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 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. The six samples show different levels of initial endogenous content, with very low (< 0.05%, 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% (WGC + YCC) 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 (WGC + YCC) 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 WGC + YCC 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

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 (5–300 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 $10^{12}$ K near the black hole), the electrons are also hot ($\sim10^{9-10.5}$ 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 world’s 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