Performance comparison of two-point linkage methods using microsatellite markers flanking known disease locations

The Genetic Analysis Workshop 14 simulated data presents an interesting, challenging, and plausible example of a complex disease interaction in a dataset. This paper summarizes the ease of detection for each of the simulated Kofendrerd Personality Disorder (KPD) genes across all of the replicates for five standard linkage statistics. Using the KPD affection status, we have analyzed the microsatellite markers flanking each of the disease genes, plus an additional 2 markers that were not linked to any of the disease loci. All markers were analyzed using the following two-point linkage methods: 1) a MMLS, which is a standard admixture LOD score maximized over θ, α, and mode of inheritance, 2) a MLS calculated by GENEHUNTER, 3) the Kong and Cox LOD score as computed by MERLIN, 4) a MOD score (standard heterogeneity LOD maximized over θ, α, and a grid of genetic model parameters), and 5) the PPL, a Bayesian statistic that directly measures the strength of evidence for linkage to a marker. All of the major loci (D1–D4) were detectable with varying probabilities in the different populations. However, the modifier genes (D5 and D6) were difficult to detect, with similar distributions under the null and alternative across populations and statistics. The pooling of the four datasets in each replicate (n = 350 pedigrees) greatly improved the chance of detecting the major genes using all five methods, but failed to increase the chance to detect D5 and D6

tert-Butyl 2-methyl-2-(4-nitro­benzo­yl)propanoate

The title compound, C15H19NO5, is bent with a dihedral angle of 61.8 (2)° between the mean planes of the benzene ring and a group encompassing the ester functionality (O=C—O—C). The dihedral angle of 0.8 (2)° between the mean planes of the nitro group and the benzene ring indicates near coplanarity. In the crystal, each mol­ecule is linked to four adjacent mol­ecules by weak C—H⋯O hydrogen-bonding inter­actions. Both benzene H atoms ortho to the ketone O atom form C—H⋯O hydrogen bonds with the keto O atoms of two neighboring mol­ecules (of the keto and ester groups, respectively), and the two other inter­actions involve the H atoms from a methyl group of the dimethyl residue, displaying C—H⋯O inter­actions with the O atoms of the nitro groups. These four inter­actions for each mol­ecule lead to the formation of two-dimensional sheets with a hydro­philic inter­ior, held together by weak hydrogen-bonded inter­actions, and a hydro­phobic exterior composed of protruding methyl groups which interst­ack with the methyl groups in adjacent sheets

tert-Butyl 2-methyl-2-(4-methyl­benzo­yl)propanoate

The title compound, C16H22O3, is bent with a dihedral angle of 75.3 (1)° between the mean planes of the benzene ring and a group encompassing the ester functionality (O=C—O—C). In the crystal, the mol­ecules are linked into infinite chains held together by weak C—H⋯O hydrogen-bonded inter­actions between an H atom on the benzene ring of one mol­ecule and an O atom on the ketone functionality of an adjacent mol­ecule. The chains are arranged with neighbouring tert-butyl and dimethyl groups on adjacent chains exhibiting hydro­phobic stacking, with short C—H⋯H—C contacts (2.37 Å) between adjacent chain

tert-Butyl 2-benzoyl-2-methyl­propanoate

The title compound, C15H20O3, is bent with a dihedral angle of 67.28 (9)° between the mean planes of the phenyl ring and a group encompassing the ester functionality (O=C—O—C). In the crystal, mol­ecules related by inversion symmetry are connected by weak C—H⋯O inter­actions into infinite chains. On one side of the mol­ecule there are two adjacent inter­actions between neighbouring mol­ecules involving the H atoms of methyl groups from the dimethyl groups and the O atoms of the ketone; on the other side, there are also two inter­actions to another adjacent mol­ecule involving the H atoms on the phenyl rings and the carbonyl O atoms of the ester functionality

Simplifying asteroseismic analysis of solar-like oscillators: An application of principal component analysis for dimensionality reduction

The asteroseismic analysis of stellar power density spectra is often computationally expensive. The models used in the analysis may use several dozen parameters to accurately describe features in the spectra caused by oscillation modes and surface granulation. Many parameters are often highly correlated, making the parameter space difficult to quickly and accurately sample. They are, however, all dependent on a smaller set of parameters, namely the fundamental stellar properties. We aim to leverage this to simplify the process of sampling the model parameter space for the asteroseismic analysis of solar-like oscillators, with an emphasis on mode identification. Using a large set of previous observations, we applied principal component analysis to the sample covariance matrix to select a new basis on which to sample the model parameters. Selecting the subset of basis vectors that explains the majority of the sample variance, we redefine the model parameter prior probability density distributions in terms of a smaller set of latent parameters. We are able to reduce the dimensionality of the sampled parameter space by a factor of two to three. The number of latent parameters needed to accurately model the stellar oscillation spectra cannot be determined exactly but is likely only between four and six. Using two latent parameters, the method is able to describe the bulk features of the oscillation spectrum, while including more latent parameters allows for a frequency precision better than $\approx10\%$ of the small frequency separation for a given target. We find that sampling a lower-rank latent parameter space still allows for accurate mode identification and parameter estimation on solar-like oscillators over a wide range of evolutionary stages. This allows for the potential to increase the complexity of spectrum models without a corresponding increase in computational expense.Comment: Accepted for publication in Astronomy & Astrophysics. 11 pages. 10 figure

Assessing the similarity of song-type transitions among birds: evidence for inter-species variation

Permission to archived accepted author manuscriptIn many species of songbird, individuals sing multiple song types, some of which are shared with their neighbours. Individuals may also share syntactical rules that govern the transitions between different song types, but few studies have attempted to study this kind of sharing. Progress has been inhibited by a lack of statistical tools to compare song-type transitions among individuals. We present a straightforward method for comparing song transitions based on Markov transition matrices. The method calculates the number of mutually preferred song-type-to-different-song-type transitions found in the song sequences of two birds, then assesses whether that number is significantly greater than would be expected if the two birds ordered their songs independently of one another. We applied this method to song sequences from five songbird species. All pairwise comparisons among male Cassin's vireos, Vireo cassinii, showed significant similarity in song transitions, as did a minority of comparisons among Adelaide's warblers, Setophaga adelaidae, and one pair of marsh wrens, Cistothorus palustris. In contrast, dyads of rock wrens, Salpinctes obsoletus, and rufous-and-white wrens, Thryophilus rufalbus, did not share song-type transitions at levels exceeding chance. Interterritory distance was not significantly related to our measure of song transition similarity in any of our study species. These results provide evidence that interindividual similarity in song-type transitions is a trait that varies considerably among species. We discuss the potential drivers of similarity in song transitions, but note that assessing its evolutionary breadth will require a larger sample of species. The application of our method to additional species will provide a more comprehensive understanding of signal use and vocal interaction in songbirds.Ye

tert-Butyl 2-(4-chloro­benzo­yl)-2-methyl­propanoate

The title compound, C15H19ClO3, is bent with a dihedral angle of 72.02 (9)° between the mean planes of the benzene ring and a group encompassing the ester functionality (O=C—O—C). In the crystal, mol­ecules related by inversion symmetry are connected by weak C—H⋯O inter­actions into infinite chains. These inter­actions involve H atoms from a methyl group of the dimethyl residue and the O atoms of the ketone on one side of a mol­ecule; on the other side there are inter­actions between H atoms of the benzene ring and the carbonyl O atoms of the ester functionality. There are no directional inter­actions between the chains