A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS

Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of basepairs across the genome. Genome-wide association studies (GWAS) may simultaneously screen for copy number-phenotype and SNP-phenotype associations as part of the analytic strategy. However, genome-wide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post-hoc quality control procedures that exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch effects and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of diallelic genotype calls from experimental data to estimate batch- and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in quantile-normalized intensities, while the latter illustrates the robustness of our approach to datasets where as many as 25% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy-number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package CRLMM available at Bioconductor (http:www.bioconductor.org).

Study of and design procedure for dual circularly polarized waveguide slot arrays

For the past sixty years, waveguide slot radiator arrays have played a critical role in microwave radar and communication systems. They feature a well-characterized antenna element capable of direct integration into a low-loss feed structure with highly developed and inexpensive manufacturing processes. Waveguide slot radiators comprise some of the highest performance—in terms of side-lobe-level, efficiency, etc. — antenna arrays ever constructed. A wealth of information is available in the open literature regarding design procedures for linearly polarized waveguide slots. By contrast, despite their presence in some of the earliest published reports, little has been presented to date on array designs for circularly polarized (CP) waveguide slots. Moreover, that which has been presented features a classic traveling wave, efficiency-reducing beam tilt. This work proposes a unique CP waveguide slot architecture which mitigates these problems and a thorough design procedure employing widely available, modern computational tools. The proposed array topology features simultaneous dual-CP operation with grating-lobe-free, broadside radiation, high aperture efficiency, and good return loss. A traditional X-Slot CP element is employed with the inclusion of a slow wave structure passive phase shifter to ensure broadside radiation without the need for performance-limiting dielectric loading. It is anticipated this technology will be advantageous for upcoming polarimetric radar and Ka-band SatCom systems. The presented design methodology represents a philosophical shift away from traditional waveguide slot radiator design practices. Rather than providing design curves and/or analytical expressions for equivalent circuit models, simple first-order design rules – generated via parametric studies — are presented with the understanding that device optimization and design will be carried out computationally. A unit-cell, S-parameter based approach provides a sufficient reduction of complexity to permit efficient, accurate device design with attention to realistic, application-specific mechanical tolerances. A transparent, start-to-finish example of the design procedure for a linear sub-array at X-Band is presented. Both unit cell and array performance is calculated via finite element method simulations. Results are confirmed via good agreement with finite difference, time domain calculations. Array performance exhibiting grating-lobe-free, broadside-scanned, dual-CP radiation with better than 20 dB return loss and over 75% aperture efficiency is presented.

Supported Cu(II) polymer catalysts for aqueous phenol oxidation

Supported Cu(II) polymer catalysts were used for the catalytic oxidation of phenol at 30 degrees C and atmospheric pressure using air and H(2)O(2) as oxidants. Heterogenisation of homogeneous Cu(II) catalysts was achieved by adsorption of Cu(II) salts onto polymeric matrices (poly(4-vinylpyridine), Chitosan). The catalytic active sites were represented by Cu(II) ions and showed to conserve their oxidative activity in heterogeneous catalysis as well as in homogeneous systems. The catalytic deactivation was evaluated by quantifying released Cu(II) ions in solution during oxidation, from where Cu-PVP(25) showed the best leaching levels no more than 5 mg L(-1). Results also indicated that Cu-PVP(25) had a catalytic activity (56% of phenol conversion when initial Cu(II) catalytic content was 200 mg L(Reaction)(-1)) comparable to that of commercial catalysts (59% of phenol conversion). Finally, the balance between activity and copper leaching was better represented by Cu-PVP(25) due to the heterogeneous catalytic activity had 86% performance in the heterogeneous phase, and the rest on the homogeneous phase, while Cu-PVP(2) had 59% and CuO/gamma-Al(2)O(3) 68%.

Preparation of highly-ordered TiO₂ nanotube arrays and their applications in Dye-sensitized solar cells

Titanium oxide is an important semiconductor, which is widely applied for solar cells. In this research, titanium oxide nanotube arrays were synthesized by anodization of Ti foil in the electrolyte composed of ethylene glycol containing 2 vol % H2O and 0.3 wt % NH4F. The voltages of 40V-50V were employed for the anodizing process. Pore diameters and lengths of the TiO2 nanotubes were evaluated by field emission scanning electron microscope (FESEM). The obtained highly-ordered titanium nanotube arrays were exploited to fabricate photoelectrode for the Dye-sensitized solar cells (DSSCS). The TiO2 nanotubes based DSSCS exhibited an excellent performance with a high short circuit current and open circuit voltage as well as a good power conversion efficiency. Those can be attributed to the high surface area and one dimensional structure of TiO2 nanotubes, which could hold a large amount of dyes to absorb light and help electron percolation process to hinder the recombination during the electrons diffusion in the electrolyte.

Enhancing Optical Isolator Performance in Nonreciprocal Waveguide Arrays

We investigate the operation of optical isolators based on magneto-optics waveguide arrays beyond the coupled mode analysis. Semi-vectorial beam propagation simulations demonstrate that evanescent tail coupling and the effects of radiation are responsible for degrading the device’s performance. Our analysis suggests that these effects can be mitigated when the array size is scaled up. In addition, we propose the use of radiation blockers in order to offset some of these effects, and we show that they provide a dramatic improvement in performance. Finally, we also study the robustness of the system with respect to fabrication tolerances using the coupled mode theory. We show that small, random variations in the system’s parameters tend to average out as the number of optical guiding channels increases.

The Effect of the Cu:Fe''' Ratio Upon the Current Efficiency in the Electrolysis of a Copper Sulfate Solution Containing Iron Sulfate

It is a well-known fact that, in the electrolysis of a CuSO4 solution containing iron sulfate, using insoluble anodes, with the depletion of copper, the point is finally reached where the current efficiency becomes zero. This decrease in current efficiency is due to the oxidation of the ferrous sulfate to the ferric condition at the anode, by the oxygen liberated. The resulting ferric sulfate diffuses over to the cathode and there dissolves copper from the cathode according to the chemical equation Cu + Fe2 (SO4)3 = CuSO4 + 2FeSO4. This copper, which has been deposited at the cathode by the electric current, is thus redissolved by the Fe2(SO4)3. The solution of the copper causes at the same time a formation of FeSO4 which in turn diffuses over to the anode and is there oxidized to Fe2(SO4)3; and so the cycle continues, using electric current without rendering useful work. E. H. Larison has noted that a definite amount of ferric salts must be reduced to the ferrous condition before all the copper will remain on the cathode; he does not state, however, just what this point is. L. Addicks has plotted the relation between current efficiency and ferric sulphate content. The existence of the results scattered the points more or less, although the decrease in current efficiency with increased ferric sulphate content is clearly indicated. E. T.Kern has likewise noted that the smaller the amount of copper in the solution, the greater is the reduction of current efficiency. In this work, therefore, it was desired to determine what amount of ferric iron was permissible in a copper sulfate solution of definite concentration before the current efficiency would drop to zero, and what, if any, was the effect of definite Cu:Fe’’’ratio upon the current efficiency of the electrolysis.

Constitution and Specific Gravity of the Ternary Mattes Cu2S-Sb2S3-PbS

The constitution of the ternary mattes Cu2S PbS Sb2S3 has never been completely investigated nor has there been any attempt to draw the complete ternary diagram. The following work is intended to [be] a contribution towards completion of this diagram by determining the specific gravity of different mattes and by pointing out some which show peculiarities of structure.

Constitution and Specific Gravity of the Ternary Mattes Cu2S-FeS-PbS.

The constitution of the ternary mattes CU2S-FeS-PbS has never been completely investigated. Fulton and Goodner 1) have investigated the binary mattes CU2S-FeS, CU2S-PbS, PbSFeS and have shown that the three binaries show eutectics. There has been no attempt however to draw the complete ternary diagram. The following work is intended to be a contribution toward the completion of this diagram by first of all pointing out those mattes which separate on melting into two layers, and second by determining the specific gravities of mattes of different compositions.