---
_id: '17723'
abstract:
- lang: eng
text: "The recent discovery of bright quasars around redshift z=6 suggests that
black holes (BHs) with masses in excess of 10^9 Msun have already assembled at
a very early stage in the evolution of the universe. An alternative interpretation
is that these quasars are powered by less massive BHs, but their fluxes are strongly
magnified through gravitational lensing by intervening galaxies. Here we analyze
the flux distribution of the Ly alpha emission of the quasar with the highest
known redshift, SDSS 1030+0524, at z=6.28. We show that this object could not
have been magnified by lensing by more than a factor of five. The constraint arises
from the large observed size, 30 (comoving) Mpc, of the ionized region around
this quasar, and relies crucially only on the assumption that the quasar is embedded
in a largely neutral IGM. Based on the line/continuum ratio of SDSS 1030+0524,
we argue further that this quasar also cannot be beamed by a significant factor.
We conclude that the minimum mass for its resident BH is 4 x 10^8 Msun (for magnification
by a factor of five); if the mass is this low, then the quasars had to switch
on prior to redshift z=9.\r\nFrom the size of the ionized region, we are also
able to place an absolute lower bound on the age of this quasar at t > 2 x 10^7
years."
article_processing_charge: No
article_type: original
author:
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Renyue
full_name: Cen, Renyue
last_name: Cen
citation:
ama: Haiman Z, Cen R. A constraint on the gravitational lensing magnification and
age of the redshift z = 6.28 Quasar SDSS 1030+0524. The Astrophysical Journal.
2002;578(2):702-707. doi:10.1086/342610
apa: Haiman, Z., & Cen, R. (2002). A constraint on the gravitational lensing
magnification and age of the redshift z = 6.28 Quasar SDSS 1030+0524. The Astrophysical
Journal. American Astronomical Society. https://doi.org/10.1086/342610
chicago: Haiman, Zoltán, and Renyue Cen. “A Constraint on the Gravitational Lensing
Magnification and Age of the Redshift z = 6.28 Quasar SDSS 1030+0524.” The
Astrophysical Journal. American Astronomical Society, 2002. https://doi.org/10.1086/342610.
ieee: Z. Haiman and R. Cen, “A constraint on the gravitational lensing magnification
and age of the redshift z = 6.28 Quasar SDSS 1030+0524,” The Astrophysical
Journal, vol. 578, no. 2. American Astronomical Society, pp. 702–707, 2002.
ista: Haiman Z, Cen R. 2002. A constraint on the gravitational lensing magnification
and age of the redshift z = 6.28 Quasar SDSS 1030+0524. The Astrophysical Journal.
578(2), 702–707.
mla: Haiman, Zoltán, and Renyue Cen. “A Constraint on the Gravitational Lensing
Magnification and Age of the Redshift z = 6.28 Quasar SDSS 1030+0524.” The
Astrophysical Journal, vol. 578, no. 2, American Astronomical Society, 2002,
pp. 702–07, doi:10.1086/342610.
short: Z. Haiman, R. Cen, The Astrophysical Journal 578 (2002) 702–707.
date_created: 2024-09-06T09:11:03Z
date_published: 2002-10-20T00:00:00Z
date_updated: 2024-09-25T14:06:28Z
day: '20'
doi: 10.1086/342610
extern: '1'
intvolume: ' 578'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/342610
month: '10'
oa: 1
oa_version: Published Version
page: 702-707
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A constraint on the gravitational lensing magnification and age of the redshift
z = 6.28 Quasar SDSS 1030+0524
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 578
year: '2002'
...
---
_id: '17739'
abstract:
- lang: eng
text: An extensive sample of galaxy clusters will be available in the coming years,
detected through their Sunyaev-Zeldovich effect (SZE). We use a semianalytic model
to study the scientific yield of combining SZE data with X-ray and optical follow-up
observations. If clusters at a given redshift z0 can be identified with virialized,
spherical halos, they populate a well-defined "fundamental plane" (FP) in the
parameter space of the three observables virial temperature (T), total Sunyaev-Zeldovich
flux decrement (ΔSν), and angular size (θ). The location and orientation of the
FP, as well as its redshift evolution, are sensitive to both the internal evolution
of clusters and to the underlying cosmological parameters. We show that if clusters
are not standard candles (e.g., because of feedback or energy injection), then
this can be inferred from the FP. Likewise, we study the dependence of the FP
on the cosmological parameters h, σ8, and Ω0, and quantify future constraints
on these parameters. We also show that in the absence of any nongravitational
effects, the scatter in the (ΔSν,T)-plane is significantly smaller than in either
the (θ,T) or the (θ,ΔSν) planes. As a result, the ΔSν-T relation can be an exceptionally
sensitive probe of both cluster physics and cosmological parameters. A comparison
of the amount of scatter in these three scaling relations will test the origin
(cosmological vs. stochastic) of the scatter.
article_processing_charge: No
article_type: original
author:
- first_name: Licia
full_name: Verde, Licia
last_name: Verde
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: David N.
full_name: Spergel, David N.
last_name: Spergel
citation:
ama: Verde L, Haiman Z, Spergel DN. Are clusters standard candles? Galaxy cluster
scaling relations with the Sunyaev‐Zeldovich effect. The Astrophysical Journal.
2002;581(1):5-19. doi:10.1086/344134
apa: Verde, L., Haiman, Z., & Spergel, D. N. (2002). Are clusters standard candles?
Galaxy cluster scaling relations with the Sunyaev‐Zeldovich effect. The Astrophysical
Journal. American Astronomical Society. https://doi.org/10.1086/344134
chicago: Verde, Licia, Zoltán Haiman, and David N. Spergel. “Are Clusters Standard
Candles? Galaxy Cluster Scaling Relations with the Sunyaev‐Zeldovich Effect.”
The Astrophysical Journal. American Astronomical Society, 2002. https://doi.org/10.1086/344134.
ieee: L. Verde, Z. Haiman, and D. N. Spergel, “Are clusters standard candles? Galaxy
cluster scaling relations with the Sunyaev‐Zeldovich effect,” The Astrophysical
Journal, vol. 581, no. 1. American Astronomical Society, pp. 5–19, 2002.
ista: Verde L, Haiman Z, Spergel DN. 2002. Are clusters standard candles? Galaxy
cluster scaling relations with the Sunyaev‐Zeldovich effect. The Astrophysical
Journal. 581(1), 5–19.
mla: Verde, Licia, et al. “Are Clusters Standard Candles? Galaxy Cluster Scaling
Relations with the Sunyaev‐Zeldovich Effect.” The Astrophysical Journal,
vol. 581, no. 1, American Astronomical Society, 2002, pp. 5–19, doi:10.1086/344134.
short: L. Verde, Z. Haiman, D.N. Spergel, The Astrophysical Journal 581 (2002) 5–19.
date_created: 2024-09-06T09:22:05Z
date_published: 2002-12-10T00:00:00Z
date_updated: 2024-09-26T14:09:02Z
day: '10'
doi: 10.1086/344134
extern: '1'
intvolume: ' 581'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/344134
month: '12'
oa: 1
oa_version: Published Version
page: 5-19
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are clusters standard candles? Galaxy cluster scaling relations with the Sunyaev‐Zeldovich
effect
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 581
year: '2002'
...
---
_id: '17746'
abstract:
- lang: eng
text: For a source of Lyα radiation embedded in a neutral intergalactic medium (IGM)
prior to the reionization epoch, the Lyα emission line is strongly suppressed
by the intervening IGM. The damping wing of the so-called Gunn-Peterson trough
can extend to the red side of the emission line and erase a significant fraction
of the total line flux. However, the transmitted fraction increases with the size
of the local cosmological H II region surrounding the source, and therefore with
the ionizing luminosity and age of the source. Motivated by the recent discovery
of a Lyα-emitting galaxy at a redshift z = 6.56 (Hu et al.), possibly prior to
the reionization of the IGM, we revisit the effects of a neutral IGM on the Lyα
emission line. We show that for faint sources with little or even no ionizing
continuum, a sufficiently broad (Δv ≳ 300 km s^-1) emission line can still remain
observable. In particular, the line detected by Hu et al. is consistent with a
source embedded in a neutral IGM. We provide characterizations of the asymmetry
and total transmitted flux of the Lyα line as functions of the ionizing emissivity
of its source. We argue that a statistical sample of Lyα emitters extending beyond
the reionization redshift can be a useful probe of reionization.
article_processing_charge: No
article_type: original
author:
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: Haiman Z. The detectability of high-redshift Lyα emission lines prior to the
reionization of the universe. The Astrophysical Journal. 2002;576(1):L1-L4.
doi:10.1086/343101
apa: Haiman, Z. (2002). The detectability of high-redshift Lyα emission lines prior
to the reionization of the universe. The Astrophysical Journal. American
Astronomical Society. https://doi.org/10.1086/343101
chicago: Haiman, Zoltán. “The Detectability of High-Redshift Lyα Emission Lines
Prior to the Reionization of the Universe.” The Astrophysical Journal.
American Astronomical Society, 2002. https://doi.org/10.1086/343101.
ieee: Z. Haiman, “The detectability of high-redshift Lyα emission lines prior to
the reionization of the universe,” The Astrophysical Journal, vol. 576,
no. 1. American Astronomical Society, pp. L1–L4, 2002.
ista: Haiman Z. 2002. The detectability of high-redshift Lyα emission lines prior
to the reionization of the universe. The Astrophysical Journal. 576(1), L1–L4.
mla: Haiman, Zoltán. “The Detectability of High-Redshift Lyα Emission Lines Prior
to the Reionization of the Universe.” The Astrophysical Journal, vol. 576,
no. 1, American Astronomical Society, 2002, pp. L1–4, doi:10.1086/343101.
short: Z. Haiman, The Astrophysical Journal 576 (2002) L1–L4.
date_created: 2024-09-06T09:34:46Z
date_published: 2002-07-31T00:00:00Z
date_updated: 2024-09-26T14:51:17Z
day: '31'
doi: 10.1086/343101
extern: '1'
intvolume: ' 576'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/343101
month: '07'
oa: 1
oa_version: Published Version
page: L1-L4
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: The detectability of high-redshift Lyα emission lines prior to the reionization
of the universe
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 576
year: '2002'
...
---
_id: '17779'
abstract:
- lang: eng
text: The first generation of stars is thought to have formed in low-mass halos
with Tvir < 10^4 K where H2 cooling is paramount. However, the efficiency of H2
formation and cooling in these halos may have been severely limited by feedback
processes. In this paper we investigate the radiative cooling and collapse of
halos with virial temperatures Tvir > 10^4 K, i.e., those that can cool in the
absence of H2 via neutral atomic lines. The evolution of these halos differs from
their less massive counterparts. Efficient atomic line radiation allows rapid
cooling to ~8000 K; subsequently the gas can contract nearly isothermally at this
temperature. In the absence of H2 molecules, the gas would likely settle into
a locally stable disk, and only disks with unusually low spin would be unstable.
However, we find that the initial atomic line cooling leaves a large, out-of-equilibrium
residual free electron fraction. This allows the molecular fraction to build up
to a universal value of x ≈ 10^-3, almost independently of initial density and
temperature. We show that this is a nonequilibrium freeze-out value that can be
understood in terms of timescale arguments. Unlike in less massive halos, H2 formation
and cooling is largely impervious to feedback from external UV fields, due to
the high initial densities achieved by atomic cooling. The newly formed molecules
cool the gas further to ~100 K and allow the gas to fragment on scales of a few
times 100 M☉. We investigate the importance of various feedback effects such as
H2 photodissociation from internal UV fields and radiation pressure due to Lyα
photon trapping, which are likely to regulate the efficiency of star formation.
article_processing_charge: No
article_type: original
author:
- first_name: S. Peng
full_name: Oh, S. Peng
last_name: Oh
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: 'Oh SP, Haiman Z. Second‐generation objects in the universe: Radiative cooling
and collapse of halos with virial temperatures above 10^4 K. The Astrophysical
Journal. 2002;569(2):558-572. doi:10.1086/339393'
apa: 'Oh, S. P., & Haiman, Z. (2002). Second‐generation objects in the universe:
Radiative cooling and collapse of halos with virial temperatures above 10^4 K.
The Astrophysical Journal. American Astronomical Society. https://doi.org/10.1086/339393'
chicago: 'Oh, S. Peng, and Zoltán Haiman. “Second‐generation Objects in the Universe:
Radiative Cooling and Collapse of Halos with Virial Temperatures above 10^4 K.”
The Astrophysical Journal. American Astronomical Society, 2002. https://doi.org/10.1086/339393.'
ieee: 'S. P. Oh and Z. Haiman, “Second‐generation objects in the universe: Radiative
cooling and collapse of halos with virial temperatures above 10^4 K,” The Astrophysical
Journal, vol. 569, no. 2. American Astronomical Society, pp. 558–572, 2002.'
ista: 'Oh SP, Haiman Z. 2002. Second‐generation objects in the universe: Radiative
cooling and collapse of halos with virial temperatures above 10^4 K. The Astrophysical
Journal. 569(2), 558–572.'
mla: 'Oh, S. Peng, and Zoltán Haiman. “Second‐generation Objects in the Universe:
Radiative Cooling and Collapse of Halos with Virial Temperatures above 10^4 K.”
The Astrophysical Journal, vol. 569, no. 2, American Astronomical Society,
2002, pp. 558–72, doi:10.1086/339393.'
short: S.P. Oh, Z. Haiman, The Astrophysical Journal 569 (2002) 558–572.
date_created: 2024-09-06T10:14:24Z
date_published: 2002-04-20T00:00:00Z
date_updated: 2024-09-30T12:04:29Z
day: '20'
doi: 10.1086/339393
extern: '1'
intvolume: ' 569'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1086/339393
month: '04'
oa: 1
oa_version: Published Version
page: 558-572
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Second‐generation objects in the universe: Radiative cooling and collapse
of halos with virial temperatures above 10^4 K'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 569
year: '2002'
...
---
OA_type: free access
_id: '17798'
abstract:
- lang: eng
text: Recent discoveries by the Sloan Digital Sky Survey (SDSS) of four bright z
~ 6 quasars could constrain the mechanism by which the supermassive black holes
powering these sources are assembled. Here we compute the probability that the
fluxes of the quasars are strongly amplified by gravitational lensing and therefore
the likelihood that the black hole masses are overestimated when they are inferred
assuming Eddington luminosities. The poorly constrained shape of the intrinsic
quasar luminosity function (LF) at redshift ~6 results in a large range of possible
lensing probabilities. If the LF is either steep or extends to faint magnitudes,
the probability for amplification by a factor μ ≳ 10 (and with only one image
detectable by SDSS) can reach essentially 100%. We show that future observations,
in particular, of either the current four quasars at the high angular resolution
provided by the Hubble Space Telescope or an increased sample of ~20 z ~ 6 quasars
at the current angular resolution, should either discover several gravitational
lenses or else provide interesting new constraints on the shape of the z ~ 6 quasar
LF.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Julia M.
full_name: Comerford, Julia M.
last_name: Comerford
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
- first_name: Joop
full_name: Schaye, Joop
last_name: Schaye
citation:
ama: Comerford JM, Haiman Z, Schaye J. Constraining the Redshift z ~ 6 quasar luminosity
function using gravitational lensing. The Astrophysical Journal. 2002;580:63-72.
doi:10.1086/343116
apa: Comerford, J. M., Haiman, Z., & Schaye, J. (2002). Constraining the Redshift
z ~ 6 quasar luminosity function using gravitational lensing. The Astrophysical
Journal. American Astronomical Society. https://doi.org/10.1086/343116
chicago: Comerford, Julia M., Zoltán Haiman, and Joop Schaye. “Constraining the
Redshift z ~ 6 Quasar Luminosity Function Using Gravitational Lensing.” The
Astrophysical Journal. American Astronomical Society, 2002. https://doi.org/10.1086/343116.
ieee: J. M. Comerford, Z. Haiman, and J. Schaye, “Constraining the Redshift z ~
6 quasar luminosity function using gravitational lensing,” The Astrophysical
Journal, vol. 580. American Astronomical Society, pp. 63–72, 2002.
ista: Comerford JM, Haiman Z, Schaye J. 2002. Constraining the Redshift z ~ 6 quasar
luminosity function using gravitational lensing. The Astrophysical Journal. 580,
63–72.
mla: Comerford, Julia M., et al. “Constraining the Redshift z ~ 6 Quasar Luminosity
Function Using Gravitational Lensing.” The Astrophysical Journal, vol.
580, American Astronomical Society, 2002, pp. 63–72, doi:10.1086/343116.
short: J.M. Comerford, Z. Haiman, J. Schaye, The Astrophysical Journal 580 (2002)
63–72.
date_created: 2024-09-06T10:29:51Z
date_published: 2002-11-20T00:00:00Z
date_updated: 2024-11-12T09:40:33Z
day: '20'
doi: 10.1086/343116
extern: '1'
external_id:
arxiv:
- astro-ph/0206441
intvolume: ' 580'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.astro-ph/0206441
month: '11'
oa: 1
oa_version: Preprint
page: 63-72
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Constraining the Redshift z ~ 6 quasar luminosity function using gravitational
lensing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 580
year: '2002'
...
---
OA_type: free access
_id: '17799'
abstract:
- lang: eng
text: The Sloan Digital Sky Survey (SDSS) is an imaging and spectroscopic survey
that will eventually cover approximately one-quarter of the celestial sphere and
collect spectra of ≈106 galaxies, 100,000 quasars, 30,000 stars, and 30,000 serendipity
targets. In 2001 June, the SDSS released to the general astronomical community
its early data release, roughly 462 deg2 of imaging data including almost 14 million
detected objects and 54,008 follow-up spectra. The imaging data were collected
in drift-scan mode in five bandpasses (u, g, r, i, and z); our 95% completeness
limits for stars are 22.0, 22.2, 22.2, 21.3, and 20.5, respectively. The photometric
calibration is reproducible to 5%, 3%, 3%, 3%, and 5%, respectively. The spectra
are flux- and wavelength-calibrated, with 4096 pixels from 3800 to 9200 Å at R
≈ 1800. We present the means by which these data are distributed to the astronomical
community, descriptions of the hardware used to obtain the data, the software
used for processing the data, the measured quantities for each observed object,
and an overview of the properties of this data set.
article_processing_charge: No
article_type: original
author:
- first_name: Chris
full_name: Stoughton, Chris
last_name: Stoughton
- first_name: Robert H.
full_name: Lupton, Robert H.
last_name: Lupton
- first_name: Mariangela
full_name: Bernardi, Mariangela
last_name: Bernardi
- first_name: Michael R.
full_name: Blanton, Michael R.
last_name: Blanton
- first_name: Scott
full_name: Burles, Scott
last_name: Burles
- first_name: Francisco J.
full_name: Castander, Francisco J.
last_name: Castander
- first_name: A. J.
full_name: Connolly, A. J.
last_name: Connolly
- first_name: Daniel J.
full_name: Eisenstein, Daniel J.
last_name: Eisenstein
- first_name: Joshua A.
full_name: Frieman, Joshua A.
last_name: Frieman
- first_name: G. S.
full_name: Hennessy, G. S.
last_name: Hennessy
- first_name: Robert B.
full_name: Hindsley, Robert B.
last_name: Hindsley
- first_name: Željko
full_name: Ivezić, Željko
last_name: Ivezić
- first_name: Stephen
full_name: Kent, Stephen
last_name: Kent
- first_name: Peter Z.
full_name: Kunszt, Peter Z.
last_name: Kunszt
- first_name: Brian C.
full_name: Lee, Brian C.
last_name: Lee
- first_name: Avery
full_name: Meiksin, Avery
last_name: Meiksin
- first_name: Jeffrey A.
full_name: Munn, Jeffrey A.
last_name: Munn
- first_name: Heidi Jo
full_name: Newberg, Heidi Jo
last_name: Newberg
- first_name: R. C.
full_name: Nichol, R. C.
last_name: Nichol
- first_name: Tom
full_name: Nicinski, Tom
last_name: Nicinski
- first_name: Jeffrey R.
full_name: Pier, Jeffrey R.
last_name: Pier
- first_name: Gordon T.
full_name: Richards, Gordon T.
last_name: Richards
- first_name: Michael W.
full_name: Richmond, Michael W.
last_name: Richmond
- first_name: David J.
full_name: Schlegel, David J.
last_name: Schlegel
- first_name: J. Allyn
full_name: Smith, J. Allyn
last_name: Smith
- first_name: Michael A.
full_name: Strauss, Michael A.
last_name: Strauss
- first_name: Mark
full_name: SubbaRao, Mark
last_name: SubbaRao
- first_name: Alexander S.
full_name: Szalay, Alexander S.
last_name: Szalay
- first_name: Aniruddha R.
full_name: Thakar, Aniruddha R.
last_name: Thakar
- first_name: Douglas L.
full_name: Tucker, Douglas L.
last_name: Tucker
- first_name: Daniel E.
full_name: Vanden Berk, Daniel E.
last_name: Vanden Berk
- first_name: Brian
full_name: Yanny, Brian
last_name: Yanny
- first_name: Jennifer K.
full_name: Adelman, Jennifer K.
last_name: Adelman
- first_name: John E.
full_name: Anderson, Jr., John E.
last_name: Anderson, Jr.
- first_name: Scott F.
full_name: Anderson, Scott F.
last_name: Anderson
- first_name: James
full_name: Annis, James
last_name: Annis
- first_name: Neta A.
full_name: Bahcall, Neta A.
last_name: Bahcall
- first_name: J. A.
full_name: Bakken, J. A.
last_name: Bakken
- first_name: Matthias
full_name: Bartelmann, Matthias
last_name: Bartelmann
- first_name: Steven
full_name: Bastian, Steven
last_name: Bastian
- first_name: Amanda
full_name: Bauer, Amanda
last_name: Bauer
- first_name: Eileen
full_name: Berman, Eileen
last_name: Berman
- first_name: Hans
full_name: Böhringer, Hans
last_name: Böhringer
- first_name: William N.
full_name: Boroski, William N.
last_name: Boroski
- first_name: Steve
full_name: Bracker, Steve
last_name: Bracker
- first_name: Charlie
full_name: Briegel, Charlie
last_name: Briegel
- first_name: John W.
full_name: Briggs, John W.
last_name: Briggs
- first_name: J.
full_name: Brinkmann, J.
last_name: Brinkmann
- first_name: Robert
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id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
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last_name: Pordes
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full_name: Schneider, Donald P.
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last_name: Sekiguchi
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last_name: Sergey
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last_name: Shimasaku
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full_name: Smee, Stephen
last_name: Smee
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full_name: Snedden, Stephanie A.
last_name: Snedden
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full_name: Stebbins, Albert
last_name: Stebbins
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full_name: Stubbs, Christopher
last_name: Stubbs
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last_name: Szapudi
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full_name: Szkody, Paula
last_name: Szkody
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full_name: Szokoly, Gyula P.
last_name: Szokoly
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full_name: Tabachnik, Serge
last_name: Tabachnik
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full_name: Tsvetanov, Zlatan
last_name: Tsvetanov
- first_name: Alan
full_name: Uomoto, Alan
last_name: Uomoto
- first_name: Michael S.
full_name: Vogeley, Michael S.
last_name: Vogeley
- first_name: Wolfgang
full_name: Voges, Wolfgang
last_name: Voges
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full_name: Waddell, Patrick
last_name: Waddell
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full_name: Walterbos, René
last_name: Walterbos
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full_name: Wang, Shu-i
last_name: Wang
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last_name: Watanabe
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full_name: Weinberg, David H.
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last_name: White
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full_name: White, Simon D. M.
last_name: White
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full_name: Wilhite, Brian
last_name: Wilhite
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full_name: Wolfe, David
last_name: Wolfe
- first_name: Naoki
full_name: Yasuda, Naoki
last_name: Yasuda
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full_name: York, Donald G.
last_name: York
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full_name: Zehavi, Idit
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last_name: Zheng
citation:
ama: 'Stoughton C, Lupton RH, Bernardi M, et al. Sloan digital sky survey: Early
data release. The Astronomical Journal. 2002;123(1):485-548. doi:10.1086/324741'
apa: 'Stoughton, C., Lupton, R. H., Bernardi, M., Blanton, M. R., Burles, S., Castander,
F. J., … Zheng, W. (2002). Sloan digital sky survey: Early data release. The
Astronomical Journal. American Astronomical Society. https://doi.org/10.1086/324741'
chicago: 'Stoughton, Chris, Robert H. Lupton, Mariangela Bernardi, Michael R. Blanton,
Scott Burles, Francisco J. Castander, A. J. Connolly, et al. “Sloan Digital Sky
Survey: Early Data Release.” The Astronomical Journal. American Astronomical
Society, 2002. https://doi.org/10.1086/324741.'
ieee: 'C. Stoughton et al., “Sloan digital sky survey: Early data release,”
The Astronomical Journal, vol. 123, no. 1. American Astronomical Society,
pp. 485–548, 2002.'
ista: 'Stoughton C et al. 2002. Sloan digital sky survey: Early data release. The
Astronomical Journal. 123(1), 485–548.'
mla: 'Stoughton, Chris, et al. “Sloan Digital Sky Survey: Early Data Release.” The
Astronomical Journal, vol. 123, no. 1, American Astronomical Society, 2002,
pp. 485–548, doi:10.1086/324741.'
short: C. Stoughton, R.H. Lupton, M. Bernardi, M.R. Blanton, S. Burles, F.J. Castander,
A.J. Connolly, D.J. Eisenstein, J.A. Frieman, G.S. Hennessy, R.B. Hindsley, Ž.
Ivezić, S. Kent, P.Z. Kunszt, B.C. Lee, A. Meiksin, J.A. Munn, H.J. Newberg, R.C.
Nichol, T. Nicinski, J.R. Pier, G.T. Richards, M.W. Richmond, D.J. Schlegel, J.A.
Smith, M.A. Strauss, M. SubbaRao, A.S. Szalay, A.R. Thakar, D.L. Tucker, D.E.
Vanden Berk, B. Yanny, J.K. Adelman, J.E. Anderson, Jr., S.F. Anderson, J. Annis,
N.A. Bahcall, J.A. Bakken, M. Bartelmann, S. Bastian, A. Bauer, E. Berman, H.
Böhringer, W.N. Boroski, S. Bracker, C. Briegel, J.W. Briggs, J. Brinkmann, R.
Brunner, L. Carey, M.A. Carr, B. Chen, D. Christian, P.L. Colestock, J.H. Crocker,
I. Csabai, P.C. Czarapata, J. Dalcanton, A.F. Davidsen, J.E. Davis, W. Dehnen,
S. Dodelson, M. Doi, T. Dombeck, M. Donahue, N. Ellman, B.R. Elms, M.L. Evans,
L. Eyer, X. Fan, G.R. Federwitz, S. Friedman, M. Fukugita, R. Gal, B. Gillespie,
K. Glazebrook, J. Gray, E.K. Grebel, B. Greenawalt, G. Greene, J.E. Gunn, E. de
Haas, Z. Haiman, M. Haldeman, P.B. Hall, M. Hamabe, B. Hansen, F.H. Harris, H.
Harris, M. Harvanek, S.L. Hawley, J.J.E. Hayes, T.M. Heckman, A. Helmi, A. Henden,
C.J. Hogan, D.W. Hogg, D.J. Holmgren, J. Holtzman, C.-H. Huang, C. Hull, S.-I.
Ichikawa, T. Ichikawa, D.E. Johnston, G. Kauffmann, R.S.J. Kim, T. Kimball, E.
Kinney, M. Klaene, S.J. Kleinman, A. Klypin, G.R. Knapp, J. Korienek, J. Krolik,
R.G. Kron, J. Krzesiński, D.Q. Lamb, R.F. Leger, S. Limmongkol, C. Lindenmeyer,
D.C. Long, C. Loomis, J. Loveday, B. MacKinnon, E.J. Mannery, P.M. Mantsch, B.
Margon, P. McGehee, T.A. McKay, B. McLean, K. Menou, A. Merelli, H.J. Mo, D.G.
Monet, O. Nakamura, V.K. Narayanan, T. Nash, E.H. Neilsen, Jr., P.R. Newman, A.
Nitta, M. Odenkirchen, N. Okada, S. Okamura, J.P. Ostriker, R. Owen, A.G. Pauls,
J. Peoples, R.S. Peterson, D. Petravick, A. Pope, R. Pordes, M. Postman, A. Prosapio,
T.R. Quinn, R. Rechenmacher, C.H. Rivetta, H.-W. Rix, C.M. Rockosi, R. Rosner,
K. Ruthmansdorfer, D. Sandford, D.P. Schneider, R. Scranton, M. Sekiguchi, G.
Sergey, R. Sheth, K. Shimasaku, S. Smee, S.A. Snedden, A. Stebbins, C. Stubbs,
I. Szapudi, P. Szkody, G.P. Szokoly, S. Tabachnik, Z. Tsvetanov, A. Uomoto, M.S.
Vogeley, W. Voges, P. Waddell, R. Walterbos, S. Wang, M. Watanabe, D.H. Weinberg,
R.L. White, S.D.M. White, B. Wilhite, D. Wolfe, N. Yasuda, D.G. York, I. Zehavi,
W. Zheng, The Astronomical Journal 123 (2002) 485–548.
date_created: 2024-09-06T10:32:06Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2024-11-12T09:51:31Z
day: '01'
doi: 10.1086/324741
extern: '1'
intvolume: ' 123'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 485-548
publication: The Astronomical Journal
publication_identifier:
eissn:
- 1538-3881
issn:
- 0004-6256
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1086/340314
scopus_import: '1'
status: public
title: 'Sloan digital sky survey: Early data release'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 123
year: '2002'
...
---
OA_place: repository
OA_type: free access
_id: '17802'
abstract:
- lang: eng
text: The Sloan Digital Sky Survey has confirmed the existence of populations of
broad absorption line (BAL) quasars with various unusual properties. We present
and discuss 23 such objects and consider the implications of their wide range
of properties for models of BAL outflows and quasars in general. We have discovered
one BAL quasar with a record number of absorption lines. Two other similarly complex
objects with many narrow troughs show broad Mg II absorption extending longward
of their systemic host galaxy redshifts. This can be explained as absorption of
an extended continuum source by the rotation-dominated base of a disk wind. Five
other objects have absorption that removes an unprecedented ∼90% of all flux shortward
of Mg II. The absorption in one of them has varied across the ultraviolet with
an amplitude and rate of change as great as ever seen. This same object may also
show broad Hβ absorption. Numerous reddened BAL quasars have been found, including
at least one reddened mini-BAL quasar with very strong Fe II emission. The five
reddest objects have continuum reddenings of E(B-V) ≃ 0.5, and in two of them
we find strong evidence that the reddening curve is even steeper than that of
the SMC. We have found at least one object with absorption from Fe III but not
Fe II. This may be due to a high column density of moderately high ionization
gas, but the Fe III level populations must also be affected by some sort of resonance.
Finally, we have found two luminous, probably reddened high-redshift objects that
may be BAL quasars whose troughs partially cover different regions of the continuum
source as a function of velocity.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Patrick B.
full_name: Hall, Patrick B.
last_name: Hall
- first_name: Scott F.
full_name: Anderson, Scott F.
last_name: Anderson
- first_name: Michael A.
full_name: Strauss, Michael A.
last_name: Strauss
- first_name: Donald G.
full_name: York, Donald G.
last_name: York
- first_name: Gordon T.
full_name: Richards, Gordon T.
last_name: Richards
- first_name: Xiaohui
full_name: Fan, Xiaohui
last_name: Fan
- first_name: G. R.
full_name: Knapp, G. R.
last_name: Knapp
- first_name: Donald P.
full_name: Schneider, Donald P.
last_name: Schneider
- first_name: Daniel E.
full_name: Vanden Berk, Daniel E.
last_name: Vanden Berk
- first_name: T. R.
full_name: Geballe, T. R.
last_name: Geballe
- first_name: Amanda E.
full_name: Bauer, Amanda E.
last_name: Bauer
- first_name: Robert H.
full_name: Becker, Robert H.
last_name: Becker
- first_name: Marc
full_name: Davis, Marc
last_name: Davis
- first_name: Hans‐Walter
full_name: Rix, Hans‐Walter
last_name: Rix
- first_name: R. C.
full_name: Nichol, R. C.
last_name: Nichol
- first_name: Neta A.
full_name: Bahcall, Neta A.
last_name: Bahcall
- first_name: J.
full_name: Brinkmann, J.
last_name: Brinkmann
- first_name: Robert
full_name: Brunner, Robert
last_name: Brunner
- first_name: A. J.
full_name: Connolly, A. J.
last_name: Connolly
- first_name: Istvan
full_name: Csabai, Istvan
last_name: Csabai
- first_name: Mamoru
full_name: Doi, Mamoru
last_name: Doi
- first_name: Masataka
full_name: Fukugita, Masataka
last_name: Fukugita
- first_name: James E.
full_name: Gunn, James E.
last_name: Gunn
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
- first_name: Michael
full_name: Harvanek, Michael
last_name: Harvanek
- first_name: Timothy M.
full_name: Heckman, Timothy M.
last_name: Heckman
- first_name: G. S.
full_name: Hennessy, G. S.
last_name: Hennessy
- first_name: Naohisa
full_name: Inada, Naohisa
last_name: Inada
- first_name: Željko
full_name: Ivezić, Željko
last_name: Ivezić
- first_name: David
full_name: Johnston, David
last_name: Johnston
- first_name: S.
full_name: Kleinman, S.
last_name: Kleinman
- first_name: Julian H.
full_name: Krolik, Julian H.
last_name: Krolik
- first_name: Jurek
full_name: Krzesinski, Jurek
last_name: Krzesinski
- first_name: Peter Z.
full_name: Kunszt, Peter Z.
last_name: Kunszt
- first_name: D. Q.
full_name: Lamb, D. Q.
last_name: Lamb
- first_name: Daniel C.
full_name: Long, Daniel C.
last_name: Long
- first_name: Robert H.
full_name: Lupton, Robert H.
last_name: Lupton
- first_name: Gajus
full_name: Miknaitis, Gajus
last_name: Miknaitis
- first_name: Jeffrey A.
full_name: Munn, Jeffrey A.
last_name: Munn
- first_name: Vijay K.
full_name: Narayanan, Vijay K.
last_name: Narayanan
- first_name: Eric
full_name: Neilsen, Eric
last_name: Neilsen
- first_name: P. R.
full_name: Newman, P. R.
last_name: Newman
- first_name: Atsuko
full_name: Nitta, Atsuko
last_name: Nitta
- first_name: Sadanori
full_name: Okamura, Sadanori
last_name: Okamura
- first_name: Laura
full_name: Pentericci, Laura
last_name: Pentericci
- first_name: Jeffrey R.
full_name: Pier, Jeffrey R.
last_name: Pier
- first_name: David J.
full_name: Schlegel, David J.
last_name: Schlegel
- first_name: S.
full_name: Snedden, S.
last_name: Snedden
- first_name: Alexander S.
full_name: Szalay, Alexander S.
last_name: Szalay
- first_name: Anirudda R.
full_name: Thakar, Anirudda R.
last_name: Thakar
- first_name: Zlatan
full_name: Tsvetanov, Zlatan
last_name: Tsvetanov
- first_name: Richard L.
full_name: White, Richard L.
last_name: White
- first_name: Wei
full_name: Zheng, Wei
last_name: Zheng
citation:
ama: Hall PB, Anderson SF, Strauss MA, et al. Unusual broad absorption line quasars
from the sloan digital sky survey. The Astrophysical Journal Supplement Series.
2002;141(2):267-309. doi:10.1086/340546
apa: Hall, P. B., Anderson, S. F., Strauss, M. A., York, D. G., Richards, G. T.,
Fan, X., … Zheng, W. (2002). Unusual broad absorption line quasars from the sloan
digital sky survey. The Astrophysical Journal Supplement Series. American
Astronomical Society. https://doi.org/10.1086/340546
chicago: Hall, Patrick B., Scott F. Anderson, Michael A. Strauss, Donald G. York,
Gordon T. Richards, Xiaohui Fan, G. R. Knapp, et al. “Unusual Broad Absorption
Line Quasars from the Sloan Digital Sky Survey.” The Astrophysical Journal
Supplement Series. American Astronomical Society, 2002. https://doi.org/10.1086/340546.
ieee: P. B. Hall et al., “Unusual broad absorption line quasars from the
sloan digital sky survey,” The Astrophysical Journal Supplement Series,
vol. 141, no. 2. American Astronomical Society, pp. 267–309, 2002.
ista: Hall PB, Anderson SF, Strauss MA, York DG, Richards GT, Fan X, Knapp GR, Schneider
DP, Vanden Berk DE, Geballe TR, Bauer AE, Becker RH, Davis M, Rix H, Nichol RC,
Bahcall NA, Brinkmann J, Brunner R, Connolly AJ, Csabai I, Doi M, Fukugita M,
Gunn JE, Haiman Z, Harvanek M, Heckman TM, Hennessy GS, Inada N, Ivezić Ž, Johnston
D, Kleinman S, Krolik JH, Krzesinski J, Kunszt PZ, Lamb DQ, Long DC, Lupton RH,
Miknaitis G, Munn JA, Narayanan VK, Neilsen E, Newman PR, Nitta A, Okamura S,
Pentericci L, Pier JR, Schlegel DJ, Snedden S, Szalay AS, Thakar AR, Tsvetanov
Z, White RL, Zheng W. 2002. Unusual broad absorption line quasars from the sloan
digital sky survey. The Astrophysical Journal Supplement Series. 141(2), 267–309.
mla: Hall, Patrick B., et al. “Unusual Broad Absorption Line Quasars from the Sloan
Digital Sky Survey.” The Astrophysical Journal Supplement Series, vol.
141, no. 2, American Astronomical Society, 2002, pp. 267–309, doi:10.1086/340546.
short: P.B. Hall, S.F. Anderson, M.A. Strauss, D.G. York, G.T. Richards, X. Fan,
G.R. Knapp, D.P. Schneider, D.E. Vanden Berk, T.R. Geballe, A.E. Bauer, R.H. Becker,
M. Davis, H. Rix, R.C. Nichol, N.A. Bahcall, J. Brinkmann, R. Brunner, A.J. Connolly,
I. Csabai, M. Doi, M. Fukugita, J.E. Gunn, Z. Haiman, M. Harvanek, T.M. Heckman,
G.S. Hennessy, N. Inada, Ž. Ivezić, D. Johnston, S. Kleinman, J.H. Krolik, J.
Krzesinski, P.Z. Kunszt, D.Q. Lamb, D.C. Long, R.H. Lupton, G. Miknaitis, J.A.
Munn, V.K. Narayanan, E. Neilsen, P.R. Newman, A. Nitta, S. Okamura, L. Pentericci,
J.R. Pier, D.J. Schlegel, S. Snedden, A.S. Szalay, A.R. Thakar, Z. Tsvetanov,
R.L. White, W. Zheng, The Astrophysical Journal Supplement Series 141 (2002) 267–309.
date_created: 2024-09-06T11:30:40Z
date_published: 2002-08-01T00:00:00Z
date_updated: 2024-11-12T10:02:25Z
day: '01'
doi: 10.1086/340546
extern: '1'
external_id:
arxiv:
- astro-ph/0203252
intvolume: ' 141'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.astro-ph/0203252
month: '08'
oa: 1
oa_version: Preprint
page: 267-309
publication: The Astrophysical Journal Supplement Series
publication_identifier:
eissn:
- 1538-4365
issn:
- 0067-0049
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unusual broad absorption line quasars from the sloan digital sky survey
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2002'
...
---
OA_place: repository
OA_type: free access
_id: '17803'
abstract:
- lang: eng
text: We reassess constraints on the cosmological baryon density from observations
of the mean decrement and power spectrum of the Lyα forest, taking into account
uncertainties in all free parameters in the simplest gravitational instability
model. The uncertainty is dominated by that of the photoionizing background, but
incomplete knowledge of the thermal state of the intergalactic medium also contributes
significantly to the error budget. While current estimates of the baryon fraction
from the forest do prefer values that are somewhat higher than the big bang nucleosynthesis
value of Ωb h2 = 0.02 ± 0.001, the discrepancy is at most about 3 σ. For instance,
assuming the highest estimate of the ionizing background, as indicated by recent
measurements of a large escape fraction from Lyman break galaxies by Steidel,
Pettini, & Adelberger, we find Ωbh2 = 0.045 ± 0.008. A recent measurement of the
ionizing background from the proximity effect by Scott et al., on the other hand,
implies Ωbh2 = 0.03 ± 0.01. We provide an expression from which future likelihoods
for Ωb h2 can be derived as measurements of the ionizing background improve—consistency
among constraints from the forest, nucleosynthesis, and the microwave background
will provide a powerful test of the gravitational instability model for the forest
and for large-scale structure in general. We also develop a formalism that treats
lower bounds on the baryon density in a statistical manner, which is appropriate
if only a lower bound on the ionizing background is known. Finally, we discuss
the implications of the escape fraction measurement for the age, structure, and
stellar content of Lyman break galaxies. We show that the observed hard spectrum
from Lyman break galaxies requires a very young age (less than about 1 million
years) and/or a top-heavy initial mass function. We also build a model in which
an extended (non-disk-like) gas distribution allows a large escape fraction.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lam
full_name: Hui, Lam
last_name: Hui
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
- first_name: Matias
full_name: Zaldarriaga, Matias
last_name: Zaldarriaga
- first_name: Tal
full_name: Alexander, Tal
last_name: Alexander
citation:
ama: Hui L, Haiman Z, Zaldarriaga M, Alexander T. Connections between the cosmic
baryon fraction, the extragalactic ionizing background, and Lyman break galaxies.
The Astrophysical Journal. 2002;564(2):525-533. doi:10.1086/324401
apa: Hui, L., Haiman, Z., Zaldarriaga, M., & Alexander, T. (2002). Connections
between the cosmic baryon fraction, the extragalactic ionizing background, and
Lyman break galaxies. The Astrophysical Journal. American Astronomical
Society. https://doi.org/10.1086/324401
chicago: Hui, Lam, Zoltán Haiman, Matias Zaldarriaga, and Tal Alexander. “Connections
between the Cosmic Baryon Fraction, the Extragalactic Ionizing Background, and
Lyman Break Galaxies.” The Astrophysical Journal. American Astronomical
Society, 2002. https://doi.org/10.1086/324401.
ieee: L. Hui, Z. Haiman, M. Zaldarriaga, and T. Alexander, “Connections between
the cosmic baryon fraction, the extragalactic ionizing background, and Lyman break
galaxies,” The Astrophysical Journal, vol. 564, no. 2. American Astronomical
Society, pp. 525–533, 2002.
ista: Hui L, Haiman Z, Zaldarriaga M, Alexander T. 2002. Connections between the
cosmic baryon fraction, the extragalactic ionizing background, and Lyman break
galaxies. The Astrophysical Journal. 564(2), 525–533.
mla: Hui, Lam, et al. “Connections between the Cosmic Baryon Fraction, the Extragalactic
Ionizing Background, and Lyman Break Galaxies.” The Astrophysical Journal,
vol. 564, no. 2, American Astronomical Society, 2002, pp. 525–33, doi:10.1086/324401.
short: L. Hui, Z. Haiman, M. Zaldarriaga, T. Alexander, The Astrophysical Journal
564 (2002) 525–533.
date_created: 2024-09-06T11:31:53Z
date_published: 2002-01-10T00:00:00Z
date_updated: 2024-11-12T10:08:42Z
day: '10'
doi: 10.1086/324401
extern: '1'
external_id:
arxiv:
- astro-ph/0104442
intvolume: ' 564'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.astro-ph/0104442
month: '01'
oa: 1
oa_version: Preprint
page: 525-533
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Connections between the cosmic baryon fraction, the extragalactic ionizing
background, and Lyman break galaxies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 564
year: '2002'
...
---
_id: '859'
abstract:
- lang: eng
text: The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats
with no spacer sequences between individual monomer units. Ubiquitin is one of
the most conserved proteins known to date, and the individual units within a number
of poly-u genes are significantly more similar to each other than would be expected
if each unit evolved independently. It has been proposed that the rather striking
similarity among poly-u monomers in some lineages is caused by a series of homogenization
events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two
mouse strains. Analysis of these sequences, as well as those of the previously
reported Chinese hamster and rat poly-u genes, supports the assertion that the
homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over
events. The sequence divergence of noncoding DNA was used to estimate the frequency
of unequal crossing-over events (6.3 x 10-5 events per generation) in the Ubc
gene, as well as to provide evidence of apparent selection in the poly-u gene.
acknowledgement: We are thankful to J.A. Southerland and P.L. Jiang for technical
assistance in DNA sequencing, as well as to Y.I. Pavlov for helpful discussions.
This work was supported by public Health Service Research Grant AI45135 from the
Institute of Allergy and Infectious Diseases, National Institutes of Health.
article_processing_charge: No
article_type: original
author:
- first_name: Andrey
full_name: Perelygin, Andrey
last_name: Perelygin
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Margo
full_name: Brinton, Margo
last_name: Brinton
citation:
ama: Perelygin A, Kondrashov F, Rogozin I, Brinton M. Evolution of the mouse polyubiquitin
C gene. Journal of Molecular Evolution. 2002;55(2):202-210. doi:10.1007/s00239-002-2318-0
apa: Perelygin, A., Kondrashov, F., Rogozin, I., & Brinton, M. (2002). Evolution
of the mouse polyubiquitin C gene. Journal of Molecular Evolution. Springer.
https://doi.org/10.1007/s00239-002-2318-0
chicago: Perelygin, Andrey, Fyodor Kondrashov, Igor Rogozin, and Margo Brinton.
“Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution.
Springer, 2002. https://doi.org/10.1007/s00239-002-2318-0.
ieee: A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the
mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no.
2. Springer, pp. 202–210, 2002.
ista: Perelygin A, Kondrashov F, Rogozin I, Brinton M. 2002. Evolution of the mouse
polyubiquitin C gene. Journal of Molecular Evolution. 55(2), 202–210.
mla: Perelygin, Andrey, et al. “Evolution of the Mouse Polyubiquitin C Gene.” Journal
of Molecular Evolution, vol. 55, no. 2, Springer, 2002, pp. 202–10, doi:10.1007/s00239-002-2318-0.
short: A. Perelygin, F. Kondrashov, I. Rogozin, M. Brinton, Journal of Molecular
Evolution 55 (2002) 202–210.
date_created: 2018-12-11T11:48:53Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-26T12:01:34Z
day: '01'
doi: 10.1007/s00239-002-2318-0
extern: '1'
external_id:
pmid:
- '12107596'
intvolume: ' 55'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 202 - 210
pmid: 1
publication: Journal of Molecular Evolution
publication_identifier:
issn:
- 0022-2844
publication_status: published
publisher: Springer
publist_id: '6787'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of the mouse polyubiquitin C gene
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 55
year: '2002'
...
---
_id: '871'
abstract:
- lang: eng
text: 'BACKGROUND: Gene duplications have a major role in the evolution of new biological
functions. Theoretical studies often assume that a duplication per se is selectively
neutral and that, following a duplication, one of the gene copies is freed from
purifying (stabilizing) selection, which creates the potential for evolution of
a new function. RESULTS: In search of systematic evidence of accelerated evolution
after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic
genomes to compare the mode and strength of selection acting on recently duplicated
genes (paralogs) and on similarly diverged, unduplicated orthologous genes in
different species. We find that the ratio of nonsynonymous to synonymous substitutions
(Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve
at similar rates, without significant asymmetry, indicating that both paralogs
produced by a duplication are subject to purifying selection. This selection is,
however, substantially weaker than the purifying selection affecting unduplicated
orthologs that have diverged to the same extent as the analyzed paralogs. Most
of the recently duplicated genes appear to be involved in various forms of environmental
response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS:
The results of this analysis indicate that recently duplicated paralogs evolve
faster than orthologs with the same level of divergence and similar functions,
but apparently do not experience a phase of neutral evolution. We hypothesize
that gene duplications that persist in an evolving lineage are beneficial from
the time of their origin, due primarily to a protein dosage effect in response
to variable environmental conditions; duplications are likely to give rise to
new functions at a later phase of their evolution once a higher level of divergence
is reached.'
acknowledgement: We are grateful to A.S. Kondrashov for numerous helpful suggestions,
to I. King Jordan, M.A. Roytberg, J.L. Spouge and D.A. Kondrashov for useful discussions
and to A.S. Kondrashov, I. King Jordan and D.J. Lipman for critical reading of the
manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Kondrashov F, Rogozin I, Wolf Y, Koonin E. Selection in the evolution of gene
duplications . Genome Biology. 2002;3(2). doi:10.1186/gb-2002-3-2-research0008
apa: Kondrashov, F., Rogozin, I., Wolf, Y., & Koonin, E. (2002). Selection in
the evolution of gene duplications . Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2002-3-2-research0008
chicago: Kondrashov, Fyodor, Igor Rogozin, Yuri Wolf, and Eugene Koonin. “Selection
in the Evolution of Gene Duplications .” Genome Biology. BioMed Central,
2002. https://doi.org/10.1186/gb-2002-3-2-research0008.
ieee: F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution
of gene duplications ,” Genome Biology, vol. 3, no. 2. BioMed Central,
2002.
ista: Kondrashov F, Rogozin I, Wolf Y, Koonin E. 2002. Selection in the evolution
of gene duplications . Genome Biology. 3(2).
mla: Kondrashov, Fyodor, et al. “Selection in the Evolution of Gene Duplications
.” Genome Biology, vol. 3, no. 2, BioMed Central, 2002, doi:10.1186/gb-2002-3-2-research0008.
short: F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
date_created: 2018-12-11T11:48:57Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-26T11:48:27Z
day: '01'
doi: 10.1186/gb-2002-3-2-research0008
extern: '1'
external_id:
pmid:
- '11864370'
intvolume: ' 3'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC65685/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1465-6906
publication_status: published
publisher: BioMed Central
publist_id: '6781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Selection in the evolution of gene duplications '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 3
year: '2002'
...
---
_id: '885'
abstract:
- lang: eng
text: We study fitness landscape in the space of protein sequences by relating sets
of human pathogenic missense mutations in 32 proteins to amino acid substitutions
that occurred in the course of evolution of these proteins. On average, ≈10% of
deviations of a nonhuman protein from its human ortholog are compensated pathogenic
deviations (CPDs), i.e., are caused by an amino acid substitution that, at this
site, would be pathogenic to humans. Normal functioning of a CPD-containing protein
must be caused by other, compensatory deviations of the nonhuman species from
humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller
incompatibility that can be visualized as the corner on a fitness ridge. Thus,
proteins evolve along fitness ridges which contain only ≈10 steps between sucessive
corners. The fraction of CPDs among all deviations of a protein from its human
ortholog does not increase with the evolutionary distance between the proteins,
indicating that subtitutions that carry evolving proteins around these corners
occur in rapid succession, driven by positive selection. Data on fitness of interspecies
hybrids suggest that the compensatory change that makes a CPD fit usually occurs
within the same protein. Data on protein structures and on cooccurrence of amino
acids at different sites of multiple orthologous proteins often make it possible
to provisionally identify the substitution that compensates a partiCUlar CPD.
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Kondrashov, Alexey
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil
last_name: Sunyaev
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov A, Sunyaev S, Kondrashov F. Dobzhansky-Muller incompatibilities
in protein evolution. PNAS. 2002;99(23):14878-14883. doi:10.1073/pnas.232565499
apa: Kondrashov, A., Sunyaev, S., & Kondrashov, F. (2002). Dobzhansky-Muller
incompatibilities in protein evolution. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.232565499
chicago: Kondrashov, Alexey, Shamil Sunyaev, and Fyodor Kondrashov. “Dobzhansky-Muller
Incompatibilities in Protein Evolution.” PNAS. National Academy of Sciences,
2002. https://doi.org/10.1073/pnas.232565499.
ieee: A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities
in protein evolution,” PNAS, vol. 99, no. 23. National Academy of Sciences,
pp. 14878–14883, 2002.
ista: Kondrashov A, Sunyaev S, Kondrashov F. 2002. Dobzhansky-Muller incompatibilities
in protein evolution. PNAS. 99(23), 14878–14883.
mla: Kondrashov, Alexey, et al. “Dobzhansky-Muller Incompatibilities in Protein
Evolution.” PNAS, vol. 99, no. 23, National Academy of Sciences, 2002,
pp. 14878–83, doi:10.1073/pnas.232565499.
short: A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883.
date_created: 2018-12-11T11:49:01Z
date_published: 2002-11-12T00:00:00Z
date_updated: 2023-07-26T09:48:37Z
day: '12'
doi: 10.1073/pnas.232565499
extern: '1'
external_id:
pmid:
- '12403824'
intvolume: ' 99'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC137512/
month: '11'
oa: 1
oa_version: Published Version
page: 14878 - 14883
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '6763'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dobzhansky-Muller incompatibilities in protein evolution
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 99
year: '2002'
...
---
_id: '897'
abstract:
- lang: eng
text: "Transcription is a slow and expensive process: in eukaryotes, approximately
20 nucleotides can be transcribed per second at the expense of at least two ATP
molecules per nucleotide. Thus, at least for highly expressed genes, transcription
of long introns, which are particularly common in mammals, is costly. Using data
on the expression of genes that encode proteins in Caenorhabditis elegans and
Homo sapiens, we show that introns in highly expressed genes are substantially
shorter than those in genes that are expressed at low levels. This difference
is greater in humans, such that introns are, on average, 14 times shorter in highly
expressed genes than in genes with low expression, whereas in C. Elegans the difference
in intron length is only twofold. In contrast, the density of introns in a gene
does not strongly depend on the level of gene expression. Thus, natural selection
appears to favor short introns in highly expressed genes to minimize the cost
of transcription and other molecular processes, such as splicing.\r\n"
acknowledgement: We are grateful to A. Kondrashov, I. Rogozin and A. Feldman for reading
the manuscript and P. Bouman, J. Cherry, J. Blumensteil and T. Kim for discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Cristian
full_name: Castillo Davis, Cristian
last_name: Castillo Davis
- first_name: Sergei
full_name: Mekhedov, Sergei
last_name: Mekhedov
- first_name: Daniel
full_name: Hartl, Daniel
last_name: Hartl
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. Selection for
short introns in highly expressed genes. Nature Genetics. 2002;31(4):415-418.
doi:10.1038/ng940
apa: Castillo Davis, C., Mekhedov, S., Hartl, D., Koonin, E., & Kondrashov,
F. (2002). Selection for short introns in highly expressed genes. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng940
chicago: Castillo Davis, Cristian, Sergei Mekhedov, Daniel Hartl, Eugene Koonin,
and Fyodor Kondrashov. “Selection for Short Introns in Highly Expressed Genes.”
Nature Genetics. Nature Publishing Group, 2002. https://doi.org/10.1038/ng940.
ieee: C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection
for short introns in highly expressed genes,” Nature Genetics, vol. 31,
no. 4. Nature Publishing Group, pp. 415–418, 2002.
ista: Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. 2002. Selection
for short introns in highly expressed genes. Nature Genetics. 31(4), 415–418.
mla: Castillo Davis, Cristian, et al. “Selection for Short Introns in Highly Expressed
Genes.” Nature Genetics, vol. 31, no. 4, Nature Publishing Group, 2002,
pp. 415–18, doi:10.1038/ng940.
short: C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, F. Kondrashov, Nature
Genetics 31 (2002) 415–418.
date_created: 2018-12-11T11:49:05Z
date_published: 2002-08-01T00:00:00Z
date_updated: 2023-07-26T09:45:30Z
day: '01'
doi: 10.1038/ng940
extern: '1'
external_id:
pmid:
- '12134150'
intvolume: ' 31'
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 415 - 418
pmid: 1
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6751'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection for short introns in highly expressed genes
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 31
year: '2002'
...
---
_id: '4631'
abstract:
- lang: eng
text: We present a theory of timed interfaces, which is capable of specifying both
the timing of the inputs a component expects from the environment, and the timing
of the outputs it can produce. Two timed interfaces are compatible if there is
a way to use them together such that their timing expectations are met. Our theory
provides algorithms for checking the compatibility between two interfaces and
for deriving the composite interface; the theory can thus be viewed as a type
system for real-time interaction. Technically, a timed interface is encoded as
a timed game between two players, representing the inputs and outputs of the component.
The algorithms for compatibility checking and interface composition are thus derived
from algorithms for solving timed games.
acknowledgement: This research was supported in part by the NSF CAREER award CCR-0132780,
the NSF grant CCR-9988172 the AFOSR MURI grant F49620-00-1-0327, the DARPA PCES
grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660, and the ONR grant N00014-02-1-0671.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'De Alfaro L, Henzinger TA, Stoelinga M. Timed interfaces. In: Proceedings
of the 2nd International Conference on Embedded Software. Vol 2491. ACM; 2002:108-122.
doi:10.1007/3-540-45828-X_9'
apa: 'De Alfaro, L., Henzinger, T. A., & Stoelinga, M. (2002). Timed interfaces.
In Proceedings of the 2nd International Conference on Embedded Software
(Vol. 2491, pp. 108–122). Grenoble, France: ACM. https://doi.org/10.1007/3-540-45828-X_9'
chicago: De Alfaro, Luca, Thomas A Henzinger, and Mariëlle Stoelinga. “Timed Interfaces.”
In Proceedings of the 2nd International Conference on Embedded Software,
2491:108–22. ACM, 2002. https://doi.org/10.1007/3-540-45828-X_9.
ieee: L. De Alfaro, T. A. Henzinger, and M. Stoelinga, “Timed interfaces,” in Proceedings
of the 2nd International Conference on Embedded Software, Grenoble, France,
2002, vol. 2491, pp. 108–122.
ista: 'De Alfaro L, Henzinger TA, Stoelinga M. 2002. Timed interfaces. Proceedings
of the 2nd International Conference on Embedded Software. EMSOFT: Embedded Software
, LNCS, vol. 2491, 108–122.'
mla: De Alfaro, Luca, et al. “Timed Interfaces.” Proceedings of the 2nd International
Conference on Embedded Software, vol. 2491, ACM, 2002, pp. 108–22, doi:10.1007/3-540-45828-X_9.
short: L. De Alfaro, T.A. Henzinger, M. Stoelinga, in:, Proceedings of the 2nd International
Conference on Embedded Software, ACM, 2002, pp. 108–122.
conference:
end_date: 2002-10-09
location: Grenoble, France
name: 'EMSOFT: Embedded Software '
start_date: 2002-10-07
date_created: 2018-12-11T12:09:51Z
date_published: 2002-10-24T00:00:00Z
date_updated: 2023-06-02T10:00:32Z
day: '24'
doi: 10.1007/3-540-45828-X_9
extern: '1'
intvolume: ' 2491'
language:
- iso: eng
month: '10'
oa_version: None
page: 108 - 122
publication: Proceedings of the 2nd International Conference on Embedded Software
publication_identifier:
isbn:
- '9783540443070'
publication_status: published
publisher: ACM
publist_id: '76'
quality_controlled: '1'
status: public
title: Timed interfaces
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2491
year: '2002'
...
---
_id: '6158'
abstract:
- lang: eng
text: Wild isolates of Caenorhabditis elegans can feed either alone or in groups1,2.
This natural variation in behaviour is associated with a single residue difference
in NPR-1, a predicted G-protein-coupled neuropeptide receptor related to Neuropeptide
Y receptors2. Here we show that the NPR-1 isoform associated with solitary feeding
acts in neurons exposed to the body fluid to inhibit social feeding. Furthermore,
suppressing the activity of these neurons, called AQR, PQR and URX, using an activated
K+ channel, inhibits social feeding. NPR-1 activity in AQR, PQR and URX neurons
seems to suppress social feeding by antagonizing signalling through a cyclic GMP-gated
ion channel encoded by tax-2 and tax-4. We show that mutations in tax-2 or tax-4
disrupt social feeding, and that tax-4 is required in several neurons for social
feeding, including one or more of AQR, PQR and URX. The AQR, PQR and URX neurons
are unusual in C. elegans because they are directly exposed to the pseudocoelomic
body fluid3. Our data suggest a model in which these neurons integrate antagonistic
signals to control the choice between social and solitary feeding behaviour.
author:
- first_name: Juliet C.
full_name: Coates, Juliet C.
last_name: Coates
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Coates JC, de Bono M. Antagonistic pathways in neurons exposed to body fluid
regulate social feeding in Caenorhabditis elegans. Nature. 2002;419(6910):925-929.
doi:10.1038/nature01170
apa: Coates, J. C., & de Bono, M. (2002). Antagonistic pathways in neurons exposed
to body fluid regulate social feeding in Caenorhabditis elegans. Nature.
Springer Nature. https://doi.org/10.1038/nature01170
chicago: Coates, Juliet C., and Mario de Bono. “Antagonistic Pathways in Neurons
Exposed to Body Fluid Regulate Social Feeding in Caenorhabditis Elegans.” Nature.
Springer Nature, 2002. https://doi.org/10.1038/nature01170.
ieee: J. C. Coates and M. de Bono, “Antagonistic pathways in neurons exposed to
body fluid regulate social feeding in Caenorhabditis elegans,” Nature,
vol. 419, no. 6910. Springer Nature, pp. 925–929, 2002.
ista: Coates JC, de Bono M. 2002. Antagonistic pathways in neurons exposed to body
fluid regulate social feeding in Caenorhabditis elegans. Nature. 419(6910), 925–929.
mla: Coates, Juliet C., and Mario de Bono. “Antagonistic Pathways in Neurons Exposed
to Body Fluid Regulate Social Feeding in Caenorhabditis Elegans.” Nature,
vol. 419, no. 6910, Springer Nature, 2002, pp. 925–29, doi:10.1038/nature01170.
short: J.C. Coates, M. de Bono, Nature 419 (2002) 925–929.
date_created: 2019-03-21T10:09:20Z
date_published: 2002-10-31T00:00:00Z
date_updated: 2021-01-12T08:06:26Z
day: '31'
doi: 10.1038/nature01170
extern: '1'
external_id:
pmid:
- '12410311'
intvolume: ' 419'
issue: '6910'
language:
- iso: eng
month: '10'
oa_version: None
page: 925-929
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Antagonistic pathways in neurons exposed to body fluid regulate social feeding
in Caenorhabditis elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 419
year: '2002'
...
---
_id: '6159'
abstract:
- lang: eng
text: 'Natural Caenorhabditis elegans isolates exhibit either social or solitary
feeding on bacteria. We show here that social feeding is induced by nociceptive
neurons that detect adverse or stressful conditions. Ablation of the nociceptive
neurons ASH and ADL transforms social animals into solitary feeders. Social feeding
is probably due to the sensation of noxious chemicals by ASH and ADL neurons;
it requires the genes ocr-2 and osm-9, which encode TRP-related transduction channels,
and odr-4 and odr-8, which are required to localize sensory chemoreceptors to
cilia. Other sensory neurons may suppress social feeding, as social feeding in
ocr-2 and odr-4 mutants is restored by mutations in osm-3, a gene required for
the development of 26 ciliated sensory neurons. Our data suggest a model for regulation
of social feeding by opposing sensory inputs: aversive inputs to nociceptive neurons
promote social feeding, whereas antagonistic inputs from neurons that express
osm-3 inhibit aggregation.'
author:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: David M.
full_name: Tobin, David M.
last_name: Tobin
- first_name: M. Wayne
full_name: Davis, M. Wayne
last_name: Davis
- first_name: Leon
full_name: Avery, Leon
last_name: Avery
- first_name: Cornelia I.
full_name: Bargmann, Cornelia I.
last_name: Bargmann
citation:
ama: de Bono M, Tobin DM, Davis MW, Avery L, Bargmann CI. Social feeding in Caenorhabditis
elegans is induced by neurons that detect aversive stimuli. Nature. 2002;419(6910):899-903.
doi:10.1038/nature01169
apa: de Bono, M., Tobin, D. M., Davis, M. W., Avery, L., & Bargmann, C. I. (2002).
Social feeding in Caenorhabditis elegans is induced by neurons that detect aversive
stimuli. Nature. Springer Nature. https://doi.org/10.1038/nature01169
chicago: Bono, Mario de, David M. Tobin, M. Wayne Davis, Leon Avery, and Cornelia
I. Bargmann. “Social Feeding in Caenorhabditis Elegans Is Induced by Neurons That
Detect Aversive Stimuli.” Nature. Springer Nature, 2002. https://doi.org/10.1038/nature01169.
ieee: M. de Bono, D. M. Tobin, M. W. Davis, L. Avery, and C. I. Bargmann, “Social
feeding in Caenorhabditis elegans is induced by neurons that detect aversive stimuli,”
Nature, vol. 419, no. 6910. Springer Nature, pp. 899–903, 2002.
ista: de Bono M, Tobin DM, Davis MW, Avery L, Bargmann CI. 2002. Social feeding
in Caenorhabditis elegans is induced by neurons that detect aversive stimuli.
Nature. 419(6910), 899–903.
mla: de Bono, Mario, et al. “Social Feeding in Caenorhabditis Elegans Is Induced
by Neurons That Detect Aversive Stimuli.” Nature, vol. 419, no. 6910, Springer
Nature, 2002, pp. 899–903, doi:10.1038/nature01169.
short: M. de Bono, D.M. Tobin, M.W. Davis, L. Avery, C.I. Bargmann, Nature 419 (2002)
899–903.
date_created: 2019-03-21T10:27:04Z
date_published: 2002-10-31T00:00:00Z
date_updated: 2021-01-12T08:06:27Z
day: '31'
doi: 10.1038/nature01169
extern: '1'
external_id:
pmid:
- '12410303'
intvolume: ' 419'
issue: '6910'
language:
- iso: eng
month: '10'
oa_version: None
page: 899-903
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Social feeding in Caenorhabditis elegans is induced by neurons that detect
aversive stimuli
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 419
year: '2002'
...
---
_id: '3448'
author:
- first_name: Sanhita
full_name: Mallick, Sanhita
last_name: Mallick
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Arif
full_name: Merchant, Arif N
last_name: Merchant
- first_name: Pallab
full_name: Dasgupta, Pallab
last_name: Dasgupta
citation:
ama: 'Mallick S, Chatterjee K, Merchant A, Dasgupta P. Implementation of shape grammar
for plan analysis. In: Elsevier; 2002.'
apa: 'Mallick, S., Chatterjee, K., Merchant, A., & Dasgupta, P. (2002). Implementation
of shape grammar for plan analysis. Presented at the IT-Built: Information Technology
For Built Environment, Elsevier.'
chicago: Mallick, Sanhita, Krishnendu Chatterjee, Arif Merchant, and Pallab Dasgupta.
“Implementation of Shape Grammar for Plan Analysis.” Elsevier, 2002.
ieee: 'S. Mallick, K. Chatterjee, A. Merchant, and P. Dasgupta, “Implementation
of shape grammar for plan analysis,” presented at the IT-Built: Information Technology
For Built Environment, 2002.'
ista: 'Mallick S, Chatterjee K, Merchant A, Dasgupta P. 2002. Implementation of
shape grammar for plan analysis. IT-Built: Information Technology For Built Environment.'
mla: Mallick, Sanhita, et al. Implementation of Shape Grammar for Plan Analysis.
Elsevier, 2002.
short: S. Mallick, K. Chatterjee, A. Merchant, P. Dasgupta, in:, Elsevier, 2002.
conference:
name: 'IT-Built: Information Technology For Built Environment'
date_created: 2018-12-11T12:03:23Z
date_published: 2002-01-15T00:00:00Z
date_updated: 2021-01-12T07:43:31Z
day: '15'
extern: 1
month: '01'
publication_status: published
publisher: Elsevier
publist_id: '2939'
quality_controlled: 0
status: public
title: Implementation of shape grammar for plan analysis
type: conference
year: '2002'
...
---
_id: '3497'
abstract:
- lang: eng
text: The use of advanced patch-clamp recording techniques in brain slices, such
as simultaneous recording from multiple neurons and recording from dendrites or
presynaptic terminals, demands slices of the highest quality. In this context
the mechanics of the tissue slicer are an important factor. Ideally, a tissue
slicer should generate large-amplitude and high-frequency movements of the cutting
blade in a horizontal axis, with minimal vibrations in the vertical axis. We developed
a vibroslicer that fulfils these in part conflicting requirements. The oscillator
is a permanent-magnet-coil-leaf-spring system. Using an auto-resonant mechano-electrical
feedback circuit, large horizontal oscillations (up to 3 mm peak-to-peak) with
high frequency (,90 Hz) are generated. To minimize vertical vibrations, an adjustment
mechanism was employed that allowed alignment of the cutting edge of the blade
with the major axis of the oscillation. A vibroprobe device was used to monitor
vertical vibrations during adjustment. The system is based on the shading of the
light path between a light-emitting diode (LED) and a photodiode. Vibroprobe monitoring
revealed that the vibroslicer, after appropriate adjustment, generated vertical
vibrations of <1 µm, significantly less than many commercial tissue slicers.
Light- and electron-microscopic analysis of surface layers of slices cut with
the vibroslicer showed that cellular elements, dendritic processes and presynaptic
terminals are well preserved under these conditions, as required for patch-clamp
recording from these structures.
acknowledgement: "We thank Dr. M. Frotscher for reading the manuscript, and H. Kressner,
R. Laufersweiler, and A. Bühler for help with the construction of several prototypes
of vibroslicer and vibroprobe. We also thank A. Blomenkamp, K. Winterhalter, B.
Joch, and A. Schneider for technical assistance. This work was supported by grants
of the Deutsche Forschungsgemeinschaft\r\n(SFB 505/C5, C6) and the Human Frontiers
Science Program Organization (RG0017/1998-B)."
article_processing_charge: No
article_type: original
author:
- first_name: Jörg
full_name: Geiger, Jörg
last_name: Geiger
- first_name: Joseph
full_name: Bischofberger, Joseph
last_name: Bischofberger
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Ulrich
full_name: Fröbe, Ulrich
last_name: Fröbe
- first_name: S
full_name: Pfitzinger, S
last_name: Pfitzinger
- first_name: H.
full_name: Weber, H.
last_name: Weber
- first_name: Klaus
full_name: Haverkampf, Klaus
last_name: Haverkampf
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Geiger J, Bischofberger J, Vida I, et al. Patch-clamp recording in brain slices
with improved slicer technology. Pflugers Archiv : European Journal of Physiology.
2002;443(3):491-501. doi:10.1007/s00424-001-0735-3'
apa: 'Geiger, J., Bischofberger, J., Vida, I., Fröbe, U., Pfitzinger, S., Weber,
H., … Jonas, P. M. (2002). Patch-clamp recording in brain slices with improved
slicer technology. Pflugers Archiv : European Journal of Physiology. Springer.
https://doi.org/10.1007/s00424-001-0735-3'
chicago: 'Geiger, Jörg, Joseph Bischofberger, Imre Vida, Ulrich Fröbe, S Pfitzinger,
H. Weber, Klaus Haverkampf, and Peter M Jonas. “Patch-Clamp Recording in Brain
Slices with Improved Slicer Technology.” Pflugers Archiv : European Journal
of Physiology. Springer, 2002. https://doi.org/10.1007/s00424-001-0735-3.'
ieee: 'J. Geiger et al., “Patch-clamp recording in brain slices with improved
slicer technology,” Pflugers Archiv : European Journal of Physiology, vol.
443, no. 3. Springer, pp. 491–501, 2002.'
ista: 'Geiger J, Bischofberger J, Vida I, Fröbe U, Pfitzinger S, Weber H, Haverkampf
K, Jonas PM. 2002. Patch-clamp recording in brain slices with improved slicer
technology. Pflugers Archiv : European Journal of Physiology. 443(3), 491–501.'
mla: 'Geiger, Jörg, et al. “Patch-Clamp Recording in Brain Slices with Improved
Slicer Technology.” Pflugers Archiv : European Journal of Physiology, vol.
443, no. 3, Springer, 2002, pp. 491–501, doi:10.1007/s00424-001-0735-3.'
short: 'J. Geiger, J. Bischofberger, I. Vida, U. Fröbe, S. Pfitzinger, H. Weber,
K. Haverkampf, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 443
(2002) 491–501.'
date_created: 2018-12-11T12:03:38Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-17T07:36:37Z
day: '01'
doi: 10.1007/s00424-001-0735-3
extern: '1'
external_id:
pmid:
- '11810221'
intvolume: ' 443'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 491 - 501
pmid: 1
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_identifier:
issn:
- 0031-6768
publication_status: published
publisher: Springer
publist_id: '2890'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Patch-clamp recording in brain slices with improved slicer technology
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 443
year: '2002'
...
---
_id: '3508'
abstract:
- lang: eng
text: A method of automatic conversion of a physical object into a three-dimensional
digital model. The method acquires a set of measured data points on the surface
of a physical model. From the measured data points, the method reconstructs a
digital model of the physical object using a Delaunay complex of the points, a
flow strcuture of the simplicies in the Delaunay complex and retracting the Delaunay
complex into a digital model of the physical object using the flow structure.
The method then outputs the digital model of the physical object.
applicant:
- Raindrop Geomagic, Inc.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
citation:
ama: Edelsbrunner H, Fu P. Methods of generating three-dimensional digital models
of objects by wrapping point cloud data points. 2002.
apa: Edelsbrunner, H., & Fu, P. (2002). Methods of generating three-dimensional
digital models of objects by wrapping point cloud data points.
chicago: Edelsbrunner, Herbert, and Ping Fu. “Methods of Generating Three-Dimensional
Digital Models of Objects by Wrapping Point Cloud Data Points,” 2002.
ieee: H. Edelsbrunner and P. Fu, “Methods of generating three-dimensional digital
models of objects by wrapping point cloud data points.” 2002.
ista: Edelsbrunner H, Fu P. 2002. Methods of generating three-dimensional digital
models of objects by wrapping point cloud data points.
mla: Edelsbrunner, Herbert, and Ping Fu. Methods of Generating Three-Dimensional
Digital Models of Objects by Wrapping Point Cloud Data Points. 2002.
short: H. Edelsbrunner, P. Fu, (2002).
date_created: 2018-12-11T12:03:42Z
date_published: 2002-04-23T00:00:00Z
date_updated: 2022-01-05T14:09:36Z
day: '23'
extern: '1'
ipc: G16Z99/00 ; G06K9/28 ; G06T17/10 ; G06T17/20
ipn: US6377865B1
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US6377865B1
month: '04'
oa: 1
oa_version: Published Version
publication_date: 2002-04-23
publist_id: '2879'
status: public
title: Methods of generating three-dimensional digital models of objects by wrapping
point cloud data points
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2002'
...
---
_id: '3533'
abstract:
- lang: eng
text: 'Information in neuronal networks is thought to be represented by the rate
of discharge and the temporal relationship between the discharging neurons. The
discharge frequency of neurons is affected by their afferents and intrinsic properties,
and shows great individual variability. The temporal coordination of neurons is
greatly facilitated by network oscillations. In the hippocampus, population synchrony
fluctuates during theta and gamma oscillations (10-100 ms scale) and can increase
almost 10-fold during sharp wave bursts. Despite these large changes in excitability
in the sub-second scale, longer-term (minute-scale) firing rates of individual
neurons are relatively constant in an unchanging environment. As a result, mean
hippocampal output remains stable over time. To understand the mechanisms responsible
for this homeostasis, we address the following issues: (i) Can firing rates of
single cells be modified? (ii) Once modified, what mechanism(s) can maintain the
changes? We show that firing rates of hippocampal pyramidal cells can be altered
in a novel environment and by Hebbian pairing of physiological input patterns
with postsynaptic burst discharge. We also illustrate a competition between single
spikes and the occurrence of spike bursts. Since spike-inducing (suprathreshold)
inputs decrease the ability of strong (''teaching'') inputs to induce a burst
discharge, we propose that the single spike versus burst competition presents
a homeostatic regulatory mechanism to maintain synaptic strength and, consequently,
firing rate in pyramidal cells.'
article_processing_charge: No
article_type: original
author:
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: George
full_name: Dragoi, George
last_name: Dragoi
- first_name: Kenneth
full_name: Harris, Kenneth
last_name: Harris
- first_name: D.
full_name: Henze, D.
last_name: Henze
- first_name: Hajima
full_name: Hirase, Hajima
last_name: Hirase
citation:
ama: Buzsáki G, Csicsvari JL, Dragoi G, Harris K, Henze D, Hirase H. Homeostatic
maintenance of neuronal excitability by burst discharges in vivo. Cerebral
Cortex. 2002;12(9):893-899. doi:10.1093/cercor/12.9.893
apa: Buzsáki, G., Csicsvari, J. L., Dragoi, G., Harris, K., Henze, D., & Hirase,
H. (2002). Homeostatic maintenance of neuronal excitability by burst discharges
in vivo. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/12.9.893
chicago: Buzsáki, György, Jozsef L Csicsvari, George Dragoi, Kenneth Harris, D.
Henze, and Hajima Hirase. “Homeostatic Maintenance of Neuronal Excitability by
Burst Discharges in Vivo.” Cerebral Cortex. Oxford University Press, 2002.
https://doi.org/10.1093/cercor/12.9.893.
ieee: G. Buzsáki, J. L. Csicsvari, G. Dragoi, K. Harris, D. Henze, and H. Hirase,
“Homeostatic maintenance of neuronal excitability by burst discharges in vivo,”
Cerebral Cortex, vol. 12, no. 9. Oxford University Press, pp. 893–899,
2002.
ista: Buzsáki G, Csicsvari JL, Dragoi G, Harris K, Henze D, Hirase H. 2002. Homeostatic
maintenance of neuronal excitability by burst discharges in vivo. Cerebral Cortex.
12(9), 893–899.
mla: Buzsáki, György, et al. “Homeostatic Maintenance of Neuronal Excitability by
Burst Discharges in Vivo.” Cerebral Cortex, vol. 12, no. 9, Oxford University
Press, 2002, pp. 893–99, doi:10.1093/cercor/12.9.893.
short: G. Buzsáki, J.L. Csicsvari, G. Dragoi, K. Harris, D. Henze, H. Hirase, Cerebral
Cortex 12 (2002) 893–899.
date_created: 2018-12-11T12:03:50Z
date_published: 2002-09-01T00:00:00Z
date_updated: 2023-07-17T07:27:12Z
day: '01'
doi: 10.1093/cercor/12.9.893
extern: '1'
external_id:
pmid:
- '12183388'
intvolume: ' 12'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 893 - 899
pmid: 1
publication: Cerebral Cortex
publication_identifier:
issn:
- 1047-3211
publication_status: published
publisher: Oxford University Press
publist_id: '2851'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Homeostatic maintenance of neuronal excitability by burst discharges in vivo
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 12
year: '2002'
...
---
_id: '3621'
abstract:
- lang: eng
text: In 1991, Barton and Turelli developed recursions to describe the evolution
of multilocus systems under arbitrary forms of selection. This article generalizes
their approach to allow for arbitrary modes of inheritance, including diploidy,
polyploidy, sex linkage, cytoplasmic inheritance, and genomic imprinting. The
framework is also extended to allow for other deterministic evolutionary forces,
including migration and mutation. Exact recursions that fully describe the state
of the population are presented; these are implemented in a computer algebra package
(available on the Web at http://helios.bto.ed.ac.uk/evolgen). Despite the generality
of our framework, it can describe evolutionary dynamics exactly by just two equations.
These recursions can be further simplified using a "quasi-linkage equilibrium"
(QLE) approximation. We illustrate the methods by finding the effect of natural
selection, sexual selection, mutation, and migration on the genetic composition
of a population.
article_processing_charge: No
article_type: original
author:
- first_name: Mark
full_name: Kirkpatrick, Mark
last_name: Kirkpatrick
- first_name: Toby
full_name: Johnson, Toby
last_name: Johnson
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kirkpatrick M, Johnson T, Barton NH. General models of multilocus evolution.
Genetics. 2002;161(4):1727-1750. doi:10.1093/genetics/161.4.1727
apa: Kirkpatrick, M., Johnson, T., & Barton, N. H. (2002). General models of
multilocus evolution. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/161.4.1727
chicago: Kirkpatrick, Mark, Toby Johnson, and Nicholas H Barton. “General Models
of Multilocus Evolution.” Genetics. Genetics Society of America, 2002.
https://doi.org/10.1093/genetics/161.4.1727.
ieee: M. Kirkpatrick, T. Johnson, and N. H. Barton, “General models of multilocus
evolution,” Genetics, vol. 161, no. 4. Genetics Society of America, pp.
1727–1750, 2002.
ista: Kirkpatrick M, Johnson T, Barton NH. 2002. General models of multilocus evolution.
Genetics. 161(4), 1727–1750.
mla: Kirkpatrick, Mark, et al. “General Models of Multilocus Evolution.” Genetics,
vol. 161, no. 4, Genetics Society of America, 2002, pp. 1727–50, doi:10.1093/genetics/161.4.1727.
short: M. Kirkpatrick, T. Johnson, N.H. Barton, Genetics 161 (2002) 1727–1750.
date_created: 2018-12-11T12:04:17Z
date_published: 2002-08-01T00:00:00Z
date_updated: 2023-07-11T13:20:26Z
day: '01'
doi: 10.1093/genetics/161.4.1727
extern: '1'
external_id:
pmid:
- '12196414'
intvolume: ' 161'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462196/
month: '08'
oa: 1
oa_version: Published Version
page: 1727 - 1750
pmid: 1
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '2762'
quality_controlled: '1'
scopus_import: '1'
status: public
title: General models of multilocus evolution
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 161
year: '2002'
...