Integration of miRNA and mRNA expression with DNA copy number of Ewing sarcoma cell lines

Ewing sarcoma is an aggressive and poorly differentiated malignancy of bone and soft tissue. It primarily affects children, adolescents, and young adults, with a slight male predominance. It is characterized by a translocation between chromosomes 11 and 22 resulting in the EWSR1-FLI1fusion transcription factor. The aim of this study is to identify putative Ewing sarcoma target genes through an integrative analysis of three microarray data sets. Array comparative genomic hybridization is used to measure changes in DNA copy number, and analyzed to detect common chromosomal aberrations. mRNA and miRNA microarrays are used to measure expression of protein-coding and miRNA genes, and these results integrated with the copy number data. Chromosomal aberrations typically contain also bystanders in addition to the driving tumor suppressor and oncogenes, and integration with expression helps to identify the true targets. Correlation between expression of miRNAs and their predicted target mRNAs is also evaluated to assess the results of post-transcriptional miRNA regulation on mRNA levels. The highest frequencies of copy number gains were identified in chromosome 8, 1q, and X. Losses were most frequent in 9p21.3, which also showed an enrichment of copy number breakpoints relative to the rest of the genome. Copy number losses in 9p21.3 were found have a statistically significant effect on the expression of MTAP, but not on CDKN2A, which is a known tumor-suppressor in the same locus. MTAP was also down-regulated in the Ewing sarcoma cell lines compared to mesenchymal stem cells. Genes exhibiting elevated expression in association with copy number gains and up-regulation compared to the reference samples included DCAF7, ENO2, MTCP1, andSTK40. Differentially expressed miRNAs were detected by comparing Ewing sarcoma cell lines against mesenchymal stem cells. 21 up-regulated and 32 down-regulated miRNAs were identified, includingmiR-145, which has been previously linked to Ewing sarcoma. The EWSR1-FLI1 fusion gene represses miR-145, which in turn targets FLI1 forming a mutually repressive feedback loop. In addition higher expression linked to copy number gains and compared to mesenchymal stem cells, STK40 was also found to be a target of four different miRNAs that were all down-regulated in Ewing sarcoma cell lines compared to the reference samples. SLCO5A1 was identified as the only up-regulated gene within a frequently gained region in chromosome 8. This region was gained in over 90 % of the cell lines, and also with a higher frequency than the neighboring regions. In addition, SLCO5A1 was found to be a target of three miRNAs that were down-regulated compared to the mesenchymal stem cells.

An accurate numerical integration scheme for finite rotations using rotation vector parametrization

A numerical integration procedure for rotational motion using a rotation vector parametrization is explored from an engineering perspective by using rudimentary vector analysis. The incremental rotation vector, angular velocity and acceleration correspond to different tangent spaces of the rotation manifold at different times and have a non-vectorial character. We rewrite the equation of motion in terms of vectors lying in the same tangent space, facilitating vector space operations consistent with the underlying geometric structure. While any integration algorithm (that works within a vector space setting) may be used, we presently employ a family of explicit Runge-Kutta algorithms to solve this equation. While this work is primarily motivated out of a need for highly accurate numerical solutions of dissipative rotational systems of engineering interest, we also compare the numerical performance of the present scheme with some of the invariant preserving schemes, namely ALGO-C1, STW, LIEMIDEA] and SUBCYC-M. Numerical results show better local accuracy via the present approach vis-a-vis the preserving algorithms. It is also noted that the preserving algorithms do not simultaneously preserve all constants of motion. We incorporate adaptive time-stepping within the present scheme and this in turn enables still higher accuracy and a `near preservation' of constants of motion over significantly longer intervals. (C) 2010 The Franklin Institute. Published by Elsevier Ltd. All rights reserved.

Symplectic integration of nonlinear Hamiltonian systems

There exist several standard numerical methods for integrating ordinary differential equations. However, if one is interested in integration of Hamiltonian systems, these methods can lead to wrong results. This is due to the fact that these methods do not explicitly preserve the so-called 'symplectic condition' (that needs to be satisfied for Hamiltonian systems) at every integration step. In this paper, we look at various methods for integration that preserve the symplectic condition.

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

Highly fluorescent GFPm2+-based genome integration-proficient promoter probe vector to study Mycobacterium tuberculosis promoters in infected macrophages

Study of activity of cloned promoters in slow-growing Mycobacterium tuberculosis during long-term growth conditions in vitro or inside macrophages, requires a genome-integration proficient promoter probe vector, which can be stably maintained even without antibiotics, carrying a substrate-independent, easily scorable and highly sensitive reporter gene. In order to meet this requirement, we constructed pAKMN2, which contains mycobacterial codon-optimized gfpm2+ gene, coding for GFPm2+ of highest fluorescence reported till date, mycobacteriophage L5 attP-int sequence for genome integration, and a multiple cloning site. pAKMN2 showed stable integration and expression of GFPm2+ from M. tuberculosis and M. smegmatis genome. Expression of GFPm2+, driven by the cloned minimal promoters of M. tuberculosis cell division gene, ftsZ (MtftsZ), could be detected in the M. tuberculosis/pAKMN2-promoter integrants, growing at exponential phase in defined medium in vitro and inside macrophages. Stable expression from genome-integrated format even without antibiotic, and high sensitivity of detection by flow cytometry and fluorescence imaging, in spite of single copy integration, make pAKMN2 useful for the study of cloned promoters of any mycobacterial species under long-term in vitro growth or stress conditions, or inside macrophages.

Electrochemical Integration of Graphene with Light-Absorbing Copper-Based Thin Films

We present an electrochemical route for the integration of graphene with light-sensitive copper-based alloys used in optoelectronic applications. Graphene grown using chemical vapor deposition (CVD) transferred to glass is found to be a robust substrate on which photoconductive CuxS films of 1-2 mu m thickness can be deposited. The effect of growth parameters on the morphology and photoconductivity of CuxS films is presented. Current-voltage (I-V) characterization and photoconductivity decay experiments are performed with graphene as one contact and silver epoxy as the other.

Surface reconstruction from disparate shading: an integration of shape-from-shading and stereopsis

A cooperative integration of stereopsis and shape-from-shading is presented. The integration makes the process of D surface reconstruction better constrained and more reliable. It also obviates the need for surface boundary conditions, and explicit information about the surface albedo and the light source direction, which can now be estimated in an iterative manner

Integration of speckle de-noising and image segmentation using synthetic aperture radar image for flood extent extraction

Flood is one of the detrimental hydro-meteorological threats to mankind. This compels very efficient flood assessment models. In this paper, we propose remote sensing based flood assessment using Synthetic Aperture Radar (SAR) image because of its imperviousness to unfavourable weather conditions. However, they suffer from the speckle noise. Hence, the processing of SAR image is applied in two stages: speckle removal filters and image segmentation methods for flood mapping. The speckle noise has been reduced with the help of Lee, Frost and Gamma MAP filters. A performance comparison of these speckle removal filters is presented. From the results obtained, we deduce that the Gamma MAP is reliable. The selected Gamma MAP filtered image is segmented using Gray Level Co-occurrence Matrix (GLCM) and Mean Shift Segmentation (MSS). The GLCM is a texture analysis method that separates the image pixels into water and non-water groups based on their spectral feature whereas MSS is a gradient ascent method, here segmentation is carried out using spectral and spatial information. As test case, Kosi river flood is considered in our study. From the segmentation result of both these methods are comprehensively analysed and concluded that the MSS is efficient for flood mapping.

Noncoherent Integration for Signal Detection: Analysis Under Model Uncertainties

The performance of postdetection integration (PDI) techniques for the detection of Global Navigation Satellite Systems (GNSS) signals in the presence of uncertainties in frequency offsets, noise variance, and unknown data-bits is studied. It is shown that the conventional PDI techniques are generally not robust to uncertainty in the data-bits and/or the noise variance. Two new modified PDI techniques are proposed, and they are shown to be robust to these uncertainties. The receiver operating characteristics (ROC) and sample complexity performance of the PDI techniques in the presence of model uncertainties are analytically derived. It is shown that the proposed methods significantly outperform existing methods, and hence they could become increasingly important as the GNSS receivers attempt to push the envelope on the minimum signal-to-noise ratio (SNR) for reliable detection.

An early in-situ stress signature of the AlN-Si pre-growth interface for successful integration of nitrides with (111) Si

The integration of Metal Organic Chemical Vapor Deposition (MOCVD) grown group III-A nitride device stacks on Si (111) substrates is critically dependent on the quality of the first AlN buffer layer grown. A Si surface that is both oxide-free and smooth is a primary requirement for nucleating such layers. A single parameter, the AlN layer growth stress, is shown to be an early (within 50 nm), clear (<0.5 GPa versus > 1GPa), and fail-safe indicator of the pre-growth surface, and the AlN quality required for successful epitaxy. Grain coalescence model for stress generation is used to correlate growth stress, the AlN-Si interface, and crystal quality. (C) 2013 AIP Publishing LLC.

AIM-Spice Integration of a Recursive Model for Threshold Voltage Shift in Thin Film Transistors

Non-crystalline semiconductor based thin film transistors are the building blocks of large area electronic systems. These devices experience a threshold voltage shift with time due to prolonged gate bias stress. In this paper we integrate a recursive model for threshold voltage shift with the open source BSIM4V4 model of AIM-Spice. This creates a tool for circuit simulation for TFTs. We demonstrate the integrity of the model using several test cases including display driver circuits.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.