Analysis of human mini-exome sequencing data from Genetic Analysis Workshop 17 using a Bayesian hierarchical mixture model

Next-generation sequencing technologies are rapidly changing the field of genetic epidemiology and enabling exploration of the full allele frequency spectrum underlying complex diseases. Although sequencing technologies have shifted our focus toward rare genetic variants, statistical methods traditionally used in genetic association studies are inadequate for estimating effects of low minor allele frequency variants. Four our study we use the Genetic Analysis Workshop 17 data from 697 unrelated individuals (genotypes for 24,487 autosomal variants from 3,205 genes). We apply a Bayesian hierarchical mixture model to identify genes associated with a simulated binary phenotype using a transformed genotype design matrix weighted by allele frequencies. A Metropolis Hasting algorithm is used to jointly sample each indicator variable and additive genetic effect pair from its conditional posterior distribution, and remaining parameters are sampled by Gibbs sampling. This method identified 58 genes with a posterior probability greater than 0.8 for being associated with the phenotype. One of these 58 genes, PIK3C2B was correctly identified as being associated with affected status based on the simulation process. This project demonstrates the utility of Bayesian hierarchical mixture models using a transformed genotype matrix to detect genes containing rare and common variants associated with a binary phenotype

Formation age of the lunar crater Giordano Bruno

Using the Terrain Camera onboard the Japanese lunar explorer, SELENE (Kaguya), we obtained new high-resolution images of the 22-kilometer-diameter lunar crater Giordano Bruno. Based on crater size-frequency measurements of small craters (<200 m in diameter) superposed on its continuous ejecta, the formation age of Giordano Bruno is estimated to be 1 to 10 Ma. This is constructive evidence against the crater's medieval age formation hypothesis.The Meteoritics & Planetary Science archives are made available by the Meteoritical Society and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202

Cross calibration between Hayabusa2/ONC-T and OSIRIS-REx/MapCam for comparative analyses between asteroids Ryugu and Bennu

Proximity observations of (162173) Ryugu by the telescopic Optical Navigation Camera onboard Hayabusa2 and (101955) Bennu by MapCam onboard Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer found opposite spectral trends of space weathering on these carbonaceous asteroids. Whether the space weathering trends on these asteroids evolved from the same starting spectra would place an important constraint for understanding their relation. However, systematic error between data obtained by the two imagers needed to be reduced for accurate comparison. To resolve this problem, we cross calibrated albedo and color data using the Moon as the common standard. We show that the cross-calibrated reflectance can be obtained by upscaling the pre-cross-calibrated reflectance of Bennu by 12 +/- 2% at v-band, reducing the systematic errors down to 2%. The cross-calibrated data show that Bennu is brighter by 16 +/- 2% at v-band and bluer in spectral slope by 0.19 +/- 0.05 (/um) than Ryugu. The spectra of fresh craters on Ryugu and Bennu before cross calibration appeared to follow two parallel trend lines with offset, but they converged to a single trend after cross calibration. Such a post-cross-calibration perspective raise the possibility that Ryugu and Bennu evolved from materials with similar visible spectra but evolved in diverging directions by space weathering. The divergent evolution can be caused by the difference in space weathering dose/process and/or composition of the starting material. Thus, comparing the composition of samples returned from Ryugu and Bennu may change the way we interpret the spectral variation of C-complex asteroids

Prospects for Genomic Selection in Cassava Breeding

Article purchased; Published online: 28 Sept 2017Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. We also evaluated the impact of increasing the training population (TP) size by phenotyping progenies selected either at random or with a genetic algorithm. Cross-validation results were mostly consistent across programs, with nonadditive models predicting of 10% better on average. Cross-population accuracy was generally low (mean = 0.18) but prediction of cassava mosaic disease increased up to 57% in one Nigerian population when data from another related population were combined. Accuracy across generations was poorer than within-generation accuracy, as expected, but accuracy for dry matter content and mosaic disease severity should be sufficient for rapid-cycling GS. Selection of a prediction model made some difference across generations, but increasing TP size was more important. With a genetic algorithm, selection of one-third of progeny could achieve an accuracy equivalent to phenotyping all progeny. We are in the early stages of GS for this crop but the results are promising for some traits. General guidelines that are emerging are that TPs need to continue to grow but phenotyping can be done on a cleverly selected subset of individuals, reducing the overall phenotyping burden

Mechanisms of cerebellar tonsil herniation in patients with Chiari malformations as guide to clinical management

Background The pathogenesis of Chiari malformations is incompletely understood. We tested the hypothesis that different etiologies have different mechanisms of cerebellar tonsil herniation (CTH), as revealed by posterior cranial fossa (PCF) morphology. Methods In 741 patients with Chiari malformation type I (CM-I) and 11 patients with Chiari malformation type II (CM-II), the size of the occipital enchondrium and volume of the PCF (PCFV) were measured on reconstructed 2D-CT and MR images of the skull. Measurements were compared with those in 80 age- and sex-matched healthy control individuals, and the results were correlated with clinical findings. Results Significant reductions of PCF size and volume were present in 388 patients with classical CM-I, 11 patients with CM-II, and five patients with CM-I and craniosynostosis. Occipital bone size and PCFV were normal in 225 patients with CM-I and occipitoatlantoaxial joint instability, 55 patients with CM-I and tethered cord syndrome (TCS), 30 patients with CM-I and intracranial mass lesions, and 28 patients with CM-I and lumboperitoneal shunts. Ten patients had miscellaneous etiologies. The size and area of the foramen magnum were significantly smaller in patients with classical CM-I and CM-I occurring with craniosynostosis and significantly larger in patients with CM-II and CM-I occurring with TCS. Conclusions Important clues concerning the pathogenesis of CTH were provided by morphometric measurements of the PCF. When these assessments were correlated with etiological factors, the following causal mechanisms were suggested: (1) cranial constriction; (2) cranial settling; (3) spinal cord tethering; (4) intracranial hypertension; and (5) intraspinal hypotension

An artificial impact on the asteroid (162173) Ryugu formed a crater in the gravity-dominated regime

The Hayabusa2 spacecraft investigated the small asteroid Ryugu, which has a rubble-pile structure. We describe an impact experiment on Ryugu using Hayabusa2’s Small Carry-on Impactor. The impact produced an artificial crater with a diameter >10 meters, which has a semicircular shape, an elevated rim, and a central pit. Images of the impact and resulting ejecta were recorded by the Deployable CAMera 3 for >8 minutes, showing the growth of an ejecta curtain (the outer edge of the ejecta) and deposition of ejecta onto the surface. The ejecta curtain was asymmetric and heterogeneous and it never fully detached from the surface. The crater formed in the gravity-dominated regime; in other words, crater growth was limited by gravity not surface strength. We discuss implications for Ryugu’s surface age

The most primitive CM chondrites, Asuka 12085, 12169, and 12236, of subtypes 3.0–2.8: Their characteristic features and classification

CM chondrites (CMs) are the most abundant group of carbonaceous chondrites. CMs experienced varying degrees of secondary aqueous alteration and heating that modified or destroyed their primitive features. We have studied three chondrites, Asuka (A) 12085, A 12169, and A 12236. Their modal compositions, chondrule size distributions, and bulk composition indicate that they are CMs. However, the common occurrence of melilite in CAIs and glass in chondrules, abundant Fe–Ni metal, the absence of tochilinite-cronstedtite intergrowths, and almost no phyllosilicates, all suggest that these chondrites, especially A 12169, experienced only minimal aqueous alteration. The textures and compositions of metal and sulfides, the lack of ferroan rims on AOA olivines, the compositional distribution of ferroan olivine, and the Raman spectra of their matrices, indicate that these chondrites experienced neither significant heating nor dehydration. These chondrites, especially A 12169, are the most primitive CMs so far reported. The degree of the alteration increases from A 12169, through A 12236, to A 12085. We propose the criteria for subtypes of 3.0–2.8 for CMs. A 12169, A 12236, and A 12085 are classified as subtype 3.0, 2.9, and 2.8, respectively. The oxygen isotopic composition of the Asuka CMs is consistent with these samples having experienced only a limited degree of aqueous alteration. The CM and CO groups are probably not derived from a single heterogeneous parent body. These chondrites are also of particular significance in view of the imminent return of sample material from the asteroids Ryugu and Bennu