_published: 2016-11-18T00:00:00Z
date_updated: 2021-01-12T06:49:06Z
day: '18'
department:
- _id: LeSa
doi: 10.1074/jbc.M116.735142
ec_funded: 1
intvolume: ' 291'
issue: '47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114416/
month: '11'
oa: 1
oa_version: Submitted Version
page: 24657 - 24675
project:
- _id: 2593EBD6-B435-11E9-9278-68D0E5697425
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(FEBS)
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '6139'
quality_controlled: '1'
scopus_import: 1
status: public
title: Purification of ovine respiratory complex i results in a highly active and
stable preparation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 291
year: '2016'
...