121 research outputs found
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations
Ice supersaturations exceeding 100% at the cold tropical tropopause: implications for cirrus formation and dehydration
International audienceRecent in situ measurements at tropical tropopause temperatures as low as 187 K indicate supersaturations with respect to ice exceeding 100% with little or no ice present. In contrast, models used to simulate cloud formation near the tropopause assume a supersaturation threshold for ice nucleation of about 65% based on laboratory measurements of sulfate aerosol freezing. The high supersaturations reported here, along with cloud simulations assuming a plausible range of temperature histories in the sampled air mass, indicate that the vast majority of aerosols in the air sampled on this flight must have had supersaturation thresholds for ice nucleation exceeding 100% (i.e. near liquid water saturation at these temperatures). Possible explanations for this high threshold are that (1) the expressions used for calculating vapor pressure over supercooled water at low temperatures give values at least 20% too low, (2) most of the available aerosols had a composition that makes them much more resistant to ice nucleation than aerosols used in laboratory experiments, and (3) organic films on the aerosol surfaces reduce their accommodation coefficient for uptake of water, resulting in aerosols with more concentrated solutions when moderate-rapid cooling occurs and correspondingly inhibited homogeneous freezing. Simulations of in situ cloud formation in the tropical tropopause layer (TTL) throughout the tropics indicate that if these decreased accommodation coefficients and resulting high thresholds for ice nucleation prevailed throughout the tropics, then the calculated occurrence frequency and areal coverage of TTL cirrus would be significantly suppressed. However, the simulations also show that even if in situ TTL cirrus form only over a very small fraction of the tropics in the western Pacific, enough air passes through them due to rapid horizontal transport such that they can still effectively freeze-dry air entering the stratosphere
Timing, rates and spectra of human germline mutation.
Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. The mutation rate increased with paternal age in all families, but the number of additional mutations per year differed by more than twofold between families. Meta-analysis of 6,570 mutations showed that germline methylation influences mutation rates. In contrast to somatic mutations, we found remarkable consistency in germline mutation spectra between the sexes and at different paternal ages. In parental germ line, 3.8% of mutations were mosaic, resulting in 1.3% of mutations being shared by siblings. The number of these shared mutations varied significantly between families. Our data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells but is reduced substantially during post-pubertal spermatogenesis. These findings have important consequences for the recurrence risks of disorders caused by de novo mutations
Ice supersaturations exceeding 100% at the cold tropical tropopause: implications for cirrus formation and dehydration
International audienceRecent in situ measurements at tropical tropopause temperatures as low as 187 K indicate supersaturations with respect to ice exceeding 100% with little or no ice present. In contrast, models used to simulate cloud formation near the tropopause assume a supersaturation threshold for ice nucleation of about 65% based on laboratory measurements of aqueous aerosol freezing. The high supersaturations reported here, along with cloud simulations assuming a plausible range of temperature histories in the sampled air mass, indicate that the vast majority of aerosols in the air sampled on this flight must have had supersaturation thresholds for ice nucleation exceeding 100% (i.e. near liquid water saturation at these temperatures). Possible explanations for this high threshold are that (1) the expressions used for calculating vapor pressure over supercooled water at low temperatures give values are at least 20% too low, (2) organic films on the aerosol surfaces reduce their accommodation coefficient for uptake of water, resulting in aerosols with more concentrated solutions when moderate-rapid cooling occurs and correspondingly inhibited homogeneous freezing, and (3) if surface freezing dominates, organic coatings may increase the surface energy of the ice embryo/vapor interface resulting in suppressed ice nucleation. Simulations of in situ cloud formation in the tropical tropopause layer (TTL) throughout the tropics indicate that if decreased accommodation coefficients and resulting high thresholds for ice nucleation prevailed throughout the tropics, then the calculated occurrence frequency and areal coverage of TTL cirrus would be significantly suppressed. However, the simulations also show that even if in situ TTL cirrus form only over a very small fraction of the tropics in the western Pacific, enough air passes through them due to rapid horizontal transport such that they can still effectively freeze-dry air entering the stratosphere. The TTL cirrus simulations show that even if very large supersaturations are required for ice nucleation, these large supersaturations should occur very rarely
The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs
We describe the design and performance of the near-infrared (1.51--1.70
micron), fiber-fed, multi-object (300 fibers), high resolution (R =
lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point
Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~
10^5 red giant stars that systematically sampled all Milky Way populations
(bulge, disk, and halo) to study the Galaxy's chemical and kinematical history.
It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014
using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New
Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV,
as well as a second spectrograph, a close copy of the first, operating at the
2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several
fiber-fed, multi-object, high resolution spectrographs have been built for
visual wavelength spectroscopy, the APOGEE spectrograph is one of the first
such instruments built for observations in the near-infrared. The instrument's
successful development was enabled by several key innovations, including a
"gang connector" to allow simultaneous connections of 300 fibers; hermetically
sealed feedthroughs to allow fibers to pass through the cryostat wall
continuously; the first cryogenically deployed mosaic volume phase holographic
grating; and a large refractive camera that includes mono-crystalline silicon
and fused silica elements with diameters as large as ~ 400 mm. This paper
contains a comprehensive description of all aspects of the instrument including
the fiber system, optics and opto-mechanics, detector arrays, mechanics and
cryogenics, instrument control, calibration system, optical performance and
stability, lessons learned, and design changes for the second instrument.Comment: 81 pages, 67 figures, PASP, accepte
Familiarization: A theory of repetition suppression predicts interference between overlapping cortical representations
Repetition suppression refers to a reduction in the cortical response to a novel stimulus that
results from repeated presentation of the stimulus. We demonstrate repetition suppression
in a well established computational model of cortical plasticity, according to which the relative
strengths of lateral inhibitory interactions are modified by Hebbian learning. We present
the model as an extension to the traditional account of repetition suppression offered by
sharpening theory, which emphasises the contribution of afferent plasticity, by instead
attributing the effect primarily to plasticity of intra-cortical circuitry. In support, repetition suppression
is shown to emerge in simulations with plasticity enabled only in intra-cortical connections.
We show in simulation how an extended ‘inhibitory sharpening theory’ can explain
the disruption of repetition suppression reported in studies that include an intermediate
phase of exposure to additional novel stimuli composed of features similar to those of the
original stimulus. The model suggests a re-interpretation of repetition suppression as a manifestation
of the process by which an initially distributed representation of a novel object
becomes a more localist representation. Thus, inhibitory sharpening may constitute a more
general process by which representation emerges from cortical re-organisation
The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey
The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic
data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data
release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median
z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar
spectra, along with the data presented in previous data releases. These spectra
were obtained with the new BOSS spectrograph and were taken between 2009
December and 2011 July. In addition, the stellar parameters pipeline, which
determines radial velocities, surface temperatures, surface gravities, and
metallicities of stars, has been updated and refined with improvements in
temperature estimates for stars with T_eff<5000 K and in metallicity estimates
for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars
presented in DR8, including stars from SDSS-I and II, as well as those observed
as part of the SDSS-III Sloan Extension for Galactic Understanding and
Exploration-2 (SEGUE-2).
The astrometry error introduced in the DR8 imaging catalogs has been
corrected in the DR9 data products. The next data release for SDSS-III will be
in Summer 2013, which will present the first data from the Apache Point
Observatory Galactic Evolution Experiment (APOGEE) along with another year of
data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at
http://www.sdss3.org/dr
The 16th Data Release of the Sloan Digital Sky Surveys: First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra
This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)
The Eleventh and Twelfth Data Releases of the Sloan Digital Sky Survey: Final Data from SDSS-III
The third generation of the Sloan Digital Sky Survey (SDSS-III) took data from 2008 to 2014 using the original SDSS wide-field imager, the original and an upgraded multi-object fiber-fed optical spectrograph, a new near-infrared high-resolution spectrograph, and a novel optical interferometer. All of the data from SDSS-III are now made public. In particular, this paper describes Data Release 11 (DR11) including all data acquired through 2013 July, and Data Release 12 (DR12) adding data acquired through 2014 July (including all data included in previous data releases), marking the end of SDSS-III observing. Relative to our previous public release (DR10), DR12 adds one million new spectra of galaxies and quasars from the Baryon Oscillation Spectroscopic Survey (BOSS) over an additional 3000 deg2 of sky, more than triples the number of H-band spectra of stars as part of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE), and includes repeated accurate radial velocity measurements of 5500 stars from the Multi-object APO Radial Velocity Exoplanet Large-area Survey (MARVELS). The APOGEE outputs now include the measured abundances of 15 different elements for each star. In total, SDSS-III added 5200 deg2 of ugriz imaging; 155,520 spectra of 138,099 stars as part of the Sloan Exploration of Galactic Understanding and Evolution 2 (SEGUE-2) survey; 2,497,484 BOSS spectra of 1,372,737 galaxies, 294,512 quasars, and 247,216 stars over 9376 deg2; 618,080 APOGEE spectra of 156,593 stars; and 197,040 MARVELS spectra of 5513 stars. Since its first light in 1998, SDSS has imaged over 1/3 of the Celestial sphere in five bands and obtained over five million astronomical spectra. © 2015. The American Astronomical Society
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