Different Types Of Arrays Research Articles

Methscore: a comprehensive R function for DNA methylation-based health predictors.

DNA methylation-based predictors of various biological metrics have been widely published and are becoming valuable tools in epidemiologic studies of epigenetics and personalized medicine. However, generating these predictors from original source software and web servers is complex and time consuming. Furthermore, different predictors were often derived based on data from different types of arrays, where array differences and batch effects can make predictors difficult to compare across studies. We integrate these published methods into a single R function to produce 158 previously published predictors for chronological age, biological age, exposures, lifestyle traits and serum protein levels using both classical and principal component-based methods. To mitigate batch and array differences, we also provide a modified RCP method (ref-RCP) that normalize input DNA methylation data to reference data prior to estimation. Evaluations in real datasets show that this approach improves estimate precision and comparability across studies. The function was included in software package ENmix, and is freely available from Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html).

Nanofluid Flow of Alumina–Copper/Water Through Isotropic Porous Arrays of Periodic Square Cylinders: Mixed Convection and Competent Array Shape

Abstract The flow of hybrid alumina–copper/water nanofluid with mixed convection heat transfer from multiple square cylinders arranged in three different types of arrays, namely equilateral triangle (ET), rotated square (RS), and rotated rhombus (RR) in a heat exchanger, has never been studied before the present study. Navier–Stokes and energy equations with a periodic boundary condition in the transverse direction for all three array types having the same porosity are solved with the finite volume methodology. The combined effect of aiding buoyancy (Richardson number 0–2), the configuration of square cylinders, and hybrid nanoparticle volume fraction (0-0.06) on the flow dynamics and their impact on the overall heat transfer phenomenon through three different array configurations is thoroughly elucidated. The arrays’ overall drag and friction coefficient increases with an increase in the strength of aiding buoyancy and nanoparticle volume fraction. An increment in Richardson number, and nanoparticle volume fraction, causes thermal boundary layer thinning and results in higher heat transfer rates across all three arrays. With an increase in Ri from 0 to 2 at a nanoparticle volume fraction of 0.06, the mean Nusselt number of ET, RS, and RR arrays is increased by 161%, 5%, and 32%, respectively. While, with an increase in nanoparticle volume fraction from 0 to 0.06 at Ri = 2, the mean Nusselt number of ET, RS, and RR arrays is augmented by 17%, 6%, and 9%, respectively. Finally, the efficient array configuration in terms of fluid-thermal behavior is proposed to design various heat-exchange systems under differing operating conditions.

Separation of nonstationary sound fields based on the time-domain equivalent source method with single layer pressure-velocity measurements.

This paper proposes a sound field separation technique based on the time-domain equivalent source method with single layer pressure-velocity measurements to extract the nonstationary sound field radiated by the target source in a reverberant environment. This technique constructs a formulation that relates the pressures and particle velocities on a measurement surface to the strengths of time-domain equivalent sources arranged for modelling the outgoing and incoming waves. By solving the strengths of time-domain equivalent sources, the sounds coming from different sides of the measurement surface can be separated independently. In the proposed technique, the use of a time-domain equivalent source model allows the measurement surface to be arbitrarily shaped, thus providing the ability to analyze the arbitrarily shaped sources in a reverberant environment. Numerical simulations investigated the performance of the proposed technique when using different types of arrays, including planar, semi-cylindrical, and semi-spherical arrays, and an experiment with three loudspeakers located at two sides of the measurement surface was carried out to test the validity of the proposed technique. Both numerical and experimental results demonstrate that the proposed technique can remove the influence of disturbing sources in both time and space domains and separate out the target sound fields effectively.

Effect of morphology of nanoparticles on performance of transparent display

Nanoparticles based transparent display is one of the most successful methods to realize transparent monitors. Also, an array of nanoparticles, especially aperiodic arrangements, plays an important role in this case. Normally, when one talks about nanoparticles, the spherical morphology appears in mind, in which it is possible to implement different morphology for nanoparticles. In this paper, six different classes of morphologies with various arrangements, such as periodic array and deterministic aperiodic arrays, have been investigated to propose a high-performance transparent display. We compare different morphologies of Si–SiO2 nanoparticles at RGB (Red, Green, Blue) wavelengths in different types of arrays to find the highest scattering cross-section. Our calculations and figure of merit depending on the optical properties of nanoparticles, such as the resonance wavelength, the extinction, scattering and absorption cross-section, and the scattering to absorption ratio (SAR). We will show that in the proposed structures, there are suitable parameters to provide higher scattering cross-section as well as narrow bandwidth in which that is equivalent to introduce the maximum transparency and contrast ratio of transparent monitor. We use the Finite-Difference Time-Domain (FDTD) numerical method to simulate and calculate the deterministic aperiodic and periodic arrays of nanoparticles. Finally, we obtain the absorption and scattering cross-sections for six classes of nanoparticles: Cube, Sphere, Disk, Oblate ellipse, Prolate ellipse, and Pyramid into aperiodic and periodic arrays.

Turbulent swirling impinging jet arrays: A numerical study on fluid flow and heat transfer

Impinging jets are generally utilized as an effective medium of heat and mass transfer. Various stream orientations and swirl effect may be a potential candidate to further improve the heat transfer characteristics. This paper numerically examines two different types of arrays of circular multiple jets and the effect of swirl on jets that impinges vertically onto a flat surface situated at a fixed vertical separation distance H = 2D, D the nozzle diameter and at Reynolds number equal to 11,600. In this regard, three-dimensional simulation was performed using finite volume method whereas turbulence was described by SST k-ω model. The results demonstrate that staggered arrangement ensures better mixing and higher velocity as well as heat transfer. The strength of recirculation for swirl jet is larger than that of non-swirl jet. Maximum pressure coefficient occurs at individual stagnation point of each jet, with a secondary peak between two neighboring jets. Strong heat transfer is predicted to occur at around the stagnation region for each non-swirling jet and between the neighboring jets for swirling jets. Turbulences are intense around the periphery of each jet and they coalesce as it moves downward.

Reduced-scale ultrasonic modelling of Rayleigh wave transmission over seismic barriers formed by periodic arrays of vertical holes

Seismic barriers are used widely to protect buildings from traffic-induced ground vibrations, mainly from propagating Rayleigh surface waves. Experimental investigations of real size seismic barriers at frequencies typical for traffic-induced ground vibrations, i.e. at 10-100 Hz, are costly and time consuming. In the present work, an alternative and much less expensive approach is proposed - a reduced-scale experimental modelling using ultrasonic Rayleigh wave propagation over very small-scale replicas of real seismic barriers. Experimental investigations of propagation of Rayleigh wave pulses with the central frequency of 1 MHz have been carried out for seismic barriers formed by periodic arrays of vertical holes in Aluminium samples. Measurements of transmission and reflection coefficients of Rayleigh waves for different types of arrays and for different incident angles have been carried out and compared with the earlier published results obtained for real seismic barriers.

Main Lobe Control of a Beam Tilting Antenna Array Laid on a Deformable Surface

The projection method (PM) is a simple and low-cost pattern recovery technique that already proved its effectiveness in retrieving the radiation properties of different types of arrays that change shape in time. However, when dealing with deformable beam-tilting arrays, this method requires to compute new compensating phase shifts every time that the main lobe is steered, since these shifts depend on both the deformation geometry and the steering angle. This tight requirement causes additional signal processing and complicates the prediction of the array behavior, especially if the deformation geometry is not a priori known: this can be an issue since the PM is mainly used for simple and low-cost systems. In this letter, we propose a simplification of this technique for beam-tilting arrays that requires only basic signal processing. In fact the phase shifts that we use are the sum of two components: one can be directly extracted from strain sensor data that measure surface deformation and the other one can be precomputed according to basic antenna theory. The effectiveness of our approach has been tested on two antennas: a 4 × 4 array (trough full-wave simulations and measurements) and on an 8 × 8 array (trough full-wave simulations) placed on a doubly wedge-shaped surface with a beam tilt up to 40 degrees.

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

BackgroundAlternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes. Unfortunately, aberrant splicing events do occur which have been linked to genetic disorders, such as several types of cancer and neurodegenerative diseases (Fan et al., Theor Biol Med Model 3:19, 2006). Therefore, understanding the mechanism of alternative splicing and identifying the difference in splicing events between diseased and healthy tissue is crucial in biomedical research with the potential of applications in personalized medicine as well as in drug development.ResultsWe propose a linear mixed model, Random Effects for the Identification of Differential Splicing (REIDS), for the identification of alternative splicing events. Based on a set of scores, an exon score and an array score, a decision regarding alternative splicing can be made. The model enables the ability to distinguish a differential expressed gene from a differential spliced exon. The proposed model was applied to three case studies concerning both exon and HTA arrays.ConclusionThe REIDS model provides a work flow for the identification of alternative splicing events relying on the established linear mixed model. The model can be applied to different types of arrays.

Seafloor mapping with a cylindrical array

Seafloor mapping is conducted with different types of arrays. Single beam mapping systems are often constructed with piston arrays. Linear arrays are used for both side scan sonar and for multibeam echo sounders. These conventional approaches to seafloor mapping are typically constrained to a single observation of any one point on the seafloor for any one pass of a moving vessel. A less conventional cylindrical array offers the opportunity to observe the majority of the seafloor from different perspectives but with the same angle with a single pass. This has the potential to improve the resulting depth estimates and seafloor backscatter products. In 2016, a Simrad Omnisonar was used to demonstrate seafloor mapping with a cylindrical array. While this array is designed for observing fish schools, a small area was successfully mapped and the results compared with a conventional bathymetric mapping system. Observations on the benefits and challenges of this approach to seafloor mapping will be discussed.

SURVEY PAPER ON ADAPTIVE BEAMFORMING LMS,NLMS AND RLS ALGORITHMS FOR SMART ANTENNA SYSTEM

Smart antenna system is used to maximize the output power of signal in desired direction and minimize the power in unwanted direction. Smart antenna system consists of multiple numbers of elements. Basic concept in smart antenna technology is beam forming, it is mainly used to improve signal to noise ratio. Beam forming signal processing technique used in sensor arrays for directional signal transmission and reception. And it possible by combining the elements in phased array in such a way that signals at particular angles experiences constructive interference and others are destructive interferences. In smart antenna system we are using various algorithms to calculate the weights of smart antenna arrays to increase the output in desired direction and reduce the power in unwanted direction We are using different types of arrays i.e. linear array, circular array, planar array . Different algorithms are used to adjust the weights of the smart antenna system Basically Weights are nothing but Amplitude and phase of the signal. Adaptive algorithms update the weights of the array elements. LMS algorithm provides less convergence speed, and that is depends on the step size. LMS algorithm is widely used in adaptive filter due to its relative low computational complexity, good stability and relatively good robustness against the implementation errors. To improve the convergence rate NLMS algorithm is used. LMS algorithm having constant step size but in NLMS algorithm step size is depends on data at each iteration. Whereas RLS algorithm having minimum bit error rate but it required more computations than the LSM algorithm.

A Dual Curvature Shell Phased Array Simulation for Delivery of High Intensity Focused Ultrasound

This paper describes the design and the evaluation for a simulation model for the dual curvature ultrasound phased array. The main goal of this simulation is to enhance the usage of dual curvature ultrasound phased array in ultrasound therapy with three dimensional phased arrays. In our simulation, focusing the total acoustic power within a specific phase can be controlled dynamically for each individual element. Moreover, a 45? steering angle in x-z plan was achieved. A software based simulation using MATLAB was performed to verify focusing and steering capability of the proposed array for three different types of arrays. The results showed a safety improvement for both of focusing and steering angle for the dual curvature phased array compared with planner and spherical types. Furthermore, the phased arrays have three different shapes; the planner phased array which was used as reference, spherical, and dual curvature shapes. Based on the conducted experiments, the results showed that the spherical and dual curvature shapes have a better focusing and steering angle generally compared with the reference phased array. As well as, the dual curvature phased array has additional capability of focusing outside the geometric volume, without any grating lobe effects.

Mutual Coupling in Phased Arrays: A Review

The mutual coupling between antenna elements affects the antenna parameters like terminal impedances, reflection coefficients and hence the antenna array performance in terms of radiation characteristics, output signal-to-interference noise ratio (SINR), and radar cross section (RCS). This coupling effect is also known to directly or indirectly influence the steady state and transient response, the resolution capability, interference rejection, and direction-of-arrival (DOA) estimation competence of the array. Researchers have proposed several techniques and designs for optimal performance of phased array in a given signal environment, counteracting the coupling effect. This paper presents a comprehensive review of the methods that model and mitigate the mutual coupling effect for different types of arrays. The parameters that get affected due to the presence of coupling thereby degrading the array performance are discussed. The techniques for optimization of the antenna characteristics in the presence of coupling are also included.

Gene Expression Profiling of Embryonic Human Neural Stem Cells and Dopaminergic Neurons from Adult Human Substantia Nigra

Neural stem cells (NSC) with self-renewal and multipotent properties serve as an ideal cell source for transplantation to treat neurodegenerative insults such as Parkinson's disease. We used Agilent's and Illumina Whole Human Genome Oligonucleotide Microarray to compare the genomic profiles of human embryonic NSC at a single time point in culture, and a multicellular tissue from postmortem adult substantia nigra (SN) which are rich in dopaminergic (DA) neurons. We identified 13525 up-regulated genes in both cell types of which 3737 (27.6%) genes were up-regulated in the hENSC, 4116 (30.4%) genes were up-regulated in the human substantia nigra dopaminergic cells, and 5672 (41.93%) were significantly up-regulated in both cell population. Careful analysis of the data that emerged using DAVID has permitted us to distinguish several genes and pathways that are involved in dopaminergic (DA) differentiation, and to identify the crucial signaling pathways that direct the process of differentiation. The set of genes expressed more highly at hENSC is enriched in molecules known or predicted to be involved in the M phase of the mitotic cell cycle. On the other hand, the genes enriched in SN cells include a different set of functional categories, namely synaptic transmission, central nervous system development, structural constituents of the myelin sheath, the internode region of axons, myelination, cell projection, cell somata, ion transport, and the voltage-gated ion channel complex. Our results were also compared with data from various databases, and between different types of arrays, Agilent versus Illumina. This approach has allowed us to confirm the consistency of our obtained results for a large number of genes that delineate the phenotypical differences of embryonic NSCs, and SN cells.

Photovoltaic generator modelling to improve numerical robustness of EMT simulation

Numerical simulation is an indispensable tool for studying photovoltaic (PV) systems, to derive component ratings, optimise protections, design controllers as well as to evaluate the impact of embedded generation on distribution system operation. In EMT simulation, the non-linear equations representing the PV generators are separated from the linear equations of the rest of the power system. This technique presents high computational efficiency but introduces a one-step delay, which can cause problems of numerical instability. These problems are particularly evident when the PV generator is represented by multiple single-diode equivalent circuits, such as in the cases of PV generators composed of different types of arrays or subject to partial shading or interfaced by multilevel inverters. To overcome such problems, in this paper a new approach is proposed to include the PV generator model into EMT simulation. A convergence analysis gives proof of the obtained improvements, which are also confirmed by numerical results. The robustness of the proposed technique is tested by simulation of an IEEE benchmark system in the cases of partial shading and of electric faults.

Biologically inspired achromatic waveplates for visible light

Waveplates are planar devices used in optics and optoelectronics to change the polarization state of light. Made of anisotropic dielectric materials such as crystals and thin films, waveplates are not known to exhibit achromatic performance over the visible regime. Inspired by the microvillar structure of R8 cells functioning as polarization converters in the eyes of stomatopod crustaceans, we conceived, designed, fabricated and tested periodically multilayered structures comprising two different types of arrays of nanorods. Morphologically analogous to the ocular cells, here we show that the periodically multilayered structures can function as achromatic waveplates over the visible regime.

Comparison of High-Density Short Oligonucleotide Microarray Platforms

Various gene expression DNA microarray platforms have been developed and often similar experiments are conducted using different types of arrays. Several investigators have explored the cross-platform comparison issues and reached mixed conclusions, ranging from discrepant to reasonably concordant results across platforms. These comparative studies, however, did not apply rigorous sequence-matching criteria. Since the sample size in each experiment is small, combining the information may help increase statistical power. Here we address this issue using the probe sequences to determine matching probes. Smooth muscle cells from the thoracic aorta of C57B46J mice treated with benzo(a)pyrene or dimethyl sulfoxide were examined using GeneChip and CodeLink arrays. Corresponding probes on the two platforms were identified by stand-alone BLAST. In general, CodeLink selected more genes as differentially expressed. For GeneChip arrays, among the various algorithms considered, more probe sets were found significantly changed using the MAS 5.0 expression estimates. The Li-Wong PM-only expression estimates led to fewer discordant results between the two platforms. We conducted quantitative RT-PCR assays on several genes to further assess the performance of each platform. We found that the use of different expression estimation algorithms led to different results within the same platform. The qRT-PCR experiments did not consistently confirm the results of either platform.

Fundamental Limitations on the Number of Resolvable Emitters Using a Geolocation System

We derive conditions for unique geolocation of multiple radio-frequency emitters using a general observation model. These conditions specify the maximum number of emitters that can be uniquely located by a geolocation system, often referred to as the resolution capacity (RC). Our derivations extend previously published results for geolocation based on angle-of-arrival (AOA) estimation. We show that with no prior information, the RC is upper bounded by the total number of antenna elements in the system, i.e., LM, where M is the number of elements in each array and L is the number of arrays. In contrast, the RC of geolocation based on AOA is upper bounded by M. In addition, if the signals are known to be uncorrelated, and the arrays are uniform and linear, the RC is upper bounded by (LM) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -L(M-1) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -1. However, more emitters can be resolved using different types of arrays. Our results lead to the inevitable conclusion that geolocation based on AOA is suboptimal, and new methods should be developed that can jointly exploit the information collected by all the antenna arrays

Using atomic force microscopy to study chromatin structure and nucleosome remodeling

Atomic force microscopy (AFM) is a technique that can directly image single molecules in solution and it therefore provides a powerful tool for obtaining unique insights into the basic properties of biological materials and the functional processes in which they are involved. We have used AFM to analyze basic features of nucleosomes in arrays, such as DNA–histone binding strength, cooperativity in template occupation, nucleosome stabilities, nucleosome locations and the effects of acetylation, to compare these features in different types of arrays and to track the response of array nucleosomes to the action of the human Swi-Snf ATP-dependent nucleosome remodeling complex. These experiments required several specific adaptations of basic AFM methods, such as repetitive imaging of the same fields of molecules in liquid, the ability to change the environmental conditions of the sample being imaged and detection of specific types of molecules within compositionally complex samples. Here, we describe the techniques that allowed such analyses to be carried out.

Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation

A critical step for DNA array analysis is data filtration, which can reduce thousands of detected signals to limited sets of genes. Commonly accepted rules for such filtration are still absent. We present a rational approach, based on thresholding of intensities with cutoff levels that are estimated by receiver operating characteristic (ROC) analysis. The technique compares test results with known distributions of positive and negative signals. We apply the method to Atlas cDNA arrays, GeneFilters, and Affymetrix GeneChip. ROC analysis demonstrates similarities in the distribution of false and true positive data for these different systems. We illustrate the estimation of an optimal cutoff level for intensity-based filtration, providing the highest ratio of true to false signals. For GeneChip arrays, we derived filtration thresholds consistent with the reported data based on replicate hybridizations. Intensity-based filtration optimized with ROC combined with other types of filtration (for example, based on significances of differences and/or ratios), should improve DNA array analysis. ROC methodology is also demonstrated for comparison of the performance of different types of arrays, imagers, and analysis software.

Development of a 950-gene DNA array for examining gene expression patterns in mouse testis.

Over the past five years, interest in and use of DNA array technology has increased dramatically, and there has been a surge in demand for different types of arrays. Although manufacturers offer a number of pre-made arrays, these are generally of utilitarian design and often cannot accommodate the specific requirements of focused research, such as a particular set of genes from a particular tissue. We found that suppliers did not provide an array to suit our particular interest in testicular toxicology, and therefore elected to design and produce our own. We describe the procedures used by members of the US Environmental Protection Agency MicroArray Consortium (EPAMAC) to produce a mouse testis expression array on both filter and glass-slide formats. The approaches used in the selection and assembly of a pertinent, nonredundant list of testis-expressed genes are detailed. Hybridization of the filter arrays with normal and bromochloroacetic acid-treated mouse testicular RNAs demonstrated that all the selected genes on the array were expressed in mouse testes. We have assembled two lists of mouse (950) and human (960) genes expressed in the mouse and/or human adult testis, essentially all of which are available as sequence-verified clones from public sources. Of these, 764 are homologous and will therefore enable close comparison of gene expression between murine models and human clinical testicular samples.