Protocols, methods, and tools for genome-wide association studies (GWAS) of dental traits

Oral health and disease are known to be influenced by complex interactions between environmental (e.g., social and behavioral) factors and innate susceptibility. Although the exact contribution of genomics and other layers of “omics” to oral health is an area of active research, it is well established that the susceptibility to dental caries, periodontal disease, and other oral and craniofacial traits is substantially influenced by the human genome. A comprehensive understanding of these genomic factors is necessary for the realization of precision medicine in the oral health domain. To aid in this direction, the advent and increasing affordability of high-throughput genotyping has enabled the simultaneous interrogation of millions of genetic polymorphisms for association with oral and craniofacial traits. Specifically, genome-wide association studies (GWAS) of dental caries and periodontal disease have provided initial insights into novel loci and biological processes plausibly implicated in these two common, complex, biofilm-mediated diseases. This paper presents a summary of protocols, methods, tools, and pipelines for the conduct of GWAS of dental caries, periodontal disease, and related traits. The protocol begins with the consideration of different traits for both diseases and outlines procedures for genotyping, quality control, adjustment for population stratification, heritability and association analyses, annotation, reporting, and interpretation. Methods and tools available for GWAS are being constantly updated and improved; with this in mind, the presented approaches have been successfully applied in numerous GWAS and meta-analyses among tens of thousands of individuals, including dental traits such as dental caries and periodontal disease. As such, they can serve as a guide or template for future genomic investigations of these and other traits

Black Hole Spin via Continuum Fitting and the Role of Spin in Powering Transient Jets

The spins of ten stellar black holes have been measured using the continuum-fitting method. These black holes are located in two distinct classes of X-ray binary systems, one that is persistently X-ray bright and another that is transient. Both the persistent and transient black holes remain for long periods in a state where their spectra are dominated by a thermal accretion disk component. The spin of a black hole of known mass and distance can be measured by fitting this thermal continuum spectrum to the thin-disk model of Novikov and Thorne; the key fit parameter is the radius of the inner edge of the black hole's accretion disk. Strong observational and theoretical evidence links the inner-disk radius to the radius of the innermost stable circular orbit, which is trivially related to the dimensionless spin parameter a_* of the black hole (|a_*| < 1). The ten spins that have so far been measured by this continuum-fitting method range widely from a_* \approx 0 to a_* > 0.95. The robustness of the method is demonstrated by the dozens or hundreds of independent and consistent measurements of spin that have been obtained for several black holes, and through careful consideration of many sources of systematic error. Among the results discussed is a dichotomy between the transient and persistent black holes; the latter have higher spins and larger masses. Also discussed is recently discovered evidence in the transient sources for a correlation between the power of ballistic jets and black hole spin.Comment: 30 pages. Accepted for publication in Space Science Reviews. Also to appear in hard cover in the Space Sciences Series of ISSI "The Physics of Accretion onto Black Holes" (Springer Publisher). Changes to Sections 5.2, 6.1 and 7.4. Section 7.4 responds to Russell et al. 2013 (MNRAS, 431, 405) who find no evidence for a correlation between the power of ballistic jets and black hole spi

Jet spectral breaks in black hole X-ray binaries

In X-ray binaries, compact jets are known to commonly radiate at radio to infrared frequencies, whereas at optical to -ray energies, the contribution of the jet is debated. The total luminosity, and hence power of the jet, is critically dependent on the position of the break in its spectrum, between optically thick (self-absorbed) and optically thin synchrotron emission. This break, or turnover, has been reported in just one black hole X-ray binary (BHXB) thus far, GX 339-4, and inferred via spectral fitting in two others, A0620-00 and Cyg X-1. Here, we collect a wealth of multi-wavelength data from the outbursts of BHXBs during hard X-ray states, in order to search for jet breaks as yet unidentified in their spectral energy distributions. In particular, we report the direct detection of the jet break in the spectrum of V404 Cyg during its 1989 outburst, at b = (1.8 ± 0.3) × 1014 Hz (1.7 ± 0.2 μm). We increase the number of BHXBs with measured jet breaks from three to eight. Jet breaks are found at frequencies spanning more than two orders of magnitude, from b = (4.5 ± 0.8) × 1012 Hz for XTE J1118+480 during its 2005 outburst, to b > 4.7 × 1014 Hz for V4641 Sgr in outburst. A positive correlation between jet break frequency and luminosity is expected theoretically; b L ~0.5 ,jet if other parameters are constant. With constraints on the jet break in a total of 12 BHXBs including two quiescent systems, we find a large range of jet break frequencies at similar luminosities and no obvious global relation (but such a relation cannot be ruled out for individual sources). We speculate that different magnetic field strengths and/or different radii of the acceleration zone in the inner regions of the jet are likely to be responsible for the observed scatter between sources. There is evidence that the high-energy cooling break in the jet spectrum shifts from UV energies at LX ~ 10-8LEdd (implying the jet may dominate the X-ray emission in quiescence) to X-ray energies at ~10-3LEdd. Finally, we find that the jet break luminosity scales as L,jet L0.56±0.05 X (very similar to the radio-X-ray correlation), and radio-faint BHXBs have fainter jet breaks. In quiescence the jet break luminosity exceeds the X-ray luminosity. © 2012 The Authors

Host Plant Records for Fruit Flies (Diptera: Tephritidae: Dacini) in the Pacific Islands: 2. Infestation Statistics on Economic Hosts

Detailed host records are listed for 39 species of Bactrocera and 2 species of Dacus fruit flies, infesting 98 species of commercial and edible fruits in the Pacific Island Countries and Territories, based on sampling and incubating in laboratory almost 13,000 field collected samples, or over 380,000 fruits. For each host-fly-country association, quantitative data are presented on the weight and number of fruits collected, the proportion of infested samples, the number of adult flies emerged per kg of fruits and, whenever available, the percentage of individual fruits infested. All the published records of each fly-host-country association are cited and erroneous or dubious published records are rectified or commented. Laboratory forced infestation data are also cited and reviewed