---
_id: '11084'
abstract:
- lang: eng
text: Protein turnover is an effective way of maintaining a functional proteome,
as old and potentially damaged polypeptides are destroyed and replaced by newly
synthesized copies. An increasing number of intracellular proteins, however, have
been identified that evade this turnover process and instead are maintained over
a cell's lifetime. This diverse group of long-lived proteins might be particularly
prone to accumulation of damage and thus have a crucial role in the functional
deterioration of key regulatory processes during ageing.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: 'Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. Nature
Reviews Molecular Cell Biology. 2013;14:55-61. doi:10.1038/nrm3496'
apa: 'Toyama, B. H., & Hetzer, M. (2013). Protein homeostasis: Live long, won’t
prosper. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/nrm3496'
chicago: 'Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long,
Won’t Prosper.” Nature Reviews Molecular Cell Biology. Springer Nature,
2013. https://doi.org/10.1038/nrm3496.'
ieee: 'B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,”
Nature Reviews Molecular Cell Biology, vol. 14. Springer Nature, pp. 55–61,
2013.'
ista: 'Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper.
Nature Reviews Molecular Cell Biology. 14, 55–61.'
mla: 'Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t
Prosper.” Nature Reviews Molecular Cell Biology, vol. 14, Springer Nature,
2013, pp. 55–61, doi:10.1038/nrm3496.'
short: B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61.
date_created: 2022-04-07T07:50:43Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2022-07-18T08:37:53Z
day: '01'
doi: 10.1038/nrm3496
extern: '1'
external_id:
pmid:
- '23258296'
intvolume: ' 14'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
month: '01'
oa_version: None
page: 55-61
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
issn:
- 1471-0072
- 1471-0080
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Protein homeostasis: Live long, won''t prosper'
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 14
year: '2013'
...
---
_id: '11085'
abstract:
- lang: eng
text: During mitotic exit, missegregated chromosomes can recruit their own nuclear
envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to
primary nuclei in the same cell, although the two compartments appear to be structurally
comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization
during interphase due to NE collapse. This disruption of the MN, which is induced
by defects in nuclear lamina assembly, drastically reduces nuclear functions and
can trigger massive DNA damage. MN disruption is associated with chromatin compaction
and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified
disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting
that disrupted MN could be a useful objective biomarker for genomic instability
in solid tumors. Our study shows that NE collapse is a key event underlying MN
dysfunction and establishes a link between aberrant NE organization and aneuploidy.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Andrew H.
full_name: Fischer, Andrew H.
last_name: Fischer
- first_name: Thomas J.
full_name: Deerinck, Thomas J.
last_name: Deerinck
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007
apa: Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic
nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007
chicago: Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer.
“Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.
ieee: E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear
envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier,
pp. 47–60, 2013.
ista: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 154(1), 47–60.
mla: Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell
Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.
short: E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.
date_created: 2022-04-07T07:50:51Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2022-07-18T08:45:47Z
day: '03'
doi: 10.1016/j.cell.2013.06.007
extern: '1'
external_id:
pmid:
- '23827674'
intvolume: ' 154'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.06.007
month: '07'
oa: 1
oa_version: Published Version
page: 47-60
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catastrophic nuclear envelope collapse in cancer cell micronuclei
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11086'
abstract:
- lang: eng
text: Faithful execution of developmental gene expression programs occurs at multiple
levels and involves many different components such as transcription factors, histone-modification
enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins,
well known components that control nucleo-cytoplasmic trafficking, have wide-ranging
functions in developmental gene regulation that potentially extend beyond their
role in nuclear transport. Whether the unexpected role of nuclear pore proteins
in transcription regulation, which initially has been described in fungi and flies,
also applies to human cells is unknown. Here we show at a genome-wide level that
the nuclear pore protein NUP98 associates with developmentally regulated genes
active during human embryonic stem cell differentiation. Overexpression of a dominant
negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes.
In addition, we identify two modes of developmental gene regulation by NUP98 that
are differentiated by the spatial localization of NUP98 target genes. Genes in
the initial stage of developmental induction can associate with NUP98 that is
embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that
are highly induced can interact with NUP98 in the nuclear interior, away from
the nuclear pores. This work demonstrates for the first time that NUP98 dynamically
associates with the human genome during differentiation, revealing a role of a
nuclear pore protein in regulating developmental gene expression programs.
article_number: e1003308
article_processing_charge: No
article_type: original
author:
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Maria C.
full_name: Marchetto, Maria C.
last_name: Marchetto
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of
NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308
apa: Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013).
Dynamic association of NUP98 with the human genome. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1003308
chicago: Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin
Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308.
ieee: Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic
association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no.
2. Public Library of Science, 2013.
ista: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association
of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308.
mla: Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS
Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308.
short: Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics
9 (2013).
date_created: 2022-04-07T07:50:59Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2022-07-18T08:45:58Z
day: '28'
doi: 10.1371/journal.pgen.1003308
extern: '1'
external_id:
pmid:
- '23468646'
intvolume: ' 9'
issue: '2'
keyword:
- Cancer Research
- Genetics (clinical)
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1003308
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic association of NUP98 with the human genome
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 9
year: '2013'
...
---
_id: '11087'
abstract:
- lang: eng
text: Intracellular proteins with long lifespans have recently been linked to age-dependent
defects, ranging from decreased fertility to the functional decline of neurons.
Why long-lived proteins exist in metabolically active cellular environments and
how they are maintained over time remains poorly understood. Here, we provide
a system-wide identification of proteins with exceptional lifespans in the rat
brain. These proteins are inefficiently replenished despite being translated robustly
throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence,
we found that nuclear pore complexes (NPCs) are maintained over a cell’s life
through slow but finite exchange of even its most stable subcomplexes. This maintenance
is limited, however, as some nucleoporin levels decrease during aging, providing
a rationale for the previously observed age-dependent deterioration of NPC function.
Our identification of a long-lived proteome reveals cellular components that are
at increased risk for damage accumulation, linking long-term protein persistence
to the cellular aging process.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Jeffrey N.
full_name: Savas, Jeffrey N.
last_name: Savas
- first_name: Sung Kyu
full_name: Park, Sung Kyu
last_name: Park
- first_name: Michael S.
full_name: Harris, Michael S.
last_name: Harris
- first_name: Nicholas T.
full_name: Ingolia, Nicholas T.
last_name: Ingolia
- first_name: John R.
full_name: Yates, John R.
last_name: Yates
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins
reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982.
doi:10.1016/j.cell.2013.07.037
apa: Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates,
J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals
exceptional stability of essential cellular structures. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.07.037
chicago: Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris,
Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived
Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.
ieee: B. H. Toyama et al., “Identification of long-lived proteins reveals
exceptional stability of essential cellular structures,” Cell, vol. 154,
no. 5. Elsevier, pp. 971–982, 2013.
ista: Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013.
Identification of long-lived proteins reveals exceptional stability of essential
cellular structures. Cell. 154(5), 971–982.
mla: Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional
Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier,
2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037.
short: B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates,
M. Hetzer, Cell 154 (2013) 971–982.
date_created: 2022-04-07T07:51:08Z
date_published: 2013-08-29T00:00:00Z
date_updated: 2022-07-18T08:50:47Z
day: '29'
doi: 10.1016/j.cell.2013.07.037
extern: '1'
external_id:
pmid:
- '23993091'
intvolume: ' 154'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.07.037
month: '08'
oa: 1
oa_version: Published Version
page: 971-982
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins reveals exceptional stability of essential
cellular structures
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11088'
abstract:
- lang: eng
text: 'The crowded intracellular environment poses a formidable challenge to experimental
and theoretical analyses of intracellular transport mechanisms. Our measurements
of single-particle trajectories in cytoplasm and their random-walk interpretations
elucidate two of these mechanisms: molecular diffusion in crowded environments
and cytoskeletal transport along microtubules. We employed acousto-optic deflector
microscopy to map out the three-dimensional trajectories of microspheres migrating
in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM),
continuous time random walk, and fractional BM were alternatively used to represent
these trajectories. The comparison of the experimental and numerical data demonstrates
that cytoskeletal transport along microtubules and diffusion in the cytosolic
fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct
signatures. Among the three random-walk models used, continuous time random walk
provides the best representation of diffusion, whereas microtubular transport
is accurately modeled with fractional BM.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin M.
full_name: Regner, Benjamin M.
last_name: Regner
- first_name: Dejan
full_name: Vučinić, Dejan
last_name: Vučinić
- first_name: Cristina
full_name: Domnisoru, Cristina
last_name: Domnisoru
- first_name: Thomas M.
full_name: Bartol, Thomas M.
last_name: Bartol
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Daniel M.
full_name: Tartakovsky, Daniel M.
last_name: Tartakovsky
- first_name: Terrence J.
full_name: Sejnowski, Terrence J.
last_name: Sejnowski
citation:
ama: Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles
in cytoplasm. Biophysical Journal. 2013;104(8):1652-1660. doi:10.1016/j.bpj.2013.01.049
apa: Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky,
D. M., & Sejnowski, T. J. (2013). Anomalous diffusion of single particles
in cytoplasm. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2013.01.049
chicago: Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol,
Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion
of Single Particles in Cytoplasm.” Biophysical Journal. Elsevier, 2013.
https://doi.org/10.1016/j.bpj.2013.01.049.
ieee: B. M. Regner et al., “Anomalous diffusion of single particles in cytoplasm,”
Biophysical Journal, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013.
ista: Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski
TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal.
104(8), 1652–1660.
mla: Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.”
Biophysical Journal, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:10.1016/j.bpj.2013.01.049.
short: B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky,
T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660.
date_created: 2022-04-07T07:51:26Z
date_published: 2013-04-16T00:00:00Z
date_updated: 2022-07-18T08:51:01Z
day: '16'
doi: 10.1016/j.bpj.2013.01.049
extern: '1'
external_id:
pmid:
- '23601312'
intvolume: ' 104'
issue: '8'
keyword:
- Biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.bpj.2013.01.049
month: '04'
oa: 1
oa_version: Published Version
page: 1652-1660
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous diffusion of single particles in cytoplasm
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 104
year: '2013'
...
---
_id: '115'
abstract:
- lang: eng
text: We present the design and performance characterization of a new experimental
technique for measuring individual particle charges in large ensembles of macroscopic
grains. The measurement principle is qualitatively similar to that used in determining
the elementary charge by Millikan in that it follows individual particle trajectories.
However, by taking advantage of new technology we are able to work with macroscopic
grains and achieve several orders of magnitude better resolution in charge to
mass ratios. By observing freely falling grains accelerated in a horizontal electric
field with a co-falling, high-speed video camera, we dramatically increase particle
tracking time and measurement precision. Keeping the granular medium under vacuum,
we eliminate air drag, leaving the electrostatic force as the primary source of
particle accelerations in the co-moving frame. Because the technique is based
on direct imaging, we can distinguish between different particle types during
the experiment, opening up the possibility of studying charge transfer processes
between different particle species. For the ∼300 μm diameter grains reported here,
we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution
of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain
(corresponding to surface charge densities ∼1 elementary charges per μm2). The
primary source of error is indeterminacy in the grain mass, but with higher resolution
cameras and better optics this can be further improved. The high degree of resolution
and the ability to visually identify particles of different species or sizes with
direct imaging make this a powerful new tool to characterize charging processes
in granular media.
acknowledgement: This work was supported financially by the National Science Foundation
(NSF) through its Materials Research Science and Engineering Center (MRSEC) program
(DMR-0820054) and by the US Army Research Office through Grant No. W911NF-12-1-0182.
S.R.W. acknowledges support from a University of Chicago Millikan Fellowship.
article_number: '025104'
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
citation:
ama: Waitukaitis SR, Jaeger H. In situ granular charge measurement by free-fall
videography. Review of Scientific Instruments. 2013;84(2). doi:10.1063/1.4789496
apa: Waitukaitis, S. R., & Jaeger, H. (2013). In situ granular charge measurement
by free-fall videography. Review of Scientific Instruments. AIP. https://doi.org/10.1063/1.4789496
chicago: Waitukaitis, Scott R, and Heinrich Jaeger. “In Situ Granular Charge Measurement
by Free-Fall Videography.” Review of Scientific Instruments. AIP, 2013.
https://doi.org/10.1063/1.4789496.
ieee: S. R. Waitukaitis and H. Jaeger, “In situ granular charge measurement by free-fall
videography,” Review of Scientific Instruments, vol. 84, no. 2. AIP, 2013.
ista: Waitukaitis SR, Jaeger H. 2013. In situ granular charge measurement by free-fall
videography. Review of Scientific Instruments. 84(2), 025104.
mla: Waitukaitis, Scott R., and Heinrich Jaeger. “In Situ Granular Charge Measurement
by Free-Fall Videography.” Review of Scientific Instruments, vol. 84, no.
2, 025104, AIP, 2013, doi:10.1063/1.4789496.
short: S.R. Waitukaitis, H. Jaeger, Review of Scientific Instruments 84 (2013).
date_created: 2018-12-11T11:44:42Z
date_published: 2013-02-07T00:00:00Z
date_updated: 2021-01-12T06:48:39Z
day: '07'
doi: 10.1063/1.4789496
extern: '1'
intvolume: ' 84'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Review of Scientific Instruments
publication_status: published
publisher: AIP
publist_id: '7939'
quality_controlled: '1'
status: public
title: In situ granular charge measurement by free-fall videography
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2013'
...
---
_id: '11520'
abstract:
- lang: eng
text: We present the spatially resolved Hα dynamics of 16 star-forming galaxies
at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the
ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging
from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc
overdensity of Hα emitters and likely reside in a group/intermediate environment,
but not a cluster. We confirm and identify a rich group of star-forming galaxies
at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven
within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies
at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star
formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close
to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα
dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can
be described by rotating disks and use the data to derive inclination corrected
rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75%
± 8%, consistent with previous results based on Hubble Space Telescope morphologies
of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density
at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation,
confirming the evolution seen in the zero point. Apart from having, on average,
higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present
the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all
disk galaxies.
acknowledgement: 'We thank the referee for many helpful comments and suggestions which
greatly improved the clarity and quality of this work. D.S. acknowledges financial
support from the Netherlands Organisation for Scientific research (NWO) through
a Veni fellowship and also funding from the European Community Seventh Framework
Programme (FP7/2007-2013) under grant agreement number RG226604 (OPTICON) which
allowed access to CFHT time (proposals: 11BO29 & 12AO19). A.M.S. gratefully acknowledges
an STFC Advanced Fellowship through grant number ST/H005234/1. I.R.S., J.P.S., and
R.G.B. acknowledge support from the UK Science and Technology Facilities Council
(STFC) under ST/I001573/1. I.R.S. acknowledges STFC (ST/J001422/1), the ERC Advanced
Investigator program DUSTYGAL and a Royal Society/Wolfson Merit Award. P.N.B. acknowledges
support from STFC. R.M.S. acknowledges support from the grant ST/1001573/1. The
data presented here are based on observations with the KMOS spectrograph on the
ESO/VLT under program 60.A-9460 and can be accessed through the ESO data archive.
The authors also wish to acknowledge the help from Michael Hilker in preparing the
KMOS observations.'
article_number: '139'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: D.
full_name: Sobral, D.
last_name: Sobral
- first_name: A. M.
full_name: Swinbank, A. M.
last_name: Swinbank
- first_name: J. P.
full_name: Stott, J. P.
last_name: Stott
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: R. G.
full_name: Bower, R. G.
last_name: Bower
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: P.
full_name: Best, P.
last_name: Best
- first_name: J. E.
full_name: Geach, J. E.
last_name: Geach
- first_name: R. M.
full_name: Sharples, R. M.
last_name: Sharples
citation:
ama: Sobral D, Swinbank AM, Stott JP, et al. The dynamics of z=0.8 H-alpha-selected
star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. 2013;779(2).
doi:10.1088/0004-637x/779/2/139
apa: Sobral, D., Swinbank, A. M., Stott, J. P., Matthee, J. J., Bower, R. G., Smail,
I., … Sharples, R. M. (2013). The dynamics of z=0.8 H-alpha-selected star-forming
galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. IOP Publishing.
https://doi.org/10.1088/0004-637x/779/2/139
chicago: Sobral, D., A. M. Swinbank, J. P. Stott, Jorryt J Matthee, R. G. Bower,
Ian Smail, P. Best, J. E. Geach, and R. M. Sharples. “The Dynamics of Z=0.8 H-Alpha-Selected
Star-Forming Galaxies from KMOS/CF-HiZELS.” The Astrophysical Journal.
IOP Publishing, 2013. https://doi.org/10.1088/0004-637x/779/2/139.
ieee: D. Sobral et al., “The dynamics of z=0.8 H-alpha-selected star-forming
galaxies from KMOS/CF-HiZELS,” The Astrophysical Journal, vol. 779, no.
2. IOP Publishing, 2013.
ista: Sobral D, Swinbank AM, Stott JP, Matthee JJ, Bower RG, Smail I, Best P, Geach
JE, Sharples RM. 2013. The dynamics of z=0.8 H-alpha-selected star-forming galaxies
from KMOS/CF-HiZELS. The Astrophysical Journal. 779(2), 139.
mla: Sobral, D., et al. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies
from KMOS/CF-HiZELS.” The Astrophysical Journal, vol. 779, no. 2, 139,
IOP Publishing, 2013, doi:10.1088/0004-637x/779/2/139.
short: D. Sobral, A.M. Swinbank, J.P. Stott, J.J. Matthee, R.G. Bower, I. Smail,
P. Best, J.E. Geach, R.M. Sharples, The Astrophysical Journal 779 (2013).
date_created: 2022-07-07T09:14:48Z
date_published: 2013-12-03T00:00:00Z
date_updated: 2022-08-18T10:43:07Z
day: '03'
doi: 10.1088/0004-637x/779/2/139
extern: '1'
external_id:
arxiv:
- '1310.3822'
intvolume: ' 779'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution – galaxies'
- high-redshift – galaxies
- starburst
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3822
month: '12'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 779
year: '2013'
...
---
_id: '116'
abstract:
- lang: eng
text: 'We describe a model experiment for dynamic jamming: a two-dimensional collection
of initially unjammed disks that are forced into the jammed state by uniaxial
compression via a rake. This leads to a stable densification front that travels
ahead of the rake, leaving regions behind it jammed. Using disk conservation in
conjunction with an upper limit to the packing fraction at jamming onset, we predict
the front speed as a function of packing fraction and rake speed. However, we
find that the jamming front has a finite width, a feature that cannot be explained
by disk conservation alone. This width appears to diverge on approach to jamming,
which suggests that it may be related to growing lengthscales encountered in other
jamming studies.'
acknowledgement: This work was supported by the National Science Foundation (NSF)
through its Materials Research Science and Engineering program (DMR-0820054). SRW
was supported by the U.S. Department of Energy, Office of Basic Energy Sciences,
Division of Materials Sciences and Engineering under Award DE-FG02-03ER46088. LKR
acknowledges support through the NSF Research Experience for Undergraduates program.
article_number: '44001'
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Leah
full_name: Roth, Leah
last_name: Roth
- first_name: Vincenzo
full_name: Vitelli, Vincenzo
last_name: Vitelli
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
citation:
ama: Waitukaitis SR, Roth L, Vitelli V, Jaeger H. Dynamic jamming fronts. EPL.
2013;102(4). doi:10.1209/0295-5075/102/44001
apa: Waitukaitis, S. R., Roth, L., Vitelli, V., & Jaeger, H. (2013). Dynamic
jamming fronts. EPL. Elsevier. https://doi.org/10.1209/0295-5075/102/44001
chicago: Waitukaitis, Scott R, Leah Roth, Vincenzo Vitelli, and Heinrich Jaeger.
“Dynamic Jamming Fronts.” EPL. Elsevier, 2013. https://doi.org/10.1209/0295-5075/102/44001.
ieee: S. R. Waitukaitis, L. Roth, V. Vitelli, and H. Jaeger, “Dynamic jamming fronts,”
EPL, vol. 102, no. 4. Elsevier, 2013.
ista: Waitukaitis SR, Roth L, Vitelli V, Jaeger H. 2013. Dynamic jamming fronts.
EPL. 102(4), 44001.
mla: Waitukaitis, Scott R., et al. “Dynamic Jamming Fronts.” EPL, vol. 102,
no. 4, 44001, Elsevier, 2013, doi:10.1209/0295-5075/102/44001.
short: S.R. Waitukaitis, L. Roth, V. Vitelli, H. Jaeger, EPL 102 (2013).
date_created: 2018-12-11T11:44:43Z
date_published: 2013-05-24T00:00:00Z
date_updated: 2021-01-12T06:48:44Z
day: '24'
doi: 10.1209/0295-5075/102/44001
extern: '1'
intvolume: ' 102'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
publication: EPL
publication_status: published
publisher: Elsevier
publist_id: '7938'
quality_controlled: '1'
status: public
title: Dynamic jamming fronts
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2013'
...
---
_id: '11671'
abstract:
- lang: eng
text: "Given only the URL of a Web page, can we identify its language? In this article
we examine this question. URL-based language classification is useful when the
content of the Web page is not available or downloading the content is a waste
of bandwidth and time.\r\nWe built URL-based language classifiers for English,
German, French, Spanish, and Italian by applying a variety of algorithms and features.
As algorithms we used machine learning algorithms which are widely applied for
text classification and state-of-art algorithms for language identification of
text. As features we used words, various sized n-grams, and custom-made features
(our novel feature set). We compared our approaches with two baseline methods,
namely classification by country code top-level domains and classification by
IP addresses of the hosting Web servers.\r\n\r\nWe trained and tested our classifiers
in a 10-fold cross-validation setup on a dataset obtained from the Open Directory
Project and from querying a commercial search engine. We obtained the lowest F1-measure
for English (94) and the highest F1-measure for German (98) with the best performing
classifiers.\r\n\r\nWe also evaluated the performance of our methods: (i) on a
set of Web pages written in Adobe Flash and (ii) as part of a language-focused
crawler. In the first case, the content of the Web page is hard to extract and
in the second page downloading pages of the “wrong” language constitutes a waste
of bandwidth. In both settings the best classifiers have a high accuracy with
an F1-measure between 95 (for English) and 98 (for Italian) for the Adobe Flash
pages and a precision between 90 (for Italian) and 97 (for French) for the language-focused
crawler."
article_number: '3'
article_processing_charge: No
article_type: original
author:
- first_name: Eda
full_name: Baykan, Eda
last_name: Baykan
- first_name: Ingmar
full_name: Weber, Ingmar
last_name: Weber
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: Baykan E, Weber I, Henzinger MH. A comprehensive study of techniques for URL-based
web page language classification. ACM Transactions on the Web. 2013;7(1).
doi:10.1145/2435215.2435218
apa: Baykan, E., Weber, I., & Henzinger, M. H. (2013). A comprehensive study
of techniques for URL-based web page language classification. ACM Transactions
on the Web. Association for Computing Machinery. https://doi.org/10.1145/2435215.2435218
chicago: Baykan, Eda, Ingmar Weber, and Monika H Henzinger. “A Comprehensive Study
of Techniques for URL-Based Web Page Language Classification.” ACM Transactions
on the Web. Association for Computing Machinery, 2013. https://doi.org/10.1145/2435215.2435218.
ieee: E. Baykan, I. Weber, and M. H. Henzinger, “A comprehensive study of techniques
for URL-based web page language classification,” ACM Transactions on the Web,
vol. 7, no. 1. Association for Computing Machinery, 2013.
ista: Baykan E, Weber I, Henzinger MH. 2013. A comprehensive study of techniques
for URL-based web page language classification. ACM Transactions on the Web. 7(1),
3.
mla: Baykan, Eda, et al. “A Comprehensive Study of Techniques for URL-Based Web
Page Language Classification.” ACM Transactions on the Web, vol. 7, no.
1, 3, Association for Computing Machinery, 2013, doi:10.1145/2435215.2435218.
short: E. Baykan, I. Weber, M.H. Henzinger, ACM Transactions on the Web 7 (2013).
date_created: 2022-07-27T12:50:18Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-09-12T08:51:57Z
day: '01'
doi: 10.1145/2435215.2435218
extern: '1'
intvolume: ' 7'
issue: '1'
keyword:
- Computer Networks and Communications
language:
- iso: eng
month: '03'
oa_version: None
publication: ACM Transactions on the Web
publication_identifier:
eissn:
- 1559-114X
issn:
- 1559-1131
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comprehensive study of techniques for URL-based web page language classification
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '117'
abstract:
- lang: eng
text: The packing arrangement of individual particles inside a granular material
and the resulting response to applied stresses depend critically on particle-particle
interactions. One aspect that recently received attention are nanoscale surface
features of particles, which play an important role in determining the strength
of cohesive van der Waals and capillary interactions and also affect tribo-charging
of grains. We describe experiments on freely falling granular streams that can
detect the contributions from all three of these forces. We show that it is possible
to measure the charge of individual grains and build up distributions that are
detailed enough to provide stringent tests of tribo-charging models currently
available. A second aspect concerns particle shape. In this case steric interactions
become important and new types of aggregate behavior can be expected when non-convex
particle shapes are considered that can interlock or entangle. However, a general
connection between the mechanical response of a granular material and the constituents\'
shape remains unknown. This has made it infeasible to tackle the "inverse
packing problem", namely to start from a given, desired behavior for the
aggregate as a whole and then find the particle shape the produces it. We discuss
a new approach, using concepts rooted in artificial evolution that provides a
way to solve this inverse problem. This approach facilitates exploring the role
of arbitrary particle geometry in jammed systems and invites the discovery and
design of granular matter with optimized properties.
acknowledgement: This work was supported by the NSF MRSEC program under DMR-0820054.
Additional support came from the US Army Research Office through W911NF-12-1-0182.
author:
- first_name: Heinrich
full_name: Jaeger, Heinrich
last_name: Jaeger
- first_name: Marc
full_name: Miskin, Marc
last_name: Miskin
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Jaeger H, Miskin M, Waitukaitis SR. From nanoscale cohesion to macroscale
entanglement: opportunities for designing granular aggregate behaviour by tailoring
grain shape and interactions. In: AIP Conference Proceedings. Vol 1542.
AIP; 2013:3-6. doi:10.1063/1.4811858'
apa: 'Jaeger, H., Miskin, M., & Waitukaitis, S. R. (2013). From nanoscale cohesion
to macroscale entanglement: opportunities for designing granular aggregate behaviour
by tailoring grain shape and interactions. In AIP Conference Proceedings
(Vol. 1542, pp. 3–6). Sydney, Australia: AIP. https://doi.org/10.1063/1.4811858'
chicago: 'Jaeger, Heinrich, Marc Miskin, and Scott R Waitukaitis. “From Nanoscale
Cohesion to Macroscale Entanglement: Opportunities for Designing Granular Aggregate
Behaviour by Tailoring Grain Shape and Interactions.” In AIP Conference Proceedings,
1542:3–6. AIP, 2013. https://doi.org/10.1063/1.4811858.'
ieee: 'H. Jaeger, M. Miskin, and S. R. Waitukaitis, “From nanoscale cohesion to
macroscale entanglement: opportunities for designing granular aggregate behaviour
by tailoring grain shape and interactions,” in AIP Conference Proceedings,
Sydney, Australia, 2013, vol. 1542, pp. 3–6.'
ista: 'Jaeger H, Miskin M, Waitukaitis SR. 2013. From nanoscale cohesion to macroscale
entanglement: opportunities for designing granular aggregate behaviour by tailoring
grain shape and interactions. AIP Conference Proceedings. Powders and Grains
vol. 1542, 3–6.'
mla: 'Jaeger, Heinrich, et al. “From Nanoscale Cohesion to Macroscale Entanglement:
Opportunities for Designing Granular Aggregate Behaviour by Tailoring Grain Shape
and Interactions.” AIP Conference Proceedings, vol. 1542, AIP, 2013, pp.
3–6, doi:10.1063/1.4811858.'
short: H. Jaeger, M. Miskin, S.R. Waitukaitis, in:, AIP Conference Proceedings,
AIP, 2013, pp. 3–6.
conference:
end_date: 2013-07-12
location: Sydney, Australia
name: Powders and Grains
start_date: 2013-07-08
date_created: 2018-12-11T11:44:43Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T06:48:49Z
day: '01'
doi: 10.1063/1.4811858
extern: '1'
intvolume: ' 1542'
language:
- iso: eng
month: '06'
oa_version: None
page: 3 - 6
publication: ' AIP Conference Proceedings'
publication_status: published
publisher: AIP
publist_id: '7937'
quality_controlled: '1'
status: public
title: 'From nanoscale cohesion to macroscale entanglement: opportunities for designing
granular aggregate behaviour by tailoring grain shape and interactions'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1542
year: '2013'
...
---
_id: '11758'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Luca
full_name: Aceto, Luca
last_name: Aceto
- 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: Jiří
full_name: Sgall, Jiří
last_name: Sgall
citation:
ama: Aceto L, Henzinger MH, Sgall J. 38th International Colloquium on Automata,
Languages and Programming. Information and Computation. 2013;222(1):1.
doi:10.1016/j.ic.2012.11.002
apa: Aceto, L., Henzinger, M. H., & Sgall, J. (2013). 38th International Colloquium
on Automata, Languages and Programming. Information and Computation. Elsevier.
https://doi.org/10.1016/j.ic.2012.11.002
chicago: Aceto, Luca, Monika H Henzinger, and Jiří Sgall. “38th International Colloquium
on Automata, Languages and Programming.” Information and Computation. Elsevier,
2013. https://doi.org/10.1016/j.ic.2012.11.002.
ieee: L. Aceto, M. H. Henzinger, and J. Sgall, “38th International Colloquium on
Automata, Languages and Programming,” Information and Computation, vol.
222, no. 1. Elsevier, p. 1, 2013.
ista: Aceto L, Henzinger MH, Sgall J. 2013. 38th International Colloquium on Automata,
Languages and Programming. Information and Computation. 222(1), 1.
mla: Aceto, Luca, et al. “38th International Colloquium on Automata, Languages and
Programming.” Information and Computation, vol. 222, no. 1, Elsevier, 2013,
p. 1, doi:10.1016/j.ic.2012.11.002.
short: L. Aceto, M.H. Henzinger, J. Sgall, Information and Computation 222 (2013)
1.
date_created: 2022-08-08T11:25:34Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2023-02-23T10:09:19Z
day: '01'
doi: 10.1016/j.ic.2012.11.002
extern: '1'
intvolume: ' 222'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: '1'
publication: Information and Computation
publication_identifier:
issn:
- 0890-5401
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 38th International Colloquium on Automata, Languages and Programming
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 222
year: '2013'
...
---
_id: '11759'
abstract:
- lang: eng
text: Matching markets play a prominent role in economic theory. A prime example
of such a market is the sponsored search market. Here, as in other markets of
that kind, market equilibria correspond to feasible, envy free, and bidder optimal
outcomes. For settings without budgets such an outcome always exists and can be
computed in polynomial-time by the so-called Hungarian Method. Moreover, every
mechanism that computes such an outcome is incentive compatible. We show that
the Hungarian Method can be modified so that it finds a feasible, envy free, and
bidder optimal outcome for settings with budgets. We also show that in settings
with budgets no mechanism that computes such an outcome can be incentive compatible
for all inputs. For inputs in general position, however, the presented mechanism—as
any other mechanism that computes such an outcome for settings with budgets—is
incentive compatible.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- 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: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and
the Hungarian Method. Information Processing Letters. 2013;113(3):67-73.
doi:10.1016/j.ipl.2012.11.006
apa: Dütting, P., Henzinger, M. H., & Weber, I. (2013). Sponsored search, market
equilibria, and the Hungarian Method. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2012.11.006
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search,
Market Equilibria, and the Hungarian Method.” Information Processing Letters.
Elsevier, 2013. https://doi.org/10.1016/j.ipl.2012.11.006.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria,
and the Hungarian Method,” Information Processing Letters, vol. 113, no.
3. Elsevier, pp. 67–73, 2013.
ista: Dütting P, Henzinger MH, Weber I. 2013. Sponsored search, market equilibria,
and the Hungarian Method. Information Processing Letters. 113(3), 67–73.
mla: Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian
Method.” Information Processing Letters, vol. 113, no. 3, Elsevier, 2013,
pp. 67–73, doi:10.1016/j.ipl.2012.11.006.
short: P. Dütting, M.H. Henzinger, I. Weber, Information Processing Letters 113
(2013) 67–73.
date_created: 2022-08-08T11:29:08Z
date_published: 2013-02-15T00:00:00Z
date_updated: 2022-09-12T09:36:15Z
day: '15'
doi: 10.1016/j.ipl.2012.11.006
extern: '1'
external_id:
arxiv:
- '0912.1934'
intvolume: ' 113'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0912.1934
month: '02'
oa: 1
oa_version: Preprint
page: 67-73
publication: Information Processing Letters
publication_identifier:
issn:
- 0020-0190
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sponsored search, market equilibria, and the Hungarian Method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2013'
...
---
_id: '11791'
abstract:
- lang: eng
text: The focus of classic mechanism design has been on truthful direct-revelation
mechanisms. In the context of combinatorial auctions the truthful direct-revelation
mechanism that maximizes social welfare is the VCG mechanism. For many valuation
spaces computing the allocation and payments of the VCG mechanism, however, is
a computationally hard problem. We thus study the performance of the VCG mechanism
when bidders are forced to choose bids from a subspace of the valuation space
for which the VCG outcome can be computed efficiently. We prove improved upper
bounds on the welfare loss for restrictions to additive bids and upper and lower
bounds for restrictions to non-additive bids. These bounds show that the welfare
loss increases in expressiveness. All our bounds apply to equilibrium concepts
that can be computed in polynomial time as well as to learning outcomes.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- 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: Martin
full_name: Starnberger, Martin
last_name: Starnberger
citation:
ama: 'Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based
combinatorial auctions. In: 9th International Conference on Web and Internet
Economics. Vol 8289. Springer Nature; 2013:146–159. doi:10.1007/978-3-642-45046-4_13'
apa: 'Dütting, P., Henzinger, M. H., & Starnberger, M. (2013). Valuation compressions
in VCG-based combinatorial auctions. In 9th International Conference on Web
and Internet Economics (Vol. 8289, pp. 146–159). Cambridge, MA, USA: Springer
Nature. https://doi.org/10.1007/978-3-642-45046-4_13'
chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions
in VCG-Based Combinatorial Auctions.” In 9th International Conference on Web
and Internet Economics, 8289:146–159. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-45046-4_13.
ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in
VCG-based combinatorial auctions,” in 9th International Conference on Web and
Internet Economics, Cambridge, MA, USA, 2013, vol. 8289, pp. 146–159.
ista: 'Dütting P, Henzinger MH, Starnberger M. 2013. Valuation compressions in VCG-based
combinatorial auctions. 9th International Conference on Web and Internet Economics.
WINE: International Conference on Web and Internet Economics, LNCS, vol. 8289,
146–159.'
mla: Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.”
9th International Conference on Web and Internet Economics, vol. 8289,
Springer Nature, 2013, pp. 146–159, doi:10.1007/978-3-642-45046-4_13.
short: P. Dütting, M.H. Henzinger, M. Starnberger, in:, 9th International Conference
on Web and Internet Economics, Springer Nature, 2013, pp. 146–159.
conference:
end_date: 2013-12-14
location: Cambridge, MA, USA
name: 'WINE: International Conference on Web and Internet Economics'
start_date: 2013-12-01
date_created: 2022-08-11T11:05:14Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2023-02-13T11:20:42Z
day: '01'
doi: 10.1007/978-3-642-45046-4_13
extern: '1'
external_id:
arxiv:
- '1310.3153'
intvolume: ' 8289'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3153
month: '12'
oa: 1
oa_version: Preprint
page: 146–159
publication: 9th International Conference on Web and Internet Economics
publication_identifier:
isbn:
- '9783642450457'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Valuation compressions in VCG-based combinatorial auctions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8289
year: '2013'
...
---
_id: '11792'
abstract:
- lang: eng
text: "We study the problem of maximizing a monotone submodular function with viability
constraints. This problem originates from computational biology, where we are
given a phylogenetic tree over a set of species and a directed graph, the so-called
food web, encoding viability constraints between these species. These food webs
usually have constant depth. The goal is to select a subset of k species that
satisfies the viability constraints and has maximal phylogenetic diversity. As
this problem is known to be NP-hard, we investigate approximation algorithm. We
present the first constant factor approximation algorithm if the depth is constant.
Its approximation ratio is (1−1\U0001D452√). This algorithm not only applies to
phylogenetic trees with viability constraints but for arbitrary monotone submodular
set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation
algorithm for our problem setting (even for additive functions) and that there
is no approximation algorithm for a slight extension of this setting."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- 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: David P.
full_name: Williamson, David P.
last_name: Williamson
citation:
ama: 'Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with
viability constraints. In: 21st Annual European Symposium on Algorithms.
Vol 8125. Springer Nature; 2013:409-420. doi:10.1007/978-3-642-40450-4_35'
apa: 'Dvořák, W., Henzinger, M. H., & Williamson, D. P. (2013). Maximizing a
submodular function with viability constraints. In 21st Annual European Symposium
on Algorithms (Vol. 8125, pp. 409–420). Sophia Antipolis, France: Springer
Nature. https://doi.org/10.1007/978-3-642-40450-4_35'
chicago: Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing
a Submodular Function with Viability Constraints.” In 21st Annual European
Symposium on Algorithms, 8125:409–20. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-40450-4_35.
ieee: W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular
function with viability constraints,” in 21st Annual European Symposium on
Algorithms, Sophia Antipolis, France, 2013, vol. 8125, pp. 409–420.
ista: 'Dvořák W, Henzinger MH, Williamson DP. 2013. Maximizing a submodular function
with viability constraints. 21st Annual European Symposium on Algorithms. ESA:
European Symposium on Algorithms, LNCS, vol. 8125, 409–420.'
mla: Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.”
21st Annual European Symposium on Algorithms, vol. 8125, Springer Nature,
2013, pp. 409–20, doi:10.1007/978-3-642-40450-4_35.
short: W. Dvořák, M.H. Henzinger, D.P. Williamson, in:, 21st Annual European Symposium
on Algorithms, Springer Nature, 2013, pp. 409–420.
conference:
end_date: 2013-09-04
location: Sophia Antipolis, France
name: 'ESA: European Symposium on Algorithms'
start_date: 2013-09-02
date_created: 2022-08-11T11:18:19Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2023-02-21T16:28:24Z
day: '01'
doi: 10.1007/978-3-642-40450-4_35
extern: '1'
external_id:
arxiv:
- '1611.05753'
intvolume: ' 8125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.05753
month: '09'
oa: 1
oa_version: Preprint
page: 409 - 420
publication: 21st Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783642404498'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11792'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Maximizing a submodular function with viability constraints
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8125
year: '2013'
...
---
_id: '11793'
abstract:
- lang: eng
text: "We study the problem of maintaining a breadth-first spanning tree (BFS tree)
in partially dynamic distributed networks modeling a sequence of either failures
or additions of communication links (but not both). We show (1 + ε)-approximation
algorithms whose amortized time (over some number of link changes) is sublinear
in D, the maximum diameter of the network. This breaks the Θ(D) time bound of
recomputing “from scratch”.\r\n\r\nOur technique also leads to a (1 + ε)-approximate
incremental algorithm for single-source shortest paths (SSSP) in the sequential
(usual RAM) model. Prior to our work, the state of the art was the classic exact
algorithm of [9] that is optimal under some assumptions [27]. Our result is the
first to show that, in the incremental setting, this bound can be beaten in certain
cases if a small approximation is allowed."
alternative_title:
- LNCS
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. Sublinear-time maintenance of breadth-first
spanning tree in partially dynamic networks. In: 40th International Colloquium
on Automata, Languages, and Programming. Vol 7966. Springer Nature; 2013:607–619.
doi:10.1007/978-3-642-39212-2_53'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Sublinear-time
maintenance of breadth-first spanning tree in partially dynamic networks. In 40th
International Colloquium on Automata, Languages, and Programming (Vol. 7966,
pp. 607–619). Riga, Latvia: Springer Nature. https://doi.org/10.1007/978-3-642-39212-2_53'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time
Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” In
40th International Colloquium on Automata, Languages, and Programming,
7966:607–619. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-39212-2_53.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance
of breadth-first spanning tree in partially dynamic networks,” in 40th International
Colloquium on Automata, Languages, and Programming, Riga, Latvia, 2013, vol.
7966, pp. 607–619.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2013. Sublinear-time maintenance
of breadth-first spanning tree in partially dynamic networks. 40th International
Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium
on Automata, Languages, and Programming, LNCS, vol. 7966, 607–619.'
mla: Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning
Tree in Partially Dynamic Networks.” 40th International Colloquium on Automata,
Languages, and Programming, vol. 7966, Springer Nature, 2013, pp. 607–619,
doi:10.1007/978-3-642-39212-2_53.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 40th International Colloquium
on Automata, Languages, and Programming, Springer Nature, 2013, pp. 607–619.
conference:
end_date: 2013-07-12
location: Riga, Latvia
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2013-07-08
date_created: 2022-08-11T11:25:13Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2023-02-21T16:28:26Z
day: '01'
doi: 10.1007/978-3-642-39212-2_53
extern: '1'
external_id:
arxiv:
- '1512.08147'
intvolume: ' 7966'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.08147
month: '07'
oa: 1
oa_version: Preprint
page: 607–619
publication: 40th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783642392115'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11793'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Sublinear-time maintenance of breadth-first spanning tree in partially dynamic
networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7966
year: '2013'
...
---
_id: '7774'
abstract:
- lang: eng
text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low
frequency vibrational properties of jammed amorphous sphere packings can be understood
in terms of a length scale, called l*, that diverges as the system becomes marginally
unstable. Despite the tremendous success of this theory, it has been difficult
to connect the counting argument that defines l* to other length scales that diverge
near the jamming transition. We present an alternate derivation of l* based on
the onset of rigidity. This phenomenological approach reveals the physical mechanism
underlying the length scale and is relevant to a range of systems for which the
original argument breaks down. It also allows us to present the first direct numerical
measurement of l*.
article_number: '10993'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Wouter G.
full_name: Ellenbroek, Wouter G.
last_name: Ellenbroek
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity
length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f'
apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of
jammed packings I: The rigidity length scale. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c3sm51095f'
chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability
of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society
of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.'
ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings
I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society
of Chemistry, 2013.'
ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I:
The rigidity length scale. Soft Matter. 9(46), 10993.'
mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity
Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51095f.'
short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).
date_created: 2020-04-30T11:43:42Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51095f
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings I: The rigidity length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7775'
abstract:
- lang: eng
text: As a function of packing fraction at zero temperature and applied stress,
an amorphous packing of spheres exhibits a jamming transition where the system
is sensitive to boundary conditions even in the thermodynamic limit. Upon further
compression, the system should become insensitive to boundary conditions provided
it is sufficiently large. Here we explore the linear response to a large class
of boundary perturbations in 2 and 3 dimensions. We consider each finite packing
with periodic-boundary conditions as the basis of an infinite square or cubic
lattice and study properties of vibrational modes at arbitrary wave vector. We
find that the stability of such modes can be understood in terms of a competition
between plane waves and the anomalous vibrational modes associated with the jamming
transition; infinitesimal boundary perturbations become irrelevant for systems
that are larger than a length scale that characterizes the transverse excitations.
This previously identified length diverges at the jamming transition.
article_number: '11000'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Oleg
full_name: Kogan, Oleg
last_name: Kogan
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed
packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d'
apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S.
R. (2013). Stability of jammed packings II: The transverse length scale. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d'
chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu,
and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.”
Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.'
ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability
of jammed packings II: The transverse length scale,” Soft Matter, vol.
9, no. 46. Royal Society of Chemistry, 2013.'
ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of
jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.'
mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse
Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51096d.'
short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter
9 (2013).
date_created: 2020-04-30T11:43:58Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51096d
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings II: The transverse length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7785'
abstract:
- lang: eng
text: Neural circuit assembly requires selection of specific cell fates, axonal
trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin,
Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified
multiple molecular and cellular mechanisms that link these events. Notch signaling
limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously
sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and
Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition,
Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice
and promote ventromedial axon-bundle formation. Selecting the correct developmental
trajectory is ultimately essential for proper target choice. These findings demonstrate
that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite
patterning well before the final target selection phase, and exemplify how a single
guidance molecule can drive consecutive stages of neural circuit assembly with
the help of sophisticated spatial and temporal regulation.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Joo, William J.
last_name: Joo
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Liang
full_name: Liang, Liang
last_name: Liang
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: 'Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice,
and target selection: Genetic analysis of sema-2b in olfactory axon targeting.
Neuron. 2013;78(4):673-686. doi:10.1016/j.neuron.2013.03.022'
apa: 'Joo, W. J., Sweeney, L. B., Liang, L., & Luo, L. (2013). Linking cell
fate, trajectory choice, and target selection: Genetic analysis of sema-2b in
olfactory axon targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.03.022'
chicago: 'Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking
Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b
in Olfactory Axon Targeting.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.03.022.'
ieee: 'W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory
choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,”
Neuron, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.'
ista: 'Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice,
and target selection: Genetic analysis of sema-2b in olfactory axon targeting.
Neuron. 78(4), 673–686.'
mla: 'Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target
Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron,
vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:10.1016/j.neuron.2013.03.022.'
short: W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.
date_created: 2020-04-30T13:19:59Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2024-01-31T10:15:25Z
day: '22'
doi: 10.1016/j.neuron.2013.03.022
extern: '1'
intvolume: ' 78'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 673-686
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Linking cell fate, trajectory choice, and target selection: Genetic analysis
of sema-2b in olfactory axon targeting'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2013'
...
---
_id: '8030'
abstract:
- lang: eng
text: While the plasticity of excitatory synaptic connections in the brain has been
widely studied, the plasticity of inhibitory connections is much less understood.
Here, we present recent experimental and theoretical findings concerning the rules
of spike timing-dependent inhibitory plasticity and their putative network function.
This is a summary of a workshop at the COSYNE conference 2012.
article_number: '119'
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R. C.
full_name: Froemke, R. C.
last_name: Froemke
- first_name: N.
full_name: Doyon, N.
last_name: Doyon
- first_name: M.
full_name: Gilson, M.
last_name: Gilson
- first_name: J. S.
full_name: Haas, J. S.
last_name: Haas
- first_name: R.
full_name: Liu, R.
last_name: Liu
- first_name: A.
full_name: Maffei, A.
last_name: Maffei
- first_name: P.
full_name: Miller, P.
last_name: Miller
- first_name: C. J.
full_name: Wierenga, C. J.
last_name: Wierenga
- first_name: M. A.
full_name: Woodin, M. A.
last_name: Woodin
- first_name: F.
full_name: Zenke, F.
last_name: Zenke
- first_name: H.
full_name: Sprekeler, H.
last_name: Sprekeler
citation:
ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike
timing-dependence and putative network function. Frontiers in Neural Circuits.
2013;7. doi:10.3389/fncir.2013.00119'
apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R.,
… Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function. Frontiers in Neural Circuits. Frontiers
Media. https://doi.org/10.3389/fncir.2013.00119'
chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu,
A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and
Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media,
2013. https://doi.org/10.3389/fncir.2013.00119.'
ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers
Media, 2013.'
ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller
P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity:
Spike timing-dependence and putative network function. Frontiers in Neural Circuits.
7, 119.'
mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence
and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119,
Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.'
short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei,
P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural
Circuits 7 (2013).
date_created: 2020-06-25T13:23:50Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T08:16:38Z
day: '18'
ddc:
- '570'
doi: 10.3389/fncir.2013.00119
extern: '1'
external_id:
pmid:
- '23882186'
file:
- access_level: open_access
checksum: 9c321cb12977d84048712eefa7f0c497
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T11:23:40Z
date_updated: 2020-07-16T11:23:40Z
file_id: '8123'
file_name: 2013_FrontNeurCirc_Vogels.pdf
file_size: 1530469
relation: main_file
success: 1
file_date_updated: 2020-07-16T11:23:40Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neural Circuits
publication_identifier:
eissn:
- 1662-5110
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
status: public
title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network
function'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '810'
abstract:
- lang: eng
text: Cryo-electron tomography combined with image processing by sub-tomogram averaging
is unique in its power to resolve the structures of proteins and macromolecular
complexes in situ. Limitations of the method, including the low signal to noise
ratio within individual images from cryo-tomographic datasets and difficulties
in determining the defocus at which the data was collected, mean that to date
the very best structures obtained by sub-tomogram averaging are limited to a resolution
of approximately 15. Å. Here, by optimizing data collection and defocus determination
steps, we have determined the structure of assembled Mason-Pfizer monkey virus
Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution
alpha-helices can be directly and clearly visualized. These data demonstrate for
the first time that high-resolution structural information can be obtained from
cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has
the potential to allow detailed studies of unsolved and biologically relevant
structures under biologically relevant conditions.
acknowledgement: The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from
Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM
grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s
IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova
for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram
reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments
on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant
BR 3635/2-1 to JAGB.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Alex
full_name: De Marco, Alex
last_name: De Marco
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015
apa: Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination
of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram
averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015
chicago: Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination
of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram
Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015.
ieee: F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein
structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,”
Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400,
2013.
ista: Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 184(3), 394–400.
mla: Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution
Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural
Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015.
short: F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology
184 (2013) 394–400.
date_created: 2018-12-11T11:48:37Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:54Z
day: '01'
doi: 10.1016/j.jsb.2013.10.015
extern: 1
intvolume: ' 184'
issue: '3'
month: '12'
page: 394 - 400
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6839'
quality_controlled: 0
status: public
title: Determination of protein structure at 8.5Å resolution using cryo-electron tomography
and sub-tomogram averaging
type: journal_article
volume: 184
year: '2013'
...