Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease. Conclusions: The MDH1 gene is not the cause of RP28-linked arRP. Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration.

Recent Advances in Low CTE and High Density System-on-a-Package (SOP) Substrate with Thin Film Component Integration

The Packaging Research Center has been developing next generation system-on-a-package (SOP) technology with digital, RF, optical, and sensor functions integrated in a single package/module. The goal of this effort is to develop a platform substrate technology providing very high wiring density and embedded thin film passive and active components using PWB compatible materials and processes. The latest SOP baseline process test vehicle has been fabricated on novel Si-matched CTE, high modulus C-SiC composite core substrates using 10mum thick BCB dielectric films with loss tangent of 0.0008 and dielectric constant of 2.65. A semi-additive plating process has been developed for multilayer microvia build-up using BCB without the use of any vacuum deposition or polishing/CMP processes. PWB and package substrate compatible processes such as plasma surface treatment/desmear and electroless/electrolytic pulse reverse plating was used. The smallest line width and space demonstrated in this paper is 6mum with microvia diameters in the 15-30mum range. This build-up process has also been developed on medium CTE organic laminates including MCL-E-679F from Hitachi Chemical and PTFE laminates with Cu-Invar-Cu core. Embedded decoupling capacitors with capacitance density of >500nF/cm2 have been integrated into the build-up layers using sol-gel synthesized BaTiO3 thin films (200-300nm film thickness) deposited on copper foils and integrated using vacuum lamination and subtractive etch processes. Thin metal alloy resistor films have been integrated into the SOP substrate using two methods: (a) NiCrAlSi thin films (25ohms per square) deposited on copper foils (Gould Electronics) laminated on the build-up layers and two step etch process for resistor definition, and (b) electroless plated Ni-W-P thin films (70 ohms to few Kohms per square) on the BCB dielectric by plasma surface treatment and activation. The electrical design and build-up layer structure along- - with key materials and processes used in the fabrication of the SOP4 test vehicle were presented in this paper. Initial results from the high density wiring and embedded thin film components were also presented. The focus of this paper is on integration of materials, processes and structures in a single package substrate for system-on-a-package (SOP) implementation

Functional analysis of ultra high information rates conveyed by rat vibrissal primary afferents

Sensory receptors determine the type and the quantity of information available for perception. Here, we quantified and characterized the information transferred by primary afferents in the rat whisker system using neural system identification. Quantification of ``how much'' information is conveyed by primary afferents, using the direct method (DM), a classical information theoretic tool, revealed that primary afferents transfer huge amounts of information (up to 529 bits/s). Information theoretic analysis of instantaneous spike-triggered kinematic stimulus features was used to gain functional insight on ``what'' is coded by primary afferents. Amongst the kinematic variables tested-position, velocity, and acceleration-primary afferent spikes encoded velocity best. The other two variables contributed to information transfer, but only if combined with velocity. We further revealed three additional characteristics that play a role in information transfer by primary afferents. Firstly, primary afferent spikes show preference for well separated multiple stimuli (i.e., well separated sets of combinations of the three instantaneous kinematic variables). Secondly, neurons are sensitive to short strips of the stimulus trajectory (up to 10 ms pre-spike time), and thirdly, they show spike patterns (precise doublet and triplet spiking). In order to deal with these complexities, we used a flexible probabilistic neuron model fitting mixtures of Gaussians to the spike triggered stimulus distributions, which quantitatively captured the contribution of the mentioned features and allowed us to achieve a full functional analysis of the total information rate indicated by the DM. We found that instantaneous position, velocity, and acceleration explained about 50% of the total information rate. Adding a 10 ms pre-spike interval of stimulus trajectory achieved 80-90%. The final 10-20% were found to be due to non-linear coding by spike bursts.

Fabrication and mechanisms of densification of ZrB2-based ultra high temperature ceramics by reactive hot pressing

Dense ZrB2-SiC (25-30 vol%) composites have been produced by reactive hot pressing using stoichiometric Zr, B4C, C and Si powder mixtures with and without Ni addition at 40 MPa, 1600 degrees C for 60 min. Nickel, a common additive to promote densification, is shown not to be essential; the presence of an ultra-fine microstructure containing a transient plastic ZrC phase is suggested to play a key role at low temperatures, while a transient liquid phase may be responsible at temperatures above 1350 degrees C. Hot Pressing of non-stoichiometric mixture of Zr, B4C and Si at 40 MPa, 1600 degrees C for 30 min resulted in ZrB2-ZrCx-SiC (15 vol%) composites of similar to 98% RD.

High vacuum tribology of polycrystalline diamond coatings

Polycrystalline diamond coatings have been grown on unpolished side of Si(100) wafers by hot filament chemical vapour deposition process. The morphology of the grown coatings has been varied from cauliflower morphology to faceted morphology by manipulation of the growth temperature from 700 degrees C to 900 degrees C and methane gas concentration from 3% to 1.5%. It is found that the coefficient of friction of the coatings under high vacuum of 133.32 x 10(-7) Pa (10(-7) torr) with nanocrystalline grains can be manipulated to 0.35 to enhance tribological behaviour of bare Si substrates.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease.

Epoxy resin chamber for high voltage breakdown studies in high vacuum

As the study of electrical breakdown phenomena in vacuum systems, gains more importance, a thorough understanding of the breakdown mechanism at high voltages necessitates a chamber for experimental studies. An epoxy-resin chamber has been constructed by casting ring sections which were joined together. The advantages of such a chamber over the conventional metal or glass chamber are given especially as regards the electric field configuration, high voltage lead-in, and the ease of construction. Special facilities can be incorporated while constructing the chamber which makes it more versatile; for example, in pre-breakdown current measurements, electron beam focusing studies, etc.

Reactive hot pressing of ZrB2-ZrCx ultra-high temperature ceramic composites with the addition of SiC particulate

Starting with non-stoichiometric Zr-B4C powder mixture ZrB2-ZrC matrix composites with SiC particulate addition have been made. It was found that variable amounts (5-25 vol%) of SiC could be incorporated and reactively hot pressed (RHPed) to relative densities of 97-99% at 1400-1500 degrees C. This technique has the potential to fabricate ZrB2-based matrices at low temperatures with a variety of reinforcements whose composition and volume fraction are not limited by stoichiometric considerations. The hardness of the composites is in the range of 17-22 GPa. (C) 2010 Elsevier Ltd. All rights reserved.

Novel Mn-doped chalcopyrites

Heavily Mn-doped II-VI-V-2 semiconductors, such as CdGeP2 and ZnGeP2 have been prepared by depositing Mn on single crystalline substrate at nearly 400 T in an ultra high vacuum chamber. Well-defined ferromagnetic hysteresis with a saturation behavior appears in the magnetization curve up to above room temperature. The chemical states of the ZDGeP(2):Mn interface has been clarified by a careful in situ photoemission spectroscopy. The as-prepared surface consists of Ge-rich, metallic Mn compound. In and below the sub-surface region, dilute divalent Mn species as precursors of the DMS phase exist. No MnP phase was observed at any stage of the depth profile. Theoretical band-calculation suggests that the system with vacancies (Cd, V-c, Mn)GeP2 or a non-stoichiometric (Cd, Ge, Mn)GeP2 are ferromagnetic and energetically stable although ferromagnetism is not stable in a stoichiometric compound (Cd, Mn)GeP2. (C) 2003 Elsevier Ltd. All rights reserved.

Physical chemistry of the reduction of calcium oxide with aluminium in vacuum

The physical chemistry of "aluminothermic" reduction of calcium oxide in vacuum is analyzed. Basic thermodynamic data required for the analysis have been generated by a variety of experiments. These include activity measurements in liquid AI-Ca alloys and determination of the Gibbs energies of formation of calcium aluminates. These data have been correlated with phase relations in the Ca-AI-0 system at 1373 K. The various stages of reduction, the end products and the corresponding equilibrium partial pressures of calcium have been established from thermodynamic considerations. In principle, the recovery of calcium can be improved by reducing the pressure in the reactor. However,, the cost of a high vacuum system and the enhanced time for reduction needed to achieve higher yields makes such a practice uneconomic. Aluminum contamination of calcium also increases at low pressures. The best compromise is to carry the reduction up to the stage where 3CaO-Al,O, is formed as the product. This corresponds to an equilibrium calcium partial pressure of 31.3 Pa at 1373 K and 91.6 Pa at 1460 K. Calcium can be extracted at this pressure using mechanical pumps in approximately 8 to 15 hr, depending on the size and the fill ratio of the retort and porosity of the charge briquettes.

Investigation on the High Vacuum Tribological Characteristics of Surface Treated Nuclear Grade Stainless Steel Type AISI 316 LN at 25 to 500 degrees C

Although some researchers have published friction and wear data of Plasma Nitride (PN) coatings, the tribological behavior of PN/PN Pairs in high vacuum environment has not been published so far In order to bridge this knowledge gap, tribological tests under dry conditions have been conducted on PN/PN Pairs for varying temperatures of 25, 200, 400 and 500 degrees C in high vacuum (1.6 x 10(-4) bar) environment. The PN coatings showed good wear resistance layer on the ring surface. The PN coatings were removed only from the pin surface for all the tests since it contacts at a point. The friction and wear were low at lower temperatures and it eliminated adhesion between the contact surfaces until the coating was completely removed from the pin surface. (C) 2011 Journal of Mechanical Engineering. All rights reserved.

Fracture Analysis of High strength and Ultra high strength Concrete beams by using Finite Element Method

This paper presents the details of nonlinear finite element analysis (FEA) of three point bending specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete (UHSC). Brief details about characterization and experimentation of HSC, HSC1 and UHSC have been provided. Cracking strength criterion has been used for simulation of crack propagation by conducting nonlinear FEA. The description about FEA using crack strength criterion has been outlined. Bi-linear tension softening relation has been used for modeling the cohesive stresses ahead of the crack tip. Numerical studies have been carried out on fracture analysis of three point bending specimens. It is observed from the studies that the computed values from FEA are in very good agreement with the corresponding experimental values. The computed values of stress vs crack width will be useful for evaluation of fracture energy, crack tip opening displacement and fracture toughness. Further, these values can also be used for crack growth study, remaining life assessment and residual strength evaluation of concrete structural components.

Evaluation of Fracture Parameters by Double-G, Double-K Models and Crack Extension Resistance for High Strength and Ultra High Strength Concrete Beams

This paper presents the advanced analytical methodologies such as Double- G and Double - K models for fracture analysis of concrete specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete. Brief details about characterization and experimentation of HSC, HSC1 and UHSC have been provided. Double-G model is based on energy concept and couples the Griffith's brittle fracture theory with the bridging softening property of concrete. The double-K fracture model is based on stress intensity factor approach. Various fracture parameters such as cohesive fracture toughness (4), unstable fracture toughness (K-Ic(c)), unstable fracture toughness (K-Ic(un)) and initiation fracture toughness (K-Ic(ini)) have been evaluated based on linear elastic fracture mechanics and nonlinear fracture mechanics principles. Double-G and double-K method uses the secant compliance at the peak point of measured P-CMOD curves for determining the effective crack length. Bi-linear tension softening model has been employed to account for cohesive stresses ahead of the crack tip. From the studies, it is observed that the fracture parameters obtained by using double - G and double - K models are in good agreement with each other. Crack extension resistance has been estimated by using the fracture parameters obtained through double - K model. It is observed that the values of the crack extension resistance at the critical unstable point are almost equal to the values of the unstable fracture toughness K-Ic(un) of the materials. The computed fracture parameters will be useful for crack growth study, remaining life and residual strength evaluation of concrete structural components.

Fatigue Crack Growth Study and Remaining Life Assessment of High Strength and Ultra High Strength Concrete Beams

This paper presents the details of crack growth study and remaining life assessment of concrete specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete (UHSC). Flexural fatigue tests have been conducted on HSC, HSC1 and UHSC beams under constant amplitude loading with a stress ratio of 0.2. It is observed from the studies that (i) the failure patterns of HSC1 and UHSC beams indicate their ductility as the member was intact till the crack propagated up to 90% of the beam depth and (ii) the remaining life decreases with increase of notch depth (iii) the failure of the specimen is influenced by the frequency of loading. A ``Net K'' model has been proposed by using non-linear fracture mechanics principles for crack growth analysis and remaining life prediction. SIF (K) has been computed by using the principle of superposition. SIP due to the cohesive forces applied on the effective crack face inside the process zone has been obtained through Green's function approach by applying bi-linear tension softening relationship to consider the cohesive the stresses acting ahead of the crack tip. Remaining life values have been have been predicted and compared with the corresponding experimental values and observed that they are in good agreement with each other.

Estimation of fracture properties for high strength and ultra high strength concrete beams and size effect

This article presents the details of estimation of fracture parameters for high strength concrete (HSC, HSC1) and ultra high strength concrete (UHSC). Brief details about characterization of ingredients of HSC, HSC1 and UHSC have been provided. Experiments have been carried out on beams made up of HSC, HSC1 and UHSC considering various sizes and notch depths. Fracture characteristics such as size independent fracture energy (G(f)), size of fracture process zone (C-f), fracture toughness (K-IC) and crack tip opening displacement (CTODc) have been estimated based on the experimental observations. From the studies, it is observed that (i) UHSC has high fracture energy and ductility inspite of having a very low value of C-f; (ii) relatively much more homogeneous than other concretes, because of absence of coarse aggregates and well-graded smaller size particles; (iii) the critical SIF (K-IC) values are increasing with increase of beam depth and decreasing with increase of notch depth. Generally, it can be noted that there is significant increase in fracture toughness and CTODc. They are about 7 times in HSC1 and about 10 times in UHSC compared to those in HSC; (iv) for notch-to-depth ratio 0.1, Bazant's size effect model slightly overestimates the maximum failure loads compared to experimental observations and Karihaloo's model slightly underestimates the maximum failure loads. For the notch-to-depth ratio ranging from 0.2 to 0.4 for the case of UHSC, it can be observed that, both the size effect models predict more or less similar maximum failure loads compared to corresponding experimental values.