1,206 research outputs found
In-solution Y-chromosome capture-enrichment on ancient DNA libraries.
As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000Â years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGCâ+âYCC) versus non-enriched (pre-capture) libraries.
The six samples show different levels of initial endogenous content, with very low (<â0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGCâ+âYCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGCâ+âYCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.
We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGCâ+âYCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round
The SuperCOSMOS Sky Survey. Paper III: Astrometry
In this, the third in a series of three papers concerning the SuperCOSMOS Sky
Survey, we describe the astrometric properties of the database. We describe the
algorithms employed in the derivation of the astrometric parameters of the
data, and demonstrate their accuracies by comparison with external datasets
using the first release of data, the South Galactic Cap survey. We show that
the celestial coordinates, which are tied to the International Celestial
Reference Frame via the Tycho-2 reference catalogue, are accurate to better
than +/- 0.2 arcsec at J,R=19,18 rising to +/- 0.3 arcsec at J,R=22,21 with
positional dependent systematic effects from bright to faint magnitudes at the
+/- 0.1 arcsec level. The proper motion measurements are shown to be accurate
to typically +/- 10 mas/yr at J,R=19,18 rising to +/- 50 mas/yr at J,R=22,21
and are tied to zero using the extragalactic reference frame. We show that the
zeropoint errors in the proper motions are 17 and are no
larger than 10 mas/yr for R < 17 mas/yr.Comment: 15 pages, 12 figures; accepted for publication in MNRA
Comorbidities, exposure to medications, and the risk of community-acquired clostridium difficile infection: A systematic review and meta-analysis
Background. Clostridium difficile infection (CDI) has been extensively escribedin healthcare settings; however, risk factor sassociated with community-acquired (CA) CDI remain uncertain. This study aimed to synthesize the current evidence for an association between commonly prescribed medications and comorbidities with CA-CDI. methods. A systematic search was conducted in 5 electronic databases for epidemiologicstudi esthatexamined the associtation between the presence of comorbidities and exposure to medications with the risk of CA-CDI. Pooled odds ratios were estimated using 3 meta-analytic methods. Subgroup analyses by location of studies and by life stages were conducted. results. Twelve publications (n=56,776 patients) met inclusion criteria. Antimicrobial (odds ratio, 6.18; 95% CI, 3.80-10.04) and corticosteroid (1.81; 1.15-2.84) exposure were associated with increased risk of CA-CDI. Among the comorbidities, inflammatory bowel disease (odds ratio, 3.72; 95% CI, 1.52-9.12), renal failure (2.64; 1.23-5.68), hematologic cancer (1.75; 1.02-5.68), and diabetes mellitus (1.15; 1.05-1.27) were associated with CA-CDI. By location, antimicrobial exposure was associated with a higher risk of CA-CDI in the United States, whereas proton-pump inhibitor exposure was associated with a higher risk in Europe. By life stages, the risk of CA-CDI associated with antimicrobial exposure greatly increased in adults older than 65 years. conclusions. Antimicrobial exposure was the strongest risk factor associated with CA-CDI. Further studies are required to investigate the risk of CA-CDI associated with medications commonly prescribed in the community. Patients with diarrhea who have inflammatory bowel disease, renal failure, hematologic cancer, or diabetes are appropriate populations for interventional studies of screening
Spectrum of the Vortex Bound States of the Dirac and Schrodinger Hamiltonian in the presence of Superconducting Gaps
We investigate the vortex bound states both Schrodinger and Dirac Hamiltonian
with the s-wave superconducting pairing gap by solving the mean-field
Bogoliubov-de-Gennes equations. The exact vortex bound states spectrum is
numerically determined by the integration method, and also accompanied by the
quasi-classical analysis. It is found that the bound state energies is
proportional to the vortex angular momentum when the chemical potential is
large enough. By applying the external magnetic field, the vortex bound state
energies of the Dirac Hamiltonian are almost unchanged; whereas the energy
shift of the Schrodinger Hamiltonian is proportional to the magnetic field.
These qualitative differences may serve as an indirect evidence of the
existence of Majorana fermions in which the zero mode exists in the case of the
Dirac Hamiltonian only.Comment: 8 pages, 9 figure
Tight-binding g-Factor Calculations of CdSe Nanostructures
The Lande g-factors for CdSe quantum dots and rods are investigated within
the framework of the semiempirical tight-binding method. We describe methods
for treating both the n-doped and neutral nanostructures, and then apply these
to a selection of nanocrystals of variable size and shape, focusing on
approximately spherical dots and rods of differing aspect ratio. For the
negatively charged n-doped systems, we observe that the g-factors for
near-spherical CdSe dots are approximately independent of size, but show strong
shape dependence as one axis of the quantum dot is extended to form rod-like
structures. In particular, there is a discontinuity in the magnitude of
g-factor and a transition from anisotropic to isotropic g-factor tensor at
aspect ratio ~1.3. For the neutral systems, we analyze the electron g-factor of
both the conduction and valence band electrons. We find that the behavior of
the electron g-factor in the neutral nanocrystals is generally similar to that
in the n-doped case, showing the same strong shape dependence and discontinuity
in magnitude and anisotropy. In smaller systems the g-factor value is dependent
on the details of the surface model. Comparison with recent measurements of
g-factors for CdSe nanocrystals suggests that the shape dependent transition
may be responsible for the observations of anomalous numbers of g-factors at
certain nanocrystal sizes.Comment: 15 pages, 6 figures. Fixed typos to match published versio
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HOx observations over West Africa during AMMA: impact of isoprene and NOx
Aircraft OH and HO2 measurements made over West Africa during the AMMA field campaign in summer 2006 have been investigated using a box model constrained to observations of long-lived species and physical parameters. "Good" agreement was found for HO2 (modelled to observed gradient of 1.23 ± 0.11). However, the model significantly overpredicts OH concentrations. The reasons for this are not clear, but may reflect instrumental instabilities affecting the OH measurements. Within the model, HOx concentrations in West Africa are controlled by relatively simple photochemistry, with production dominated by ozone photolysis and reaction of O(1D) with water vapour, and loss processes dominated by HO2 + HO2 and HO2 + RO2. Isoprene chemistry was found to influence forested regions. In contrast to several recent field studies in very low NOx and high isoprene environments, we do not observe any dependence of model success for HO2 on isoprene and attribute this to efficient recycling of HOx through RO2 + NO reactions under the moderate NOx concentrations (5â300 ppt NO in the boundary layer, median 76 ppt) encountered during AMMA. This suggests that some of the problems with understanding the impact of isoprene on atmospheric composition may be limited to the extreme low range of NOx concentrations
Low-Luminosity Accretion in Black Hole X-ray Binaries and Active Galactic Nuclei
At luminosities below a few percent of Eddington, accreting black holes
switch to a hard spectral state which is very different from the soft
blackbody-like spectral state that is found at higher luminosities. The hard
state is well-described by a two-temperature, optically thin, geometrically
thick, advection-dominated accretion flow (ADAF) in which the ions are
extremely hot (up to K near the black hole), the electrons are also
hot ( K), and thermal Comptonization dominates the X-ray
emission. The radiative efficiency of an ADAF decreases rapidly with decreasing
mass accretion rate, becoming extremely low when a source reaches quiescence.
ADAFs are expected to have strong outflows, which may explain why relativistic
jets are often inferred from the radio emission of these sources. It has been
suggested that most of the X-ray emission also comes from a jet, but this is
less well established.Comment: To appear in "From X-ray Binaries to Quasars: Black Hole Accretion on
All Mass Scales" edited by T. Maccarone, R. Fender, L. Ho, to be published as
a special edition of "Astrophysics and Space Science" by Kluwe
What works to increase charitable donations? A meta-review with meta-meta-analysis
Many charities rely on donations to support their work addressing some of the worldâs most pressing problems. We conducted a meta-review to determine what interventions work to increase charitable donations. We found 21 systematic reviews incorporating 1339 primary studies and over 2,139,938 participants. Our meta-meta-analysis estimated the average effect of an intervention on charitable donation size and incidence: r = 0.08 (95% CI [0.03, 0.12]). Due to limitations in the included systematic reviews, we are not certain this estimate reflects the true overall effect size. The most robust evidence found suggests charities could increase donations by (1) emphasising individual beneficiaries, (2) increasing the visibility of donations, (3) describing the impact of the donation, and (4) enacting or promoting tax-deductibility of the charity. We make recommendations for improving primary research and reviews about charitable donations, and how to apply the meta-review findings to increase charitable donations
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