Detection of suspicious interactions of spiking covariates in methylation data

BACKGROUND: In methylation analyses like epigenome-wide association studies, a high amount of biomarkers is tested for an association between the measured continuous outcome and different covariates. In the case of a continuous covariate like smoking pack years (SPY), a measure of lifetime exposure to tobacco toxins, a spike at zero can occur. Hence, all non-smokers are generating a peak at zero, while the smoking patients are distributed over the other SPY values. Additionally, the spike might also occur on the right side of the covariate distribution, if a category "heavy smoker" is designed. Here, we will focus on methylation data with a spike at the left or the right of the distribution of a continuous covariate. After the methylation data is generated, analysis is usually performed by preprocessing, quality control, and determination of differentially methylated sites, often performed in pipeline fashion. Hence, the data is processed in a string of methods, which are available in one software package. The pipelines can distinguish between categorical covariates, i.e. for group comparisons or continuous covariates, i.e. for linear regression. The differential methylation analysis is often done internally by a linear regression without checking its inherent assumptions. A spike in the continuous covariate is ignored and can cause biased results. RESULTS: We have reanalysed five data sets, four freely available from ArrayExpress, including methylation data and smoking habits reported by smoking pack years. Therefore, we generated an algorithm to check for the occurrences of suspicious interactions between the values associated with the spike position and the non-spike positions of the covariate. Our algorithm helps to decide if a suspicious interaction can be found and further investigations should be carried out. This is mostly important, because the information on the differentially methylated sites will be used for post-hoc analyses like pathway analyses. CONCLUSIONS: We help to check for the validation of the linear regression assumptions in a methylation analysis pipeline. These assumptions should also be considered for machine learning approaches. In addition, we are able to detect outliers in the continuous covariate. Therefore, more statistical robust results should be produced in methylation analysis using our algorithm as a preprocessing step

Optical dispersion relations for diamondlike carbon films

Ellipsometric measurements on plasma deposited diamondlike amorphous carbon (a-C:H) films were taken in the visible, (E = 1.75 to 3.5 eV). The films were deposited on Si and their properties were varied using high temperature (up to 750 C) anneals. The real (n) and imaginary (k) parts of the complex index of refraction, N, were obtained simultaneously. Following the theory of Forouhi and Bloomer, a least squares fit was used to find the dispersion relations n(E) and k(E). Reasonably good fits were obtained, showing that the theory can be used for a-C:H films. Moreover, the value of the energy gap, Eg, obtained in this way was compared the the Eg value using conventional Tauc plots and reasonably good agreement was obtained

A new technique for oil backstreaming contamination measurements

Due to the large size and the number of diffusion pumps, space simulation chambers cannot be easily calibrated by the usual test dome method for measuring backstreaming from oil diffusion pumps. In addition, location dependent contamination may be an important parameter of the test. The backstreaming contamination was measured in the Space Power Facility (SPF) near Sandusky, OH, the largest space simulation vacuum test chamber in the U.S.. Small clean silicon wafers placed at all desired measurement sites were used as contamination sensors. The facility used diffusion pumps with DC 705 oil. The thickness of the contamination oil film was measured using ellipsometry. Since the oil did not wet the silicon substrate uniformly, two analysis models were developed to measure the oil film: (1) continuous, homogeneous film; and (2) islands of oil with the islands varying in coverage fraction and height. In both cases, the contamination film refractive index was assumed to be that of DC 705. The second model improved the ellipsometric analysis quality parameter by up to two orders of magnitude, especially for the low coverage cases. Comparison of the two models shows that the continuous film model overestimates the oil volume by less than 50 percent. Absolute numbers for backstreaming are in good agreement with published results for diffusion pumps. Good agreement was also found between the ellipsometric results and measurements done by x-ray photoelectron spectroscopy (XPS) and by scanning electron microscopy (SEM) on examples exposed to the same vacuum runs

Stability of antiphase line defects in nanometer-sized boron-nitride cones

We investigate the stability of boron nitride conical sheets of nanometer size, using first-principles calculations. Our results indicate that cones with an antiphase boundary (a line defect that contains either B-B or N-N bonds) can be more stable than those without one. We also find that doping the antiphase boundaries with carbon can enhance their stability, leading also to the appearance of localized states in the bandgap. Among the structures we considered, the one with the smallest formation energy is a cone with a carbon-modified antiphase boundary that presents a spin splitting of about 0.5 eV at the Fermi level.Comment: 5 two-column pages with 2 figures Accepted for publication in Physical Review B (vol 70, 15 Nov.

Ellipsometric study of InGaAs MODFET material

In(x)Ga(1-x)As based MODFET (modulation doped field effect transistor) material was grown by molecular beam epitaxy on semi-insulating InP substrates. Several structures were made, including lattice matched and strained layer InGaAs. All structures also included several layers of In(0.52)Al(0.48)As. Variable angle spectroscopic ellipsometry was used to characterize the structures. The experimental data, together with the calibration function for the constituent materials, were analyzed to yield the thickness of all the layers of the MODFET structure. Results of the ellipsometrically determined thicknesses compare very well with the reflection high energy electron diffraction in situ thickness measurements

Erratum: ‘‘Ellipsometric characterization of In0.52Al0.48As and of modulation doped field effect transistor structures on InP substrates’’ [Appl. Phys. Lett. 62, 1411 (1993)]

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69682/2/APPLAB-63-1-121-1.pd

Dielectric function of InGaAs in the visible

Measurements are reported of the dielectric function of thermodynamically stable In(x)Ga(1-x)As in the composition range 0.3 equal to or less than X = to or less than 0.7. The optically thick samples of InGaAs were made by molecular beam epitaxy (MBE) in the range 0.4 = to or less than X = to or less than 0.7 and by metal-organic chemical vapor deposition (MOCVD) for X = 0.3. The MBE made samples, usually 1 micron thick, were grown on semi-insulating InP and included a strain release structure. The MOCVD sample was grown on GaAs and was 2 microns thick. The dielectric functions were measured by variable angle spectroscopic ellipsometry in the range 1.55 to 4.4 eV. The data was analyzed assuming an optically thick InGaAs material with an oxide layer on top. The thickness of this layer was estimated by comparing the results for the InP lattice matched material, i.e., X = 0.53, with results published in the literature. The top oxide layer mathematically for X = 0.3 and X = 0.53 was removed to get the dielectric function of the bare InGaAs. In addition, the dielectric function of GaAs in vacuum, after a protective arsenic layer was removed. The dielectric functions for X = 0, 0.3, and 0.53 together with the X = 1 result from the literature to evaluate an algorithm for calculating the dielectric function of InGaAs for an arbitrary value of X(0 = to or less than X = to or less than 1) were used. Results of the dielectric function calculated using the algorithm were compared with experimental data

Study of InGaAs based MODFET structures using variable angle spectroscopic ellipsometry

Variable angle spectroscopic ellipsometry was used to estimate the thicknesses of all layers within the optical penetration depth of InGaAs based MODFET structures. Strained and unstrained InGaAs channels were made by MBE on InP substrates and by MOCVD on GaAs substrates. In most cases, ellipsometrically determined thicknesses were within 10 percent of the growth calibration results. The MBE made InGaAs strained layers showed large strain effects, indicating a probable shift in the critical points of their dielectric function toward the InP lattice matched concentration

Cluster: Mission Overview and End-of-Life Analysis

The Cluster mission is part of the scientific programme of the European Space Agency (ESA) and its purpose is the analysis of the Earth's magnetosphere. The Cluster project consists of four satellites. The selected polar orbit has a shape of 4.0 and 19.2 Re which is required for performing measurements near the cusp and the tail of the magnetosphere. When crossing these regions the satellites form a constellation which in most of the cases so far has been a regular tetrahedron. The satellite operations are carried out by the European Space Operations Centre (ESOC) at Darmstadt, Germany. The paper outlines the future orbit evolution and the envisaged operations from a Flight Dynamics point of view. In addition a brief summary of the LEOP and routine operations is included beforehand

Ellipsometric study of Si(0.5)Ge(0.5)/Si strained-layer superlattices

An ellipsometric study of two Si(0.5)Ge(0.5)/Si strained-layer super lattices grown by MBE at low temperature (500 C) is presented, and results are compared with x ray diffraction (XRD) estimates. Excellent agreement is obtained between target values, XRD, and ellipsometry when one of two available Si(x)Ge(1-x) databases is used. It is shown that ellipsometry can be used to nondestructively determine the number of superlattice periods, layer thicknesses, Si(x)Ge(1-x) composition, and oxide thickness without resorting to additional sources of information. It was also noted that we do not observe any strain effect on the E(sub 1) critical point