Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization

PubMed Central

2009-01-01

Background Array genomic hybridization is being used clinically to detect pathogenic copy number variants in children with intellectual disability and other birth defects. However, there is no agreement regarding the kind of array, the distribution of probes across the genome, or the resolution that is most appropriate for clinical use. Results We performed 500 K Affymetrix GeneChip® array genomic hybridization in 100 idiopathic intellectual disability trios, each comprised of a child with intellectual disability of unknown cause and both unaffected parents. We found pathogenic genomic imbalance in 16 of these 100 individuals with idiopathic intellectual disability. In comparison, we had found pathogenic genomic imbalance in 11 of 100 children with idiopathic intellectual disability in a previous cohort who had been studied by 100 K GeneChip® array genomic hybridization. Among 54 intellectual disability trios selected from the previous cohort who were re-tested with 500 K GeneChip® array genomic hybridization, we identified all 10 previously-detected pathogenic genomic alterations and at least one additional pathogenic copy number variant that had not been detected with 100 K GeneChip® array genomic hybridization. Many benign copy number variants, including one that was de novo, were also detected with 500 K array genomic hybridization, but it was possible to distinguish the benign and pathogenic copy number variants with confidence in all but 3 (1.9%) of the 154 intellectual disability trios studied. Conclusion Affymetrix GeneChip® 500 K array genomic hybridization detected pathogenic genomic imbalance in 10 of 10 patients with idiopathic developmental disability in whom 100 K GeneChip® array genomic hybridization had found genomic imbalance, 1 of 44 patients in whom 100 K GeneChip® array genomic hybridization had found no abnormality, and 16 of 100 patients who had not previously been tested. Effective clinical interpretation of these studies requires considerable skill and experience. PMID:19917086

Genome-wide array-based comparative genomic hybridization (array-CGH) analysis in Aicardi Syndrome

USDA-ARS?s Scientific Manuscript database

Aicardi syndrome is characterized by agenesis of the corpus callosum, chorioretinal lacunae, severe seizures (starting as infantile spasms), neuronal migration defects, mental retardation, costovertebral defects, and typical facial features. Because Aicardi syndrome is sporadic and affects only fem...

A Novel Approach to Beam Steering Using Arrays Composed of Multiple Unique Radiating Modes

NASA Astrophysics Data System (ADS)

Labadie, Nathan Richard

Phased array antennas have found wide application in both radar and wireless communications systems particularly as implementation costs continue to decrease. The primary advantages of electronically scanned arrays are speed of beam scan and versatility of beamforming compared to mechanically scanned fixed beam antennas. These benefits come at the cost of a few well known design issues including element pattern rolloff and mutual coupling between elements. Our primary contribution to the field of research is the demonstration of significant improvement in phased array scan performance using multiple unique radiating modes. In short, orthogonal radiating modes have minimal coupling by definition and can also be generated with reduced rolloff at wide scan angles. In this dissertation, we present a combination of analysis, full-wave electromagnetic simulation and measured data to support our claims. The novel folded ring resonator (FRR) antenna is introduced as a wideband and multi-band element embedded in a grounded dielectric substrate. Multiple radiating modes of a small ground plane excited by a four element FRR array were also investigated. A novel hemispherical null steering antenna composed of two collocated radiating elements, each supporting a unique radiating mode, is presented in the context of an anti-jam GPS receiver application. Both the antenna aperture and active feed network were fabricated and measured showing excellent agreement with analytical and simulated data. The concept of using an antenna supporting multiple radiating modes for beam steering is also explored. A 16 element hybrid linear phased array was fabricated and measured demonstrating significantly improved scan range and scanned gain compared to a conventional phased array. This idea is expanded to 2 dimensional scanning arrays by analysis and simulation of a hybrid phased array composed of novel multiple mode monopole on patch antenna sub-arrays. Finally, we fabricated and characterized the 2D scanning hybrid phased array demonstrating wide angle scanning with high antenna efficiency.

A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays

PubMed Central

2012-01-01

Background DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. Results For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. Conclusions To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These two factors are sequence dependent and have a large impact on probe intensity. The results presented here provide novel insight into the effect of probe synthesis errors on Affymetrix microarrays; furthermore, the algorithms developed in this work provide useful tools for the analysis of cross-hybridization, probe synthesis efficiency, fragmentation, wash stringency, temperature, and salt concentration on microarray intensities. PMID:23270536

An integrated analysis-synthesis array system for spatial sound fields.

PubMed

Bai, Mingsian R; Hua, Yi-Hsin; Kuo, Chia-Hao; Hsieh, Yu-Hao

2015-03-01

An integrated recording and reproduction array system for spatial audio is presented within a generic framework akin to the analysis-synthesis filterbanks in discrete time signal processing. In the analysis stage, a microphone array "encodes" the sound field by using the plane-wave decomposition. Direction of arrival of plane-wave components that comprise the sound field of interest are estimated by multiple signal classification. Next, the source signals are extracted by using a deconvolution procedure. In the synthesis stage, a loudspeaker array "decodes" the sound field by reconstructing the plane-wave components obtained in the analysis stage. This synthesis stage is carried out by pressure matching in the interior domain of the loudspeaker array. The deconvolution problem is solved by truncated singular value decomposition or convex optimization algorithms. For high-frequency reproduction that suffers from the spatial aliasing problem, vector panning is utilized. Listening tests are undertaken to evaluate the deconvolution method, vector panning, and a hybrid approach that combines both methods to cover frequency ranges below and above the spatial aliasing frequency. Localization and timbral attributes are considered in the subjective evaluation. The results show that the hybrid approach performs the best in overall preference. In addition, there is a trade-off between reproduction performance and the external radiation.

Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls

PubMed Central

Miller, Allison J.; Matasci, Naim; Schwaninger, Heidi; Aradhya, Mallikarjuna K.; Prins, Bernard; Zhong, Gan-Yuan; Simon, Charles; Buckler, Edward S.; Myles, Sean

2013-01-01

Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction. PMID:24236035

Theory and design of compact hybrid microphone arrays on two-dimensional planes for three-dimensional soundfield analysis.

PubMed

Chen, Hanchi; Abhayapala, Thushara D; Zhang, Wen

2015-11-01

Soundfield analysis based on spherical harmonic decomposition has been widely used in various applications; however, a drawback is the three-dimensional geometry of the microphone arrays. In this paper, a method to design two-dimensional planar microphone arrays that are capable of capturing three-dimensional (3D) spatial soundfields is proposed. Through the utilization of both omni-directional and first order microphones, the proposed microphone array is capable of measuring soundfield components that are undetectable to conventional planar omni-directional microphone arrays, thus providing the same functionality as 3D arrays designed for the same purpose. Simulations show that the accuracy of the planar microphone array is comparable to traditional spherical microphone arrays. Due to its compact shape, the proposed microphone array greatly increases the feasibility of 3D soundfield analysis techniques in real-world applications.

Application of Nexus copy number software for CNV detection and analysis.

PubMed

Darvishi, Katayoon

2010-04-01

Among human structural genomic variation, copy number variants (CNVs) are the most frequently known component, comprised of gains/losses of DNA segments that are generally 1 kb in length or longer. Array-based comparative genomic hybridization (aCGH) has emerged as a powerful tool for detecting genomic copy number variants (CNVs). With the rapid increase in the density of array technology and with the adaptation of new high-throughput technology, a reliable and computationally scalable method for accurate mapping of recurring DNA copy number aberrations has become a main focus in research. Here we introduce Nexus Copy Number software, a platform-independent tool, to analyze the output files of all types of commercial and custom-made comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) arrays, such as those manufactured by Affymetrix, Agilent Technologies, Illumina, and Roche NimbleGen. It also supports data generated by various array image-analysis software tools such as GenePix, ImaGene, and BlueFuse. (c) 2010 by John Wiley & Sons, Inc.

Telescope Array Low energy Extension: TALE

NASA Astrophysics Data System (ADS)

Ogio, Shoichi

TALE, the Telescope Array Low Energy extension was designed to lower the energy threshold to about 1016.5 eV. TALE has a surface detector (SD) array made up of 103 scintillation counters (40 with 400 m spacing, 36 with 600 m spacing and 27 with 1.2 km spacing) and a Fluorescence Detector (FD) station consisting of ten FD telescopes working with the Telescope Array Middle Drum FD station, which is made up of 14 telescopes. TALE-FD full operation started in 2013 and the SD array was partially-completed with 16 SDs and continues the operation from 2014. We will describe the history and the current status of the detectors and will make a brief report about the FD and the hybrid analysis results. TALE detector will be completed as a hybrid air shower detector in 2018. We will report the technical details of the detectors, the schedule and the expected performances.

Novel fabrication technique of hybrid structure lens array for 3D images

NASA Astrophysics Data System (ADS)

Lee, Junsik; Kim, Junoh; Kim, Cheoljoong; Shin, Dooseub; Koo, Gyohyun; Won, Yong Hyub

2016-03-01

Tunable liquid lens arrays can produce three dimensional images by using electrowetting principle that alters surface tensions by applying voltage. This method has advantages of fast response time and low power consumption. However, it is challenging to fabricate a high fill factor liquid lens array and operate three dimensional images which demand high diopter. This study describes a hybrid structure lens array which has not only a liquid lens array but a solid lens array. A concave-shape lens array is unavoidable when using only the liquid lens array and some voltages are needed to make the lens flat. By placing the solid lens array on the liquid lens array, initial diopter can be positive. To fabricate the hybrid structure lens array, a conventional lithographic process in semiconductor manufacturing is needed. A negative photoresist SU-8 was used as chamber master molds. PDMS and UV adhesive replica molding are done sequentially. Two immiscible liquids, DI water and dodecane, are injected in the fabricated chamber, followed by sealing. The fabricated structure has a 20 by 20 pattern of cylindrical shaped circle array and the aperture size of each lens is 1mm. The thickness of the overall hybrid structure is about 2.8mm. Hybrid structure lens array has many advantages. Solid lens array has almost 100% fill factor and allow high efficiency. Diopter can be increased by more than 200 and negative diopter can be shifted to the positive region. This experiment showed several properties of the hybrid structure and demonstrated its superiority.

[Application of array-based comparative genomic hybridization technique in genetic analysis of patients with spontaneous abortion].

PubMed

Chu, Y; Wu, D; Hou, Q F; Huo, X D; Gao, Y; Wang, T; Wang, H D; Yang, Y L; Liao, S X

2016-08-25

To investigate the value of array-based comparative genomic hybridization (array-CGH) technique for the detection of chromosomal analysis of miscarried embryo, and to provide genetic counseling for couples with spontaneous abortion. Totally 382 patients who underwent miscarriage were enrolled in this study. All aborted tissues were analyzed with conventional cytogenetic karyotyping and array-CGH, respectively. Through genetic analysis, all of the 382 specimens were successfully analyzed by array-CGH (100.0%, 382/382), and the detection rate of chromosomal aberrations was 46.6% (178/382). However, conventional karyotype analysis was successfully performed in 281 cases (73.6%, 281/382), and 113 (40.2%, 113/281) were found with chromosomal aberrations. Of these 178 samples identified by array-CGH, 163 samples (91.6%, 163/178) were aneuploidy, 15 samples (8.4%, 15/178) were segmental deletion and (or) duplication cases. Four of 10 cases with small segmental deletion and duplication were validated to be transferred from their fathers or mathers who were carriers of submicroscopic reciprocal translocation. Of these 113 abnormal karyotypes founded by conventional karyotyping, 108 cases (95.6%, 108/113) were aneuploidy and 5 cases (4.4%, 5/113) had chromosome structural aberrations. Most array-CGH results were consistent with conventional karyotyping but with 3 cases of discrepancy, which included 2 cases of triploids, 1 case of low-level mosaicism that undetcted by array-CGH. Compared with conventional karyotyping, there is an increased detection rate of chromosomal abnormalities when array-CGH is used to analyse the products of conception, primarilly because of its sucess with nonviable tissues. It could be a first-line method to determine the reason of miscarrage with higher accuracy and sensitivity.

High-density fiber-optic DNA random microsphere array.

PubMed

Ferguson, J A; Steemers, F J; Walt, D R

2000-11-15

A high-density fiber-optic DNA microarray sensor was developed to monitor multiple DNA sequences in parallel. Microarrays were prepared by randomly distributing DNA probe-functionalized 3.1-microm-diameter microspheres in an array of wells etched in a 500-microm-diameter optical imaging fiber. Registration of the microspheres was performed using an optical encoding scheme and a custom-built imaging system. Hybridization was visualized using fluorescent-labeled DNA targets with a detection limit of 10 fM. Hybridization times of seconds are required for nanomolar target concentrations, and analysis is performed in minutes.

Comparative Genomic Hybridization–Array Analysis Enhances the Detection of Aneuploidies and Submicroscopic Imbalances in Spontaneous Miscarriages

PubMed Central

Schaeffer, Anthony J. ; Chung, June ; Heretis, Konstantina ; Wong, Andrew ; Ledbetter, David H. ; Lese Martin, Christa 

2004-01-01

Miscarriage is a condition that affects 10%–15% of all clinically recognized pregnancies, most of which occur in the first trimester. Approximately 50% of first-trimester miscarriages result from fetal chromosome abnormalities. Currently, G-banded chromosome analysis is used to determine if large-scale genetic imbalances are the cause of these pregnancy losses. This technique relies on the culture of cells derived from the fetus, a technique that has many limitations, including a high rate of culture failure, maternal overgrowth of fetal cells, and poor chromosome morphology. Comparative genomic hybridization (CGH)–array analysis is a powerful new molecular cytogenetic technique that allows genomewide analysis of DNA copy number. By hybridizing patient DNA and normal reference DNA to arrays of genomic clones, unbalanced gains or losses of genetic material across the genome can be detected. In this study, 41 product-of-conception (POC) samples, which were previously analyzed by G-banding, were tested using CGH arrays to determine not only if the array could identify all reported abnormalities, but also whether any previously undetected genomic imbalances would be discovered. The array methodology detected all abnormalities as reported by G-banding analysis and revealed new abnormalities in 4/41 (9.8%) cases. Of those, one trisomy 21 POC was also mosaic for trisomy 20, one had a duplication of the 10q telomere region, one had an interstitial deletion of chromosome 9p, and the fourth had an interstitial duplication of the Prader-Willi/Angelman syndrome region on chromosome 15q, which, if maternally inherited, has been implicated in autism. This retrospective study demonstrates that the DNA-based CGH-array technology overcomes many of the limitations of routine cytogenetic analysis of POC samples while enhancing the detection of fetal chromosome aberrations. PMID:15127362

Study of Ultra-High Energy Cosmic Ray composition using Telescope Array's Middle Drum detector and surface array in hybrid mode

NASA Astrophysics Data System (ADS)

Abbasi, R. U.; Abe, M.; Abu-Zayyad, T.; Allen, M.; Anderson, R.; Azuma, R.; Barcikowski, E.; Belz, J. W.; Bergman, D. R.; Blake, S. A.; Cady, R.; Chae, M. J.; Cheon, B. G.; Chiba, J.; Chikawa, M.; Cho, W. R.; Fujii, T.; Fukushima, M.; Goto, T.; Hanlon, W.; Hayashi, Y.; Hayashida, N.; Hibino, K.; Honda, K.; Ikeda, D.; Inoue, N.; Ishii, T.; Ishimori, R.; Ito, H.; Ivanov, D.; Jui, C. C. H.; Kadota, K.; Kakimoto, F.; Kalashev, O.; Kasahara, K.; Kawai, H.; Kawakami, S.; Kawana, S.; Kawata, K.; Kido, E.; Kim, H. B.; Kim, J. H.; Kim, J. H.; Kitamura, S.; Kitamura, Y.; Kuzmin, V.; Kwon, Y. J.; Lan, J.; Lim, S. I.; Lundquist, J. P.; Machida, K.; Martens, K.; Matsuda, T.; Matsuyama, T.; Matthews, J. N.; Minamino, M.; Mukai, Y.; Myers, I.; Nagasawa, K.; Nagataki, S.; Nakamura, T.; Nonaka, T.; Nozato, A.; Ogio, S.; Ogura, J.; Ohnishi, M.; Ohoka, H.; Oki, K.; Okuda, T.; Ono, M.; Oshima, A.; Ozawa, S.; Park, I. H.; Pshirkov, M. S.; Rodriguez, D. C.; Rubtsov, G.; Ryu, D.; Sagawa, H.; Sakurai, N.; Sampson, A. L.; Scott, L. M.; Shah, P. D.; Shibata, F.; Shibata, T.; Shimodaira, H.; Shin, B. K.; Shin, H. S.; Smith, J. D.; Sokolsky, P.; Springer, R. W.; Stokes, B. T.; Stratton, S. R.; Stroman, T.; Suzawa, T.; Takamura, M.; Takeda, M.; Takeishi, R.; Taketa, A.; Takita, M.; Tameda, Y.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Thomas, S. B.; Thomson, G. B.; Tinyakov, P.; Tkachev, I.; Tokuno, H.; Tomida, T.; Troitsky, S.; Tsunesada, Y.; Tsutsumi, K.; Uchihori, Y.; Udo, S.; Urban, F.; Vasiloff, G.; Wong, T.; Yamane, R.; Yamaoka, H.; Yamazaki, K.; Yang, J.; Yashiro, K.; Yoneda, Y.; Yoshida, S.; Yoshii, H.; Zollinger, R.; Zundel, Z.

2015-04-01

Previous measurements of the composition of Ultra-High Energy Cosmic Rays (UHECRs) made by the High Resolution Fly's Eye (HiRes) and Pierre Auger Observatory (PAO) are seemingly contradictory, but utilize different detection methods, as HiRes was a stereo detector and PAO is a hybrid detector. The five year Telescope Array (TA) Middle Drum hybrid composition measurement is similar in some, but not all, respects in methodology to PAO, and good agreement is evident between data and a light, largely protonic, composition when comparing the measurements to predictions obtained with the QGSJetII-03 and QGSJet-01c models. These models are also in agreement with previous HiRes stereo measurements, confirming the equivalence of the stereo and hybrid methods. The data is incompatible with a pure iron composition, for all models examined, over the available range of energies. The elongation rate and mean values of Xmax are in good agreement with Pierre Auger Observatory data. This analysis is presented using two methods: data cuts using simple geometrical variables and a new pattern recognition technique.

Glossary

MedlinePlus

... array, and oligo/SNP combination array. Related terms: comparative genomic hybridization ; copy number variant ; SNP array chromosome ... for example, the AB blood groups in humans comparative genomic hybridization Method in which two DNA samples ( ...

Multiple period s-p hybridization in nano-strip embedded photonic crystal.

PubMed

Han, Seunghoon; Lee, Il-Min; Kim, Hwi; Lee, Byoungho

2005-04-04

We report and analyze hybridization of s-state and p-state modes in photonic crystal one-dimensional defect cavity array. When embedding a nano-strip into a dielectric rod photonic crystal, an effective cavity array is made, where each cavity possesses two cavity modes: s-state and p-state. The two modes are laterally even versus the nano-strip direction, and interact with each other, producing defect bands, of which the group velocity becomes zero within the first Brillouin zone. We could model and describe the phenomena by using the tight-binding method, well agreeing with the plane-wave expansion method analysis. We note that the reported s- and p-state mode interaction corresponds to the hybridization of atomic orbital in solid-state physics. The concept of multiple period s-p hybridization and the proposed model can be useful for analyzing and developing novel photonic crystal waveguides and devices.

Electrochemical DNA biosensor based on the BDD nanograss array electrode.

PubMed

Jin, Huali; Wei, Min; Wang, Jinshui

2013-04-10

The development of DNA biosensor has attracted considerable attention due to their potential applications, including gene analysis, clinical diagnostics, forensic study and more medical applications. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry in this study. Electrochemical DNA biosensor was developed based on the BDD film electrode (fBDD) and BDD nanograss array electrode (nBDD). In comparison with fBDD and AuNPs/CA/fBDD electrode, the lower semicircle diameter of electrochemical impedance spectroscopy obtained on nBDD and AuNPs/CA/nBDD electrode indicated that the presence of nanograss array improved the reactive site, reduced the interfacial resistance, and made the electron transfer easier. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry. The experimental results demonstrated that the prepared AuNPs/CA/nBDD electrode was suitable for DNA hybridization with favorable performance of faster response, higher sensitivity, lower detection limit and satisfactory selectivity, reproducibility and stability.

Electrochemical DNA biosensor based on the BDD nanograss array electrode

PubMed Central

2013-01-01

Background The development of DNA biosensor has attracted considerable attention due to their potential applications, including gene analysis, clinical diagnostics, forensic study and more medical applications. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry in this study. Results Electrochemical DNA biosensor was developed based on the BDD film electrode (fBDD) and BDD nanograss array electrode (nBDD). In comparison with fBDD and AuNPs/CA/fBDD electrode, the lower semicircle diameter of electrochemical impedance spectroscopy obtained on nBDD and AuNPs/CA/nBDD electrode indicated that the presence of nanograss array improved the reactive site, reduced the interfacial resistance, and made the electron transfer easier. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry. Conclusions The experimental results demonstrated that the prepared AuNPs/CA/nBDD electrode was suitable for DNA hybridization with favorable performance of faster response, higher sensitivity, lower detection limit and satisfactory selectivity, reproducibility and stability. PMID:23575250

DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays

PubMed Central

Jobs, Magnus; Howell, W. Mathias; Strömqvist, Linda; Mayr, Torsten; Brookes, Anthony J.

2003-01-01

Genotyping technologies need to be continually improved in terms of their flexibility, cost-efficiency, and throughput, to push forward genome variation analysis. To this end, we have leveraged the inherent simplicity of dynamic allele-specific hybridization (DASH) and coupled it to recent innovations of centrifugal arrays and iFRET. We have thereby created a new genotyping platform we term DASH-2, which we demonstrate and evaluate in this report. The system is highly flexible in many ways (any plate format, PCR multiplexing, serial and parallel array processing, spectral-multiplexing of hybridization probes), thus supporting a wide range of application scales and objectives. Precision is demonstrated to be in the range 99.8–100%, and assay costs are 0.05 USD or less per genotype assignment. DASH-2 thus provides a powerful new alternative for genotyping practice, which can be used without the need for expensive robotics support. PMID:12727908

A low-power small-area ADC array for IRFPA readout

NASA Astrophysics Data System (ADS)

Zhong, Shengyou; Yao, Libin

2013-09-01

The readout integrated circuit (ROIC) is a bridge between the infrared focal plane array (IRFPA) and image processing circuit in an infrared imaging system. The ROIC is the first part of signal processing circuit and connected to detectors directly, so its performance will greatly affect the detector or even the whole imaging system performance. With the development of CMOS technologies, it's possible to digitalize the signal inside the ROIC and develop the digital ROIC. Digital ROIC can reduce complexity of the whole system and improve the system reliability. More importantly, it can accommodate variety of digital signal processing techniques which the traditional analog ROIC cannot achieve. The analog to digital converter (ADC) is the most important building block in the digital ROIC. The requirements for ADCs inside the ROIC are low power, high dynamic range and small area. In this paper we propose an RC hybrid Successive Approximation Register (SAR) ADC as the column ADC for digital ROIC. In our proposed ADC structure, a resistor ladder is used to generate several voltages. The proposed RC hybrid structure not only reduces the area of capacitor array but also releases requirement for capacitor array matching. Theory analysis and simulation show RC hybrid SAR ADC is suitable for ADC array applications

Composition Studies with the Telescope Array Surface Detector

NASA Astrophysics Data System (ADS)

Kuznetsov, Mikhail; Piskunov, Maxim; Rubtsov, Grigory; Troitsky, Sergey; Zhezher, Yana

The results on ultra-high-energy cosmic-ray chemical composition based on the data from the Telescope Array surface-detector are presented. The method is based on the multivariate boosted decision tree (BDT) analysis which uses surface-detector observables. The results on average atomic mass in the energy range 1018.0-1020.0 eV are presented. A comparison with the Telescope Array hybrid results and the Pierre Auger Observatory surface detector results is shown.

Application of Array Comparative Genomic Hybridization in Newborns with Multiple Congenital Anomalies.

PubMed

Szczałuba, Krzysztof; Nowakowska, Beata; Sobecka, Katarzyna; Smyk, Marta; Castaneda, Jennifer; Klapecki, Jakub; Kutkowska-Kaźmierczak, Anna; Śmigiel, Robert; Bocian, Ewa; Radkowski, Marek; Demkow, Urszula

2016-01-01

Major congenital anomalies are detectable in 2-3 % of the newborn population. Some of their genetic causes are attributable to copy number variations identified by array comparative genomic hybridization (aCGH). The value of aCGH screening as a first-tier test in children with multiple congenital anomalies has been studied and consensus adopted. However, array resolution has not been agreed upon, specifically in the newborn or infant population. Moreover, most array studies have been focused on mixed populations of intellectual disability/developmental delay with or without multiple congenital anomalies, making it difficult to assess the value of microarrays in newborns. The aim of the study was to determine the optimal quality and clinical sensitivity of high-resolution array comparative genomic hybridization in neonates with multiple congenital anomalies. We investigated a group of 54 newborns with multiple congenital anomalies defined as two or more birth defects from more than one organ system. Cytogenetic studies were performed using OGT CytoSure 8 × 60 K microarray. We found ten rearrangements in ten newborns. Of these, one recurrent syndromic microduplication was observed, whereas all other changes were unique. Six rearrangements were definitely pathogenic, including one submicroscopic and five that could be seen on routine karyotype analysis. Four other copy number variants were likely pathogenic. The candidate genes that may explain the phenotype were discussed. In conclusion, high-resolution array comparative hybridization can be applied successfully in newborns with multiple congenital anomalies as the method detects a significant number of pathogenic changes, resulting in early diagnoses. We hypothesize that small changes previously considered benign or even inherited rearrangements should be classified as potentially pathogenic at least until a subsequent clinical assessment would exclude a developmental delay or dysmorphism.

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

PubMed Central

Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

2010-01-01

Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181

Scattering and radiation analysis of three-dimensional cavity arrays via a hybrid finite element method

NASA Technical Reports Server (NTRS)

Jin, Jian-Ming; Volakis, John L.

1992-01-01

A hybrid numerical technique is presented for a characterization of the scattering and radiation properties of three-dimensional cavity arrays recessed in a ground plane. The technique combines the finite element and boundary integral methods and invokes Floquet's representation to formulate a system of equations for the fields at the apertures and those inside the cavities. The system is solved via the conjugate gradient method in conjunction with the Fast Fourier Transform (FFT) thus achieving an O(N) storage requirement. By virtue of the finite element method, the proposed technique is applicable to periodic arrays comprised of cavities having arbitrary shape and filled with inhomogeneous dielectrics. Several numerical results are presented, along with new measured data, which demonstrate the validity, efficiency, and capability of the technique.

Two Siblings with Alternate Unbalanced Recombinants Derived from a Large Cryptic Maternal Pericentric Inversion of Chromosome 20

PubMed Central

DeScipio, Cheryl; Morrissette, Jennifer J.D.; Conlin, Laura K.; Clark, Dinah; Kaur, Maninder; Coplan, James; Riethman, Harold; Spinner, Nancy B.; Krantz, Ian D.

2009-01-01

Two brothers, with dissimilar clinical features, were each found to have different abnormalities of chromosome 20 by subtelomere fluorescence in situ hybridization (FISH). The proband had deletion of 20p subtelomere and duplication of 20q subtelomere, while his brother was found to have a duplication of 20p subtelomere and deletion of 20q subtelomere. Parental cytogenetic studies were initially thought to be normal, both by G-banding and by subtelomere FISH analysis. Since chromosome 20 is a metacentric chromosome and an inversion was suspected, we used anchored FISH to assist in identifying a possible inversion. This approach employed concomitant hybridization of a FISH probe to the short (p) arm of chromosome 20 with the 20q subtelomere probe. We identified a cytogenetically non-visible, mosaic pericentric inversion of one of the maternal chromosome 20 homologues, providing a mechanistic explanation for the chromosomal abnormalities present in these brothers. Array comparative genomic hybridization (CGH) with both a custom-made BAC and cosmid-based subtelomere specific array (TEL array) and a commercially-available SNP-based array confirmed and further characterized these rearrangements, identifying this as the largest pericentric inversion of chromosome 20 described to date. TEL array data indicate that the 20p breakpoint is defined by BAC RP11-978M13, ~900 kb from the pter; SNP array data reveal this breakpoint to occur within BAC RP11-978M13. The 20q breakpoint is defined by BAC RP11-93B14, ~1.7 Mb from the qter, by TEL array; SNP array data refine this breakpoint to within a gap between BACs on the TEL array (i.e. between RP11-93B14 and proximal BAC RP11-765G16). PMID:20101690

Two siblings with alternate unbalanced recombinants derived from a large cryptic maternal pericentric inversion of chromosome 20.

PubMed

Descipio, Cheryl; Morrissette, Jennifer D; Conlin, Laura K; Clark, Dinah; Kaur, Maninder; Coplan, James; Riethman, Harold; Spinner, Nancy B; Krantz, Ian D

2010-02-01

Two brothers, with dissimilar clinical features, were each found to have different abnormalities of chromosome 20 by subtelomere fluorescence in situ hybridization (FISH). The proband had deletion of 20p subtelomere and duplication of 20q subtelomere, while his brother was found to have a duplication of 20p subtelomere and deletion of 20q subtelomere. Parental cytogenetic studies were initially thought to be normal, both by G-banding and by subtelomere FISH analysis. Since chromosome 20 is a metacentric chromosome and an inversion was suspected, we used anchored FISH to assist in identifying a possible inversion. This approach employed concomitant hybridization of a FISH probe to the short (p) arm of chromosome 20 with the 20q subtelomere probe. We identified a cytogenetically non-visible, mosaic pericentric inversion of one of the maternal chromosome 20 homologs, providing a mechanistic explanation for the chromosomal abnormalities present in these brothers. Array comparative genomic hybridization (CGH) with both a custom-made BAC and cosmid-based subtelomere specific array (TEL array) and a commercially available SNP-based array confirmed and further characterized these rearrangements, identifying this as the largest pericentric inversion of chromosome 20 described to date. TEL array data indicate that the 20p breakpoint is defined by BAC RP11-978M13, approximately 900 kb from the pter; SNP array data reveal this breakpoint to occur within BAC RP11-978M13. The 20q breakpoint is defined by BAC RP11-93B14, approximately 1.7 Mb from the qter, by TEL array; SNP array data refine this breakpoint to within a gap between BACs on the TEL array (i.e., between RP11-93B14 and proximal BAC RP11-765G16). Copyright 2010 Wiley-Liss, Inc.

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

PubMed Central

Sumer, Huseyin; Craig, Jeffrey M.; Sibson, Mandy; Choo, K.H. Andy

2003-01-01

Human neocentromeres are fully functional centromeres that arise at previously noncentromeric regions of the genome. We have tested a rapid procedure of genomic array analysis of chromosome scaffold/matrix attachment regions (S/MARs), involving the isolation of S/MAR DNA and hybridization of this DNA to a genomic BAC/PAC array. Using this procedure, we have defined a 2.5-Mb domain of S/MAR-enriched chromatin that fully encompasses a previously mapped centromere protein-A (CENP-A)-associated domain at a human neocentromere. We have independently verified this procedure using a previously established fluorescence in situ hybridization method on salt-treated metaphase chromosomes. In silico sequence analysis of the S/MAR-enriched and surrounding regions has revealed no outstanding sequence-related predisposition. This study defines the S/MAR-enriched domain of a higher eukaryotic centromere and provides a method that has broad application for the mapping of S/MAR attachment sites over large genomic regions or throughout a genome. PMID:12840048

Method for performing site-specific affinity fractionation for use in DNA sequencing

DOEpatents

Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Dubley, Svetlana A.

1999-01-01

A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between said cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting said extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to said extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from said array.

Miniaturized reaction vessel system, method for performing site-specific biochemical reactions and affinity fractionation for use in DNA sequencing

DOEpatents

Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Dubley, Svetlana A.

2000-01-01

A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between said cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting said extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to said extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from said array.

Method for performing site-specific affinity fractionation for use in DNA sequencing

DOEpatents

Mirzabekov, A.D.; Lysov, Y.P.; Dubley, S.A.

1999-05-18

A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between the cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting the extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to the extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from the array. 14 figs.

Analysis of L-band Multi-Channel Sea Clutter

DTIC Science & Technology

2010-08-01

Some researchers found that the use of a hybrid algorithm of PS and GA could accelerate the convergence for array beamforming designs (Yeo and Lu...to be shown is array failure correction using the PS algorithm . Assume element 5 of a 32 half-wavelength spacing linear array is in failure. The goal... algorithm . The blue one is the 20 dB Chebyshev pattern and the template in red is the goal pattern to achieve. Two corrected beam patterns are

Design of Hybrid Nanostructural Arrays to Manipulate SERS-Active Substrates by Nanosphere Lithography.

PubMed

Zhao, Xiaoyu; Wen, Jiahong; Zhang, Mengning; Wang, Dunhui; Wang, Yaxin; Chen, Lei; Zhang, Yongjun; Yang, Jinghai; Du, Youwei

2017-03-01

An easy-handling and low-cost method is utilized to controllably fabricate nanopattern arrays as the surface-enhanced Raman scattering (SERS) active substrates with high density of SERS-active areas (hot spots). A hybrid silver array of nanocaps and nanotriangles are prepared by combining magnetron sputtering and plasma etching. By adjusting the etching time of polystyrene (PS) colloid spheres array in silver nanobowls, the morphology of the arrays can be easily manipulated to control the formation and distribution of hot spots. The experimental results show that the hybrid nanostructural arrays have large enhancement factor, which is estimated to be seven times larger than that in the array of nanocaps and three times larger than that in the array of nanorings and nanoparticles. According to the results of finite-difference time-domain simulation, the excellent SERS performance of this array is ascribed to the high density of hot spots and enhanced electromagnetic field.

A new normalizing algorithm for BAC CGH arrays with quality control metrics.

PubMed

Miecznikowski, Jeffrey C; Gaile, Daniel P; Liu, Song; Shepherd, Lori; Nowak, Norma

2011-01-01

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose "SmoothArray", a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package "aCGHplus," this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

Synthesis of porous NiO/CeO2 hybrid nanoflake arrays as a platform for electrochemical biosensing

NASA Astrophysics Data System (ADS)

Cui, Jiewu; Luo, Jinbao; Peng, Bangguo; Zhang, Xinyi; Zhang, Yong; Wang, Yan; Qin, Yongqiang; Zheng, Hongmei; Shu, Xia; Wu, Yucheng

2015-12-01

Porous NiO/CeO2 hybrid nanoflake arrays fabricated by a facile hydrothermal method were employed as substrates for electrochemical biosensors. The resulting NiO/CeO2 hybrid nanoflake arrays with a large specific surface area and good biocompatibility presented an excellent platform for electrochemical biosensing.Porous NiO/CeO2 hybrid nanoflake arrays fabricated by a facile hydrothermal method were employed as substrates for electrochemical biosensors. The resulting NiO/CeO2 hybrid nanoflake arrays with a large specific surface area and good biocompatibility presented an excellent platform for electrochemical biosensing. Electronic supplementary information (ESI) available: Optical photographs of the as-prepared samples, SEM, TEM, EDS, XRD and BET data of the samples are presented, I-t curves of glucose biosensors based on NiO and NiO/CeO2 NFAs, EIS results of different electrodes. See DOI: 10.1039/c5nr05924k

Primary gamma ray selection in a hybrid timing/imaging Cherenkov array

NASA Astrophysics Data System (ADS)

Postnikov, E. B.; Grinyuk, A. A.; Kuzmichev, L. A.; Sveshnikova, L. G.

2017-06-01

This work is a methodical study on hybrid reconstruction techniques for hybrid imaging/timing Cherenkov observations. This type of hybrid array is to be realized at the gamma-observatory TAIGA intended for very high energy gamma-ray astronomy (> 30 TeV). It aims at combining the cost-effective timing-array technique with imaging telescopes. Hybrid operation of both of these techniques can lead to a relatively cheap way of development of a large area array. The joint approach of gamma event selection was investigated on both types of simulated data: the image parameters from the telescopes, and the shower parameters reconstructed from the timing array. The optimal set of imaging parameters and shower parameters to be combined is revealed. The cosmic ray background suppression factor depending on distance and energy is calculated. The optimal selection technique leads to cosmic ray background suppression of about 2 orders of magnitude on distances up to 450 m for energies greater than 50 TeV.

Analysis of LH Launcher Arrays (Like the ITER One) Using the TOPLHA Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maggiora, R.; Milanesio, D.; Vecchi, G.

2009-11-26

TOPLHA (Torino Polytechnic Lower Hybrid Antenna) code is an innovative tool for the 3D/1D simulation of Lower Hybrid (LH) antennas, i.e. accounting for realistic 3D waveguides geometry and for accurate 1D plasma models, and without restrictions on waveguide shape, including curvature. This tool provides a detailed performances prediction of any LH launcher, by computing the antenna scattering parameters, the current distribution, electric field maps and power spectra for any user-specified waveguide excitation. In addition, a fully parallelized and multi-cavity version of TOPLHA permits the analysis of large and complex waveguide arrays in a reasonable simulation time. A detailed analysis ofmore » the performances of the proposed ITER LH antenna geometry has been carried out, underlining the strong dependence of the antenna input parameters with respect to plasma conditions. A preliminary optimization of the antenna dimensions has also been accomplished. Electric current distribution on conductors, electric field distribution at the interface with plasma, and power spectra have been calculated as well. The analysis shows the strong capabilities of the TOPLHA code as a predictive tool and its usefulness to LH launcher arrays detailed design.« less

Graphene quantum dots-carbon nanotube hybrid arrays for supercapacitors

NASA Astrophysics Data System (ADS)

Hu, Yue; Zhao, Yang; Lu, Gewu; Chen, Nan; Zhang, Zhipan; Li, Hui; Shao, Huibo; Qu, Liangti

2013-05-01

Graphene quantum dots (GQDs) have been successfully deposited onto aligned carbon nanotubes (CNTs) by a benign electrochemical method and the capacitive properties of the as-formed GQD/CNT hybrid arrays were evaluated in symmetrical supercapacitors. It was found that supercapacitors fabricated from GQD/CNT hybrid arrays exhibited a high capacitance of 44 mF cm-2, representing a more than 200% improvement over that of bare CNT electrodes.

Graphene quantum dots-carbon nanotube hybrid arrays for supercapacitors.

PubMed

Hu, Yue; Zhao, Yang; Lu, Gewu; Chen, Nan; Zhang, Zhipan; Li, Hui; Shao, Huibo; Qu, Liangti

2013-05-17

Graphene quantum dots (GQDs) have been successfully deposited onto aligned carbon nanotubes (CNTs) by a benign electrochemical method and the capacitive properties of the as-formed GQD/CNT hybrid arrays were evaluated in symmetrical supercapacitors. It was found that supercapacitors fabricated from GQD/CNT hybrid arrays exhibited a high capacitance of 44 mF cm(-2), representing a more than 200% improvement over that of bare CNT electrodes.

A Hybrid, Large-Scale Wireless Sensor Network for Real-Time Acquisition and Tracking

DTIC Science & Technology

2007-06-01

multicolor, Quantum Well Infrared Photodetector ( QWIP ), step-stare, large-format Focal Plane Array (FPA) is proposed and evaluated through performance...Photodetector ( QWIP ), step-stare, large-format Focal Plane Array (FPA) is proposed and evaluated through performance analysis. The thesis proposes...7 1. Multi-color IR Sensors - Operational Advantages ...........................8 2. Quantum-Well IR Photodetector ( QWIP

An oligonucleotide array for the identification and differentiation of bacteria pathogenic on potato.

PubMed

Fessehaie, Anania; De Boer, Solke H; Lévesque, C André

2003-03-01

ABSTRACT Oligonucleotides, 16 to 24 bases long, were selected from the 3' end of the 16S gene and the 16S-23S intergenic spacer regions of bacteria pathogenic on potato, including Clavibacter michiganensis subsp. sepedonicus, Ralstonia solanacearum, and the pectolytic erwinias, including Erwinia carotovora subsp. atroseptica and carotovora and E. chrysanthemi. Oligonucleotides were designed and formatted into an array by pin spotting on nylon membranes. Genomic DNA from bacterial cultures was amplified by polymerase chain reaction using conserved ribosomal primers and labeled simultaneously with digoxigenin-dUTP. Hybridization of amplicons to the array and subsequent serological detection of digoxigenin label revealed different hybridization patterns that were distinct for each species and subspecies tested. Hybridization of amplicons generally was restricted to appropriate homologous oligonucleotides and cross-hybridization with heterologous oligonucleotides was rare. Hybridization patterns were recorded as separate gray values for each hybridized spot and revealed a consistent pattern for multiple strains of each species or subspecies isolated from diverse geographical regions. In preliminary tests, bacteria could be correctly identified and detected by hybridizing to the array amplicons from mixed cultures and inoculated potato tissue.

Feasibility of microelectrode array (MEA) based on silicone-polyimide hybrid for retina prosthesis.

PubMed

Kim, Eui Tae; Kim, Cinoo; Lee, Seung Woo; Seo, Jong-Mo; Chung, Hum; Kim, Sung June

2009-09-01

To adopt micropatterning technology in manufacturing silicone elastomer-based microelectrode arrays for retinal stimulation, a silicone-polyimide hybrid microelectrode array was proposed and tested in vivo. Gold microelectrodes were created by semiconductor manufacturing technology based on polyimide and were hybridized with silicone elastomer by spin coating. The stability of the hybrid between the two materials was flex and blister tested. The feasibility of the hybrid electrode was evaluated in the rabbit eye by reviewing optical coherence tomography (OCT) findings after suprachoroidal implantation. The flex test showed no dehiscence between the two materials for 24 hours of alternative flexion and extension from -45.0 degrees to +45.0 degrees . During the blister test, delamination was observed at 8.33 +/- 1.36 psi of pressure stress; however, this property was improved to 11.50 +/- 1.04 psi by oxygen plasma treatment before hybridization. OCT examination revealed that the implanted electrodes were safely located in the suprachoroidal space during the 4-week follow-up period. The silicone-polyimide hybrid microelectrode array showed moderate physical properties, which are suitable for in vivo application. Appropriate pretreatment before hybridization improved electrode stability. In vivo testing indicated that this electrode is suitable as a stimulation electrode in artificial retina.

Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thissen, James B.; McLoughlin, Kevin; Gardner, Shea

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA wasmore » able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.« less

Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray

DOE PAGES

Thissen, James B.; McLoughlin, Kevin; Gardner, Shea; ...

2014-06-01

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA wasmore » able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.« less

Power System Mass Analysis for Hydrogen Reduction Oxygen Production on the Lunar Surface

NASA Technical Reports Server (NTRS)

Colozza, Anthony J.

2009-01-01

The production of oxygen from the lunar regolith requires both thermal and electrical power in roughly similar proportions. This unique power requirement is unlike most applications on the lunar surface. To efficiently meet these requirements, both solar PV array and solar concentrator systems were evaluated. The mass of various types of photovoltaic and concentrator based systems were calculated to determine the type of power system that provided the highest specific power. These were compared over a range of oxygen production rates. Also a hybrid type power system was also considered. This system utilized a photovoltaic array to produce the electrical power and a concentrator to provide the thermal power. For a single source system the three systems with the highest specific power were a flexible concentrator/Stirling engine system, a rigid concentrator/Stirling engine system and a tracking triple junction solar array system. These systems had specific power values of 43, 34, and 33 W/kg, respectively. The hybrid power system provided much higher specific power values then the single source systems. The best hybrid combinations were the triple junction solar array with the flexible concentrator and the rigid concentrator. These systems had a specific power of 81 and 68 W/kg, respectively.

HIA: a genome mapper using hybrid index-based sequence alignment.

PubMed

Choi, Jongpill; Park, Kiejung; Cho, Seong Beom; Chung, Myungguen

2015-01-01

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools. HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table and suffix array (hybrid index) is much faster than the suffix array method for finding a substring in the reference sequence. Here, we defined the matching region (MR) is a longest common substring between a reference and a read. And, we also defined the candidate alignment regions (CARs) as a list of MRs that is close to each other. The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read. We found that aligning only the unmatched regions in the CAR is much faster than aligning the whole CAR. In benchmark analysis, HIA outperformed in mapping speed compared with the other aligners, without significant loss of mapping accuracy. Our experiments show that the hybrid of hash table and suffix array is useful in terms of speed for mapping NGS sequencing reads to the human reference genome sequence. In conclusion, our tool is appropriate for aligning massive data sets generated by NGS sequencing.

The Utility of Chromosomal Microarray Analysis in Developmental and Behavioral Pediatrics

ERIC Educational Resources Information Center

Beaudet, Arthur L.

2013-01-01

Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism…

Solid phase sequencing of biopolymers

DOEpatents

Cantor, Charles; Koster, Hubert

2010-09-28

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array.

PubMed

Rizzi, Giovanni; Lee, Jung-Rok; Dahl, Christina; Guldberg, Per; Dufva, Martin; Wang, Shan X; Hansen, Mikkel F

2017-09-26

Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.

An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples

PubMed Central

Zhang, Xiao; Chen, Jiamin; Radcliffe, Tom; LeBrun, Dave P.; Tron, Victor A.; Feilotter, Harriet

2008-01-01

MicroRNAs (miRNAs) are small, noncoding RNAs that suppress gene expression at the posttranscriptional level via an antisense RNA-RNA interaction. miRNAs used for array-based profiling are generally purified from either snap-frozen or fresh samples. Because tissues found in most pathology departments are available only in formalin-fixed and paraffin-embedded (FFPE) states, we sought to evaluate miRNA derived from FFPE samples for microarray analysis. In this study, miRNAs extracted from matched snap-frozen and FFPE samples were profiled using the Agilent miRNA array platform (Agilent, Santa Clara, CA). Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. Seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling, and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results; technical replicates showed high correlations with one another (Kendall tau, 0.722 to 0.853; Spearman rank correlation coefficient, 0.891 to 0.954). Our results showed consistent high correlations between matched frozen and FFPE samples (Kendall tau, 0.669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling. PMID:18832457

Monitoring of beer fermentation based on hybrid electronic tongue.

PubMed

Kutyła-Olesiuk, Anna; Zaborowski, Michał; Prokaryn, Piotr; Ciosek, Patrycja

2012-10-01

Monitoring of biotechnological processes, including fermentation is extremely important because of the rapidly occurring changes in the composition of the samples during the production. In the case of beer, the analysis of physicochemical parameters allows for the determination of the stage of fermentation process and the control of its possible perturbations. As a tool to control the beer production process a sensor array can be used, composed of potentiometric and voltammetric sensors (so-called hybrid Electronic Tongue, h-ET). The aim of this study is to apply electronic tongue system to distinguish samples obtained during alcoholic fermentation. The samples originate from batch of homemade beer fermentation and from two stages of the process: fermentation reaction and maturation of beer. The applied sensor array consists of 10 miniaturized ion-selective electrodes (potentiometric ET) and silicon based 3-electrode voltammetric transducers (voltammetric ET). The obtained results were processed using Partial Least Squares (PLS) and Partial Least Squares-Discriminant Analysis (PLS-DA). For potentiometric data, voltammetric data, and combined potentiometric and voltammetric data, comparison of the classification ability was conducted based on Root Mean Squared Error (RMSE), sensitivity, specificity, and coefficient F calculation. It is shown, that in the contrast to the separately used techniques, the developed hybrid system allowed for a better characterization of the beer samples. Data fusion in hybrid ET enables to obtain better results both in qualitative analysis (RMSE, specificity, sensitivity) and in quantitative analysis (RMSE, R(2), a, b). Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis of NiMn-LDH Nanosheet@Ni3S2 Nanorod Hybrid Structures for Supercapacitor Electrode Materials with Ultrahigh Specific Capacitance.

PubMed

Yu, Shuai; Zhang, Yingxi; Lou, Gaobo; Wu, Yatao; Zhu, Xinqiang; Chen, Hao; Shen, Zhehong; Fu, Shenyuan; Bao, Binfu; Wu, Limin

2018-03-27

One of the key challenges for pseudocapacitive electrode materials with highly effective capacitance output and future practical applications is how to rationally construct hierarchical and ordered hybrid nanoarchitecture through the simple process. Herein, we design and synthesize a novel NiMn-layered double hydroxide nanosheet@Ni 3 S 2 nanorod hybrid array supported on porous nickel foam via a one-pot hydrothermal method. Benefited from the ultrathin and rough nature, the well-defined porous structure of the hybrid array, as well as the synergetic effect between NiMn-layered double hydroxide nanosheets and Ni 3 S 2 nanorods, the as-fabricated hybrid array-based electrode exhibits an ultrahigh specific capacitance of 2703 F g -1 at 3 A g -1 . Moreover, the asymmetric supercapacitor with this hybrid array as a positive electrode and wood-derived activated carbon as a negative electrode demonstrates high energy density (57 Wh Kg -1 at 738 W Kg -1 ) and very good electrochemical cycling stability.

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH

PubMed Central

2009-01-01

Background Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through genotype-phenotype association, it is also an important technique towards the discovery of disease causing genes and genomewide functional annotation in human. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient against a normal reference sample. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the "normal" reference instead of a patient aberration. Instead, we apply an experimental loop design that compares three patients in three hybridizations. Results We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of 27 patients seen at our genetics center, we observed that the linear models of the log ratios are advantageous over the mixed models of the absolute intensities. Conclusion The loop design and the performance of the statistical analysis contribute to the quick adoption of array CGH as a routine diagnostic tool. They lower the detection limit of mosaicisms and improve the assignment of copy number variation for genetic association studies. PMID:19925645

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

PubMed

Allemeersch, Joke; Van Vooren, Steven; Hannes, Femke; De Moor, Bart; Vermeesch, Joris Robert; Moreau, Yves

2009-11-19

Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through genotype-phenotype association, it is also an important technique towards the discovery of disease causing genes and genomewide functional annotation in human. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient against a normal reference sample. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the "normal" reference instead of a patient aberration. Instead, we apply an experimental loop design that compares three patients in three hybridizations. We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of 27 patients seen at our genetics center, we observed that the linear models of the log ratios are advantageous over the mixed models of the absolute intensities. The loop design and the performance of the statistical analysis contribute to the quick adoption of array CGH as a routine diagnostic tool. They lower the detection limit of mosaicisms and improve the assignment of copy number variation for genetic association studies.

Performance measurements of hybrid PIN diode arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jernigan, J.G.; Arens, J.F.; Kramer, G.

We report on the successful effort to develop hybrid PIN diode arrays and to demonstrate their potential as components of vertex detectors. Hybrid pixel arrays have been fabricated by the Hughes Aircraft Co. by bump bonding readout chips developed by Hughes to an array of PIN diodes manufactured by Micron Semiconductor Inc. These hybrid pixel arrays were constructed in two configurations. One array format having 10 {times} 64 pixels, each 120 {mu}m square, and the other format having 256 {times} 256 pixels, each 30 {mu}m square. In both cases, the thickness of the PIN diode layer is 300 {mu}m. Measurementsmore » of detector performance show that excellent position resolution can be achieved by interpolation. By determining the centroid of the charge cloud which spreads charge into a number of neighboring pixels, a spatial resolution of a few microns has been attained. The noise has been measured to be about 300 electrons (rms) at room temperature, as expected from KTC and dark current considerations, yielding a signal-to-noise ratio of about 100 for minimum ionizing particles. 4 refs., 13 figs.« less

The hybrid energy spectrum of Telescope Array's Middle Drum Detector and surface array

NASA Astrophysics Data System (ADS)

Abbasi, R. U.; Abe, M.; Abu-Zayyad, T.; Allen, M. G.; Anderson, R.; Azuma, R.; Barcikowski, E.; Belz, J. W.; Bergman, D. R.; Blake, S. A.; Cady, R.; Chae, M. J.; Cheon, B. G.; Chiba, J.; Chikawa, M.; Cho, W. R.; Fujii, T.; Fukushima, M.; Goto, T.; Hanlon, W.; Hayashi, Y.; Hayashida, N.; Hibino, K.; Honda, K.; Ikeda, D.; Inoue, N.; Ishii, T.; Ishimori, R.; Ito, H.; Ivanov, D.; Jui, C. C. H.; Kadota, K.; Kakimoto, F.; Kalashev, O.; Kasahara, K.; Kawai, H.; Kawakami, S.; Kawana, S.; Kawata, K.; Kido, E.; Kim, H. B.; Kim, J. H.; Kim, J. H.; Kitamura, S.; Kitamura, Y.; Kuzmin, V.; Kwon, Y. J.; Lan, J.; Lim, S. I.; Lundquist, J. P.; Machida, K.; Martens, K.; Matsuda, T.; Matsuyama, T.; Matthews, J. N.; Minamino, M.; Mukai, K.; Myers, I.; Nagasawa, K.; Nagataki, S.; Nakamura, T.; Nonaka, T.; Nozato, A.; Ogio, S.; Ogura, J.; Ohnishi, M.; Ohoka, H.; Oki, K.; Okuda, T.; Ono, M.; Oshima, A.; Ozawa, S.; Park, I. H.; Pshirkov, M. S.; Rodriguez, D. C.; Rubtsov, G.; Ryu, D.; Sagawa, H.; Sakurai, N.; Sampson, A. L.; Scott, L. M.; Shah, P. D.; Shibata, F.; Shibata, T.; Shimodaira, H.; Shin, B. K.; Shin, H. S.; Smith, J. D.; Sokolsky, P.; Springer, R. W.; Stokes, B. T.; Stratton, S. R.; Stroman, T. A.; Suzawa, T.; Takamura, M.; Takeda, M.; Takeishi, R.; Taketa, A.; Takita, M.; Tameda, Y.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Thomas, S. B.; Thomson, G. B.; Tinyakov, P.; Tkachev, I.; Tokuno, H.; Tomida, T.; Troitsky, S.; Tsunesada, Y.; Tsutsumi, K.; Uchihori, Y.; Udo, S.; Urban, F.; Vasiloff, G.; Wong, T.; Yamane, R.; Yamaoka, H.; Yamazaki, K.; Yang, J.; Yashiro, K.; Yoneda, Y.; Yoshida, S.; Yoshii, H.; Zollinger, R.; Zundel, Z.

2015-08-01

The Telescope Array experiment studies ultra high energy cosmic rays using a hybrid detector. Fluorescence telescopes measure the longitudinal development of the extensive air shower generated when a primary cosmic ray particle interacts with the atmosphere. Meanwhile, scintillator detectors measure the lateral distribution of secondary shower particles that hit the ground. The Middle Drum (MD) fluorescence telescope station consists of 14 telescopes from the High Resolution Fly's Eye (HiRes) experiment, providing a direct link back to the HiRes measurements. Using the scintillator detector data in conjunction with the telescope data improves the geometrical reconstruction of the showers significantly, and hence, provides a more accurate reconstruction of the energy of the primary particle. The Middle Drum hybrid spectrum is presented and compared to that measured by the Middle Drum station in monocular mode. Further, the hybrid data establishes a link between the Middle Drum data and the surface array. A comparison between the Middle Drum hybrid energy spectrum and scintillator Surface Detector (SD) spectrum is also shown.

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array

PubMed Central

Kawakami, Takeshi; Backström, Niclas; Burri, Reto; Husby, Arild; Olason, Pall; Rice, Amber M; Ålund, Murielle; Qvarnström, Anna; Ellegren, Hans

2014-01-01

With the access to draft genome sequence assemblies and whole-genome resequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million single-nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17 kb, but the extent of LD varied markedly within the genome and was more than 10-fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 Ma, this suggests strong selection against F1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system. PMID:24784959

Arrays of probes for positional sequencing by hybridization

DOEpatents

Cantor, Charles R [Boston, MA; Prezetakiewiczr, Marek [East Boston, MA; Smith, Cassandra L [Boston, MA; Sano, Takeshi [Waltham, MA

2008-01-15

This invention is directed to methods and reagents useful for sequencing nucleic acid targets utilizing sequencing by hybridization technology comprising probes, arrays of probes and methods whereby sequence information is obtained rapidly and efficiently in discrete packages. That information can be used for the detection, identification, purification and complete or partial sequencing of a particular target nucleic acid. When coupled with a ligation step, these methods can be performed under a single set of hybridization conditions. The invention also relates to the replication of probe arrays and methods for making and replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

A functional hybrid memristor crossbar-array/CMOS system for data storage and neuromorphic applications.

PubMed

Kim, Kuk-Hwan; Gaba, Siddharth; Wheeler, Dana; Cruz-Albrecht, Jose M; Hussain, Tahir; Srinivasa, Narayan; Lu, Wei

2012-01-11

Crossbar arrays based on two-terminal resistive switches have been proposed as a leading candidate for future memory and logic applications. Here we demonstrate a high-density, fully operational hybrid crossbar/CMOS system composed of a transistor- and diode-less memristor crossbar array vertically integrated on top of a CMOS chip by taking advantage of the intrinsic nonlinear characteristics of the memristor element. The hybrid crossbar/CMOS system can reliably store complex binary and multilevel 1600 pixel bitmap images using a new programming scheme. © 2011 American Chemical Society

Tilted pillar array fabrication by the combination of proton beam writing and soft lithography for microfluidic cell capture Part 2: Image sequence analysis based evaluation and biological application.

PubMed

Járvás, Gábor; Varga, Tamás; Szigeti, Márton; Hajba, László; Fürjes, Péter; Rajta, István; Guttman, András

2018-02-01

As a continuation of our previously published work, this paper presents a detailed evaluation of a microfabricated cell capture device utilizing a doubly tilted micropillar array. The device was fabricated using a novel hybrid technology based on the combination of proton beam writing and conventional lithography techniques. Tilted pillars offer unique flow characteristics and support enhanced fluidic interaction for improved immunoaffinity based cell capture. The performance of the microdevice was evaluated by an image sequence analysis based in-house developed single-cell tracking system. Individual cell tracking allowed in-depth analysis of the cell-chip surface interaction mechanism from hydrodynamic point of view. Simulation results were validated by using the hybrid device and the optimized surface functionalization procedure. Finally, the cell capture capability of this new generation microdevice was demonstrated by efficiently arresting cells from a HT29 cell-line suspension. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-time, multiplexed electrochemical DNA detection using an active complementary metal-oxide-semiconductor biosensor array with integrated sensor electronics.

PubMed

Levine, Peter M; Gong, Ping; Levicky, Rastislav; Shepard, Kenneth L

2009-03-15

Optical biosensing based on fluorescence detection has arguably become the standard technique for quantifying extents of hybridization between surface-immobilized probes and fluorophore-labeled analyte targets in DNA microarrays. However, electrochemical detection techniques are emerging which could eliminate the need for physically bulky optical instrumentation, enabling the design of portable devices for point-of-care applications. Unlike fluorescence detection, which can function well using a passive substrate (one without integrated electronics), multiplexed electrochemical detection requires an electronically active substrate to analyze each array site and benefits from the addition of integrated electronic instrumentation to further reduce platform size and eliminate the electromagnetic interference that can result from bringing non-amplified signals off chip. We report on an active electrochemical biosensor array, constructed with a standard complementary metal-oxide-semiconductor (CMOS) technology, to perform quantitative DNA hybridization detection on chip using targets conjugated with ferrocene redox labels. A 4 x 4 array of gold working electrodes and integrated potentiostat electronics, consisting of control amplifiers and current-input analog-to-digital converters, on a custom-designed 5 mm x 3 mm CMOS chip drive redox reactions using cyclic voltammetry, sense DNA binding, and transmit digital data off chip for analysis. We demonstrate multiplexed and specific detection of DNA targets as well as real-time monitoring of hybridization, a task that is difficult, if not impossible, with traditional fluorescence-based microarrays.

High-MTF hybrid ferroelectric IRFPA

NASA Astrophysics Data System (ADS)

Evans, Scott B.; Hayden, Terrence

1998-07-01

Low cost, uncooled hybrid infrared focal plane arrays (IRFPA's) are in full-scale production at Raytheon Systems Company (RSC), formerly Texas Instruments Defense Systems and Electronics Group. Detectors consist of reticulated ceramic barium strontium titanate (BST) arrays of 320 X 240 pixels on 48.5 micrometer pitch. The principal performance shortcoming of the hybrid arrays has been low MTF due to thermal crosstalk between pixels. In the past two years, significant improvements have been made to increase MTF making hybrids more competitive in performance with monolithic arrays. The improvements are (1) the reduction of the thickness of the IR absorbing layer electrode that maintains electrical continuity and increases thermal isolation between pixels, (2) reduction of the electrical crosstalk from the ROIC, and (3) development of a process to increase the thermal path-length between pixels called 'elevated optical coat.' This paper describes all three activities and their efficacy. Also discussed is the uncooled IRFPA production capability at RSC.

A handy motion driven hybrid energy harvester: dual Halbach array based electromagnetic and triboelectric generators

NASA Astrophysics Data System (ADS)

Salauddin, M.; Park, J. Y.

2016-11-01

In this work, we have proposed and experimentally validated of hybrid electromagnetic and triboelectric energy harvester using dual Halbach magnets array excited by human handy motion. Hybrid electromagnetic (EM) and triboelectric (TE) generator that can deliver an output performance much higher than that of the individual energy-harvesting unit due to the combination operation of EM and TE mechanisms under the same mechanical movements. A Halbach array concentrates the magnetic flux lines on one side of the array while suppressing the flux lines on the other side. Dual Halbach array allows the concentrated magnetic flux lines to interact with the same coil in a way where maximum flux linkage occurs. When an external mechanical vibration is applied to the hybrid structure in the axial direction of the harvester, the suspended mass (two sided dual-Halbach-array frame) starts to oscillate within the magnetic springs and TEG part. Therefore, the TEG part, the Al film and microstructure PDMS film are collected into full contact with each other, generating triboelectric charges due to the various triboelectricities between them. A prototype of the hybrid harvester has been fabricated and tested. The EMG is capable of delivering maximum 11.5mW peak power at 32.5Ω matching load resistance and the TEG delivering 88μW peak power at 10MΩ load resistance.

REopt Improves the Operations of Alcatraz's Solar PV-Battery-Diesel Hybrid System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olis, Daniel R; Walker, H. A; Van Geet, Otto D

This poster identifies operations improvement strategies for a photovoltaic (PV)-battery-diesel hybrid system at the National Park Service's Alcatraz Island using NREL's REopt analysis tool. The current 'cycle charging' strategy results in significant curtailing of energy production from the PV array, requiring excessive diesel use, while also incurring high wear on batteries without benefit of improved efficiency. A simple 'load following' strategy results in near optimal operating cost reduction.

SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data.

PubMed

Chi, Bryan; DeLeeuw, Ronald J; Coe, Bradley P; MacAulay, Calum; Lam, Wan L

2004-02-09

Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles. We have developed a visualization tool for displaying whole genome array CGH data in the context of chromosomal location. SeeGH is an application that translates spot signal ratio data from array CGH experiments to displays of high resolution chromosome profiles. Data is imported from a simple tab delimited text file obtained from standard microarray image analysis software. SeeGH processes the signal ratio data and graphically displays it in a conventional CGH karyotype diagram with the added features of magnification and DNA segment annotation. In this process, SeeGH imports the data into a database, calculates the average ratio and standard deviation for each replicate spot, and links them to chromosome regions for graphical display. Once the data is displayed, users have the option of hiding or flagging DNA segments based on user defined criteria, and retrieve annotation information such as clone name, NCBI sequence accession number, ratio, base pair position on the chromosome, and standard deviation. SeeGH represents a novel software tool used to view and analyze array CGH data. The software gives users the ability to view the data in an overall genomic view as well as magnify specific chromosomal regions facilitating the precise localization of genetic alterations. SeeGH is easily installed and runs on Microsoft Windows 2000 or later environments.

Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

PubMed

Xu, Y; Ehringer, M; Yang, F; Sikela, J M

2001-06-01

Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and efficient way to discover potential genes and pathways involved in alcoholism and alcohol-related physiologic processes.

Multi-segment detector array for hybrid reflection-mode ultrasound and optoacoustic tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Merčep, Elena; Burton, Neal C.; Deán-Ben, Xosé Luís.; Razansky, Daniel

2017-02-01

The complementary contrast of the optoacoustic (OA) and pulse-echo ultrasound (US) modalities makes the combined usage of these imaging technologies highly advantageous. Due to the different physical contrast mechanisms development of a detector array optimally suited for both modalities is one of the challenges to efficient implementation of a single OA-US imaging device. We demonstrate imaging performance of the first hybrid detector array whose novel design, incorporating array segments of linear and concave geometry, optimally supports image acquisition in both reflection-mode ultrasonography and optoacoustic tomography modes. Hybrid detector array has a total number of 256 elements and three segments of different geometry and variable pitch size: a central 128-element linear segment with pitch of 0.25mm, ideally suited for pulse-echo US imaging, and two external 64-elements segments with concave geometry and 0.6mm pitch optimized for OA image acquisition. Interleaved OA and US image acquisition with up to 25 fps is facilitated through a custom-made multiplexer unit. Spatial resolution of the transducer was characterized in numerical simulations and validated in phantom experiments and comprises 230 and 300 μm in the respective OA and US imaging modes. Imaging performance of the multi-segment detector array was experimentally shown in a series of imaging sessions with healthy volunteers. Employing mixed array geometries allows at the same time achieving excellent OA contrast with a large field of view, and US contrast for complementary structural features with reduced side-lobes and improved resolution. The newly designed hybrid detector array that comprises segments of linear and concave geometries optimally fulfills requirements for efficient US and OA imaging and may expand the applicability of the developed hybrid OPUS imaging technology and accelerate its clinical translation.

Novel applications of array comparative genomic hybridization in molecular diagnostics.

PubMed

Cheung, Sau W; Bi, Weimin

2018-05-31

In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

Detection of recurrent transmission of 17q12 microdeletion by array comparative genomic hybridization in a fetus with prenatally diagnosed hydronephrosis, hydroureter, and multicystic kidney, and variable clinical spectrum in the family.

PubMed

Chen, Chih-Ping; Chang, Shuenn-Dyh; Wang, Tzu-Hao; Wang, Liang-Kai; Tsai, Jeng-Daw; Liu, Yu-Peng; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chen, Yu-Ting; Wang, Wayseen

2013-12-01

This study was aimed at detection of recurrent transmission of the 17q12 microdeletion in a fetus with congenital anomalies of the kidney and urinary tract. A 35-year-old woman was referred to the hospital at 20 weeks' gestation because of hydronephrosis in the fetus. The mother was normal and healthy. Her second child was a girl who had bilateral dysplastic kidneys that required hemodialysis, and died at the age of 5 years. During this pregnancy, the woman underwent amniocentesis at 18 weeks' gestation because of advanced maternal age. Cytogenetic analysis revealed a karyotype of 46,XY. Prenatal ultrasound showed left hydronephrosis with a tortuous ureter, right hydronephrosis, and increased echogenicity of the kidneys. Fetal magnetic resonance imaging showed right dilated renal calyces, left hydronephrosis, hydroureter, and multicystic kidney. The pregnancy was subsequently terminated. Array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization were applied for genetic analysis using umbilical cord, maternal blood, and cultured amniocytes. aCGH analysis on umbilical cord detected a 1.75-Mb deletion at 17q12 including haploinsufficiency of LHX1 and HNF1B. aCGH analysis on maternal blood detected a 1.54-Mb deletion at 17q12 including haploinsufficiency of LHX1 and HNF1B. Metaphase fluorescence in situ hybridization analysis on cultured amniocytes and maternal blood lymphocytes using 17q12-specific bacterial artificial chromosome probe showed 17q12 microdeletion in the fetus and the mother. Prenatal diagnosis of recurrent renal and urinary tract abnormalities in the fetus should include a differential diagnosis of familial 17q12 microdeletion. Copyright © 2013. Published by Elsevier B.V.

Nucleic Acid Detection Methods

DOEpatents

Smith, Cassandra L.; Yaar, Ron; Szafranski, Przemyslaw; Cantor, Charles R.

1998-05-19

The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3'-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated.

Surface plasmon resonance imaging system with Mach-Zehnder phase-shift interferometry for DNA micro-array hybridization

NASA Astrophysics Data System (ADS)

Hsiu, Feng-Ming; Chen, Shean-Jen; Tsai, Chien-Hung; Tsou, Chia-Yuan; Su, Y.-D.; Lin, G.-Y.; Huang, K.-T.; Chyou, Jin-Jung; Ku, Wei-Chih; Chiu, S.-K.; Tzeng, C.-M.

2002-09-01

Surface plasmon resonance (SPR) imaging system is presented as a novel technique based on modified Mach-Zehnder phase-shifting interferometry (PSI) for biomolecular interaction analysis (BIA), which measures the spatial phase variation of a resonantly reflected light in biomolecular interaction. In this technique, the micro-array SPR biosensors with over a thousand probe NDA spots can be detected simultaneously. Owing to the feasible and swift measurements, the micro-array SPR biosensors can be extensively applied to the nonspecific adsorption of protein, the membrane/protein interactions, and DNA hybridization. The detection sensitivity of the SPR PSI imaging system is improved to about 1 pg/mm2 for each spot over the conventional SPR imaging systems. The SPR PSI imaging system and its SPR sensors have been successfully used to observe slightly index change in consequence of argon gas flow through the nitrogen in real time, with high sensitivity, and at high-throughout screening rates.

[Analysis of genetics mechanism for the phenotypic diversity in a patient carrying a rare ring chromosome 9].

PubMed

Qin, Shengfang; Wang, Xueyan; Li, Yunxing; Wei, Ping; Chen, Chun; Zeng, Lan

2016-02-01

To explore the genetics mechanism for the phenotypic variability in a patient carrying a rare ring chromosome 9. The karyotype of the patient was analyzed with cytogenetics method. Presence of sex chromosome was confirmed with fluorescence in situ hybridization. The SRY gene was subjected to PCR amplification and direct sequencing. Potential deletion and duplication were detected with array-based comparative genomic hybridization (array-CGH). The karyotype of the patient has comprised 6 types of cell lines containing a ring chromosome 9. The SRY gene sequence was normal. By array-CGH, the patient has carried a hemizygous deletion at 9p24.3-p23 (174 201-9 721 761) encompassing 30 genes from Online Mendelian Inheritance in Man. The phenotypic variability of the 9p deletion syndrome in conjunct with ring chromosome 9 may be attributable to multiple factors including loss of chromosomal material, insufficient dosage of genes, instability of ring chromosome, and pattern of inheritance.

Design, processing and testing of LSI arrays: Hybrid microelectronics task

NASA Technical Reports Server (NTRS)

Himmel, R. P.; Stuhlbarg, S. M.; Ravetti, R. G.; Zulueta, P. J.

1979-01-01

Mathematical cost factors were generated for both hybrid microcircuit and printed wiring board packaging methods. A mathematical cost model was created for analysis of microcircuit fabrication costs. The costing factors were refined and reduced to formulae for computerization. Efficient methods were investigated for low cost packaging of LSI devices as a function of density and reliability. Technical problem areas such as wafer bumping, inner/outer leading bonding, testing on tape, and tape processing, were investigated.

Energy and charge transfer effects in two-dimensional van der Waals hybrid nanostructures on periodic gold nanopost array

NASA Astrophysics Data System (ADS)

Kim, Jun Young; Kim, Sun Gyu; Youn, Jong Won; Lee, Yongjun; Kim, Jeongyong; Joo, Jinsoo

2018-05-01

Two-dimensional (2D) semiconducting MoS2 and WSe2 flakes grown by chemical vapor deposition were mechanically hybridized. A hexagonal boron nitride (h-BN) dielectric flake was inserted between MoS2 and WSe2 flakes to investigate the nanoscale optical properties of 2D van der Waals hybrid nanostructures. The fabricated MoS2/WSe2 and MoS2/h-BN/WSe2 van der Waals hybrid nanostructures were loaded on a periodic gold nanopost (Au-NPo) array to study energy and charge transfer effects at the surface plasmon resonance (SPR) condition. Nanoscale photoluminescence (PL) spectra of the 2D hybrid nanostructures were measured using a high-resolution laser confocal microscope (LCM). A shift of the LCM PL peak of the MoS2/WSe2 n-p hybrid nanostructures was observed owing to the charge transfer. In contrast, the shift of the LCM PL peak of the MoS2/h-BN/WSe2 n-insulator-p hybrid nanostructure was not considerable, as the inserted h-BN dielectric layer prevented the charge transfer. The intensity of the LCM PL peak of the MoS2/h-BN/WSe2 hybrid nanostructure considerably increased once the nanostructure was loaded on the Au-NPo array, owing to the energy transfer between the 2D materials and the Au-NPo array at the SPR condition, which was confirmed by the increase in the LCM Raman intensity.

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

PubMed

Cook, Michael A; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-02-06

Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base) unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

Performance and economics of the PV hybrid power system at Dangling Rope Marina, Utah

NASA Astrophysics Data System (ADS)

Rosenthal, Andrew L.

1999-03-01

The National Park Service has operated a large photovoltaic (PV) hybrid power system at the Dangling Rope Marina since August 1996. Performance and economic analyses for this system based on its first year of operation have been published elsewhere [1,2]. Now, as the system enters its third year of operation, recent changes to the site electrical load and impending additions to the PV array raise new interest in this site as the subject of analysis and evaluation. In 1998, energy conservation measures reduced the site electrical load by 10-12%. At the same time, funding has been allocated to expand the PV array by 40% in 1999. This paper analyzes the effects that these changes will have on the site's fuel use and 20-year life cycle cost.

In-vitro biocompatibility and corrosion resistance of electrochemically assembled PPy/TNTA hybrid material for biomedical applications

NASA Astrophysics Data System (ADS)

Simi, V. S.; Satish, Aishwarya; Korrapati, Purna Sai; Rajendran, N.

2018-07-01

Nanostructured hybrid materials composed of inorganic and organic constituents of different chemistry and functionality have attracted wide range of biomedical applications. The uniform electrodeposition of polypyrrole into titania nanotube arrays was achieved by normal pulse voltammetry technique in lithium perchlorate electrolyte by varying the pulse period. The electrochemically assembled polypyrrole/titania nanotube arrays (PPy/TNTA) surface was characterized by structural characterizations including attenuated total reflectance -fourier transform infrared spectroscopy, Raman and X-ray photoelectron spectroscopy analysis. Morphological study carried out by high resolution scanning electron microscopy demonstrates the influence of varying pulse period in achieving the controlled deposition of polypyrrole into the nanotube frame work. Cyclic voltammetry study reveals the electroactive nature of the hybrid material. The contact angle measurements and In-vitro immersion studies in stimulated body fluid hanks' solution were carried out to evaluate the wettability and apatite forming ability of the developed hybrid material. The deposition of polypyrrole enhanced the corrosion resistance of TNTA as evidenced from the lower icorr value observed for PPy/TNTA. The corrosion protection behavior of the hybrid material revealed from the electrochemical impedance spectroscopic studies was clearly noticed from the increase in impedance and maximum phase angle values. Further In-vitro cell culture studies were carried out using MG63 osteoblast cells to evaluate the biocompatibility of the hybrid material. Noticeable improvement in corrosion protection and biocompatibility performance suggest the possible application of PPy/TNTA hybrid material for biomedical applications.

Soft Lithography for Oligonucleotide Arrays Fabrication

DTIC Science & Technology

2001-10-25

adenosine; Abbreviated T, C, G, A respectively), the other synthesis reagents and solvents except oxidation agent (seen in Table 1) were purchased...dried by cold blowing before hybridization. Oligonucleotide arrays were hybridized in 200 nM 3’-TCC TCC GAT TCA GAG AGT CC- HEX (PE Biosystems... citrate buffer), 0.1% SDS in 0.1xSSC respectively. The probe array was scanned on the Scanarray Microarray Systems (Packard Biochip Technologies, USA

Experimental study of surface insulated-standard hybrid tungsten planar wire array Z-pinches at "QiangGuang-I" facility

NASA Astrophysics Data System (ADS)

Sheng, Liang; Peng, Bodong; Li, Yang; Yuan, Yuan; Li, Mo; Zhang, Mei; Zhao, Chen; Zhao, Jizhen; Wang, Liangping

2016-01-01

The experimental results of the insulated-standard hybrid wire array Z pinches carried out on "QiangGuang-I" facility at Northwest Institute of Nuclear Technology were presented and discussed. The surface insulating can impose a significant influence on the dynamics and radiation characteristics of the hybrid wire array Z pinches, especially on the early stage (t/timp < 0.6). The expansion of insulated wires at the ablation stage is suppressed, while the streams stripped from the insulated wires move faster than that from the standard wires. The foot radiation of X-ray is enhanced by increment of the number of insulated wires, 19.6 GW, 33.6 GW, and 68.6 GW for shots 14037S, 14028H, and 14039I, respectively. The surface insulation also introduces nonhomogeneity along the single wire—the streams move much faster near the electrodes. The colliding boundary of the hybrid wire array Z pinches is bias to the insulated side approximately 0.6 mm.

Recombination between Streptococcus suis ICESsu32457 and Streptococcus agalactiae ICESa2603 yields a hybrid ICE transferable to Streptococcus pyogenes.

PubMed

Marini, Emanuela; Palmieri, Claudio; Magi, Gloria; Facinelli, Bruna

2015-07-09

Integrative conjugative elements (ICEs) are mobile genetic elements that reside in the chromosome but retain the ability to undergo excision and to transfer by conjugation. Genes involved in drug resistance, virulence, or niche adaptation are often found among backbone genes as cargo DNA. We recently characterized in Streptococcus suis an ICE (ICESsu32457) carrying resistance genes [tet(O/W/32/O), tet(40), erm(B), aphA, and aadE] in the 15K unstable genetic element, which is flanked by two ∼1.3kb direct repeats. Remarkably, ∼1.3-kb sequences are conserved in ICESa2603 of Streptococcus agalactiae 2603V/R, which carry heavy metal resistance genes cadC/cadA and mer. In matings between S. suis 32457 (donor) and S. agalactiae 2603V/R (recipient), transconjugants were obtained. PCR experiments, PFGE, and sequence analysis of transconjugants demonstrated a tandem array between ICESsu32457 and ICESa2603. Matings between tandem array-containing S. agalactiae 2603V/R (donor) and Streptococcus pyogenes RF12 (recipient) yielded a single transconjugant containing a hybrid ICE, here named ICESa2603/ICESsu32457. The hybrid formed by recombination of the left ∼1.3-kb sequence of ICESsu32457 and the ∼1.3-kb sequence of ICESa2603. Interestingly, the hybrid ICE was transferable between S. pyogenes strains, thus demonstrating that it behaves as a conventional ICE. These findings suggest that both tandem arrays and hybrid ICEs may contribute to the evolution of antibiotic resistance in streptococci, creating novel mobile elements capable of disseminating new combinations of antibiotic resistance genes. Copyright © 2015 Elsevier B.V. All rights reserved.

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

[Prenatal genetic diagnosis for a fetus with atypical neurofibromatosis type 1 microdeletion].

PubMed

Lin, Shaobin; Wu, Jianzhu; Zhang, Zhiqiang; Ji, Yuanjun; Fang, Qun; Chen, Baojiang; Luo, Yanmin

2016-04-01

To analyze the correlation between atypical neurofibromatosis type 1(NF1) microdeletion and fetal phenotype. Fetal blood sampling was carried out for a woman bearing a fetus with talipes equinovarus. G-banded karyotyping and single nucleotide polymorphism array (SNP-array) were performed on the fetal blood sample. Fluorescence in situ hybridization (FISH) was used to confirm the result of SNP array analysis. FISH assay was also carried out on peripheral blood specimens from the parents to ascertain the origin of mutation. The karyotype of fetus was found to be 46, XY by G-banding analysis. However, a 3.132 Mb microdeletion was detected in chromosome region 17q11.2 by SNP array, which overlaped with the region of NF1 microdeletion syndrome. Analyzing of the specimens from the fetus and its parents with FISH has confirmed it to be a de novo deletion. Talipes equinovarus may be an abnormal sonographic feature of fetus with atypical NF1 microdeletion which can be accurately diagnosed with SNP array.

Micro-dressing of a carbon nanotube array with MoS2 gauze

NASA Astrophysics Data System (ADS)

Lim, Sharon Xiaodai; Woo, Kah Whye; Ng, Junju; Lu, Junpeng; Kwang, Siu Yi; Zhang, Zheng; Tok, Eng Soon; Sow, Chorng-Haur

2015-10-01

Few-layer MoS2 film has been successfully assembled over an array of CNTs. Using different focused laser beams with different wavelengths, site selective patterning of either the MoS2 film or the supporting CNT array is achieved. This paves the way for applications and investigations into the fundamental properties of the hybrid MoS2/CNT material with a controlled architecture. Through Raman mapping, straining and electron doping of the MoS2 film as a result of interaction with the supporting CNT array are detected. The role of the MoS2 film was further emphasized with a lower work function being detected from Ultra-violet Photoelectron Spectrsocopy (UPS) measurements of the hybrid material, compared to the CNT array. The effect of the changes in the work function was illustrated through the optoelectronic behavior of the hybrid material. At 0 V, 3.49 nA of current is measured upon illuminating the sample with a broad laser beam emitting laser light with a wavelength of 532 nm. With a strong response to external irradiation of different wavelengths, and changes to the power of the excitation source, the hybrid material has shown potential for applications in optoelectronic devices.

Population sequencing reveals breed and sub-species specific CNVs in cattle

USDA-ARS?s Scientific Manuscript database

Individualized copy number variation (CNV) maps have highlighted the need for population surveys of cattle to detect rare and common variants. While SNP and comparative genomic hybridization (CGH) arrays have provided preliminary data, next-generation sequence (NGS) data analysis offers an increased...

Heterologous Array Analysis in Pinaceae: Hybridization of Pinus Taeda cDNA Arrays With cDNA From Needles and Embryogenic Cultures of P. Taeda, P. Sylvestris or Picea Abies

PubMed Central

van Zyl, Leonel; von Arnold, Sara; Bozhkov, Peter; Chen, Yongzhong; Egertsdotter, Ulrika; MacKay, John; Sederoff, Ronald R.; Shen, Jing; Zelena, Lyubov

2002-01-01

Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces. PMID:18629264

Characterization and quantitative analysis of phenylpropanoid amides in eggplant (Solanum melongena L.) by high performance liquid chromatography coupled with diode array detection and hybrid ion trap time-of-flight mass spectrometry.

PubMed

Sun, Jing; Song, Yue-Lin; Zhang, Jing; Huang, Zheng; Huo, Hui-Xia; Zheng, Jiao; Zhang, Qian; Zhao, Yun-Fang; Li, Jun; Tu, Peng-Fei

2015-04-08

Eggplant (Solanum melongena L.) is a famous edible and medicinal plant. Despite being widely cultivated and used, data on certain parts other than the fruit are limited. The present study focused on the qualitative and quantitative analysis of the chemical constituents, particularly phenylpropanoid amides (PAs), in eggplant. The mass fragmentation patterns of PAs were proposed using seven authentic compounds with the assistance of a hybrid ion trap time-of-flight mass spectrometer. Thirty-seven compounds (27 PAs and 10 others) were detected and plausibly assigned in the different parts of eggplant. Afterward, a reliable method based on liquid chromatography coupled with diode array detection was developed, validated, and applied for the simultaneous determination of seven PAs and three caffeoylquinic acids in 17 batches of eggplant roots with satisfactory accuracy, precision, and reproducibility, which could not only provide global chemical insight of eggplant but also offer a reliable tool for quality control.

Hybrid magnet devices for molecule manipulation and small scale high gradient-field applications

DOEpatents

Humphries, David E [El Cerrito, CA; Hong, Seok-Cheol [Seoul, KR; Cozzarelli, legal representative, Linda A.; Pollard, Martin J [El Cerrito, CA; Cozzarelli, Nicholas R [Berkeley, CA

2009-01-06

The present disclosure provides a high performance hybrid magnetic structure made from a combination of permanent magnets and ferromagnetic pole materials which are assembled in a predetermined array. The hybrid magnetic structure provides means for separation and other biotechnology applications involving holding, manipulation, or separation of magnetizable molecular structures and targets. Also disclosed are hybrid magnetic tweezers able to exert approximately 1 nN of force to 4.5 .mu.m magnetic bead. The maximum force was experimentally measured to be .about.900 pN which is in good agreement with theoretical estimations and other measurements. In addition, a new analysis scheme that permits fast real-time position measurement in typical geometry of magnetic tweezers has been developed and described in detail.

Assessing the Battery Cost at Which Plug-In Hybrid Medium-Duty Parcel Delivery Vehicles Become Cost-Effective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramroth, L. A.; Gonder, J. D.; Brooker, A. D.

2013-04-01

The National Renewable Energy Laboratory (NREL) validated diesel-conventional and diesel-hybrid medium-duty parcel delivery vehicle models to evaluate petroleum reductions and cost implications of hybrid and plug-in hybrid diesel variants. The hybrid and plug-in hybrid variants are run on a field data-derived design matrix to analyze the effect of drive cycle, distance, engine downsizing, battery replacements, and battery energy on fuel consumption and lifetime cost. For an array of diesel fuel costs, the battery cost per kilowatt-hour at which the hybridized configuration becomes cost-effective is calculated. This builds on a previous analysis that found the fuel savings from medium duty plug-inmore » hybrids more than offset the vehicles' incremental price under future battery and fuel cost projections, but that they seldom did so under present day cost assumptions in the absence of purchase incentives. The results also highlight the importance of understanding the application's drive cycle specific daily distance and kinetic intensity.« less

Blocked impurity band hybrid infrared focal plane arrays for astronomy

NASA Technical Reports Server (NTRS)

Reynolds, D. B.; Seib, D. H.; Stetson, S. B.; Herter, T.; Rowlands, N.

1989-01-01

High-performance infrared hybrid focal plane arrays using 10- x 50-element Si:As blocked-impurity-band (BIB) detectors (cutoff wavelength = 28 microns) and matching switched MOSFET multiplexers have been developed and characterized for space astronomy. Use of impurity-band-conduction technology provides detectors which are nuclear-radiation-hard and free of the many anomalies associated with conventional silicon photoconductive detectors. Emphasis in the present work is on recent advances in detector material quality which have led to significantly improved detector and hybrid characteristics. Results demonstrating increased quantum efficiency (particularly at short-wavelength infrared), obtained by varying the BIB detector properties (infrared active layer thickness and arsenic doping profile), are summarized. Measured read noise and dark current for different temperatures are reported. The hybrid array performance achieved demonstrates that BIB detectors are well suited for use in astronomical instrumentation.

Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort.

PubMed

Retterer, Kyle; Scuffins, Julie; Schmidt, Daniel; Lewis, Rachel; Pineda-Alvarez, Daniel; Stafford, Amanda; Schmidt, Lindsay; Warren, Stephanie; Gibellini, Federica; Kondakova, Anastasia; Blair, Amanda; Bale, Sherri; Matyakhina, Ludmila; Meck, Jeanne; Aradhya, Swaroop; Haverfield, Eden

2015-08-01

Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing. Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array. In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons. These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array.Genet Med 17 8, 623-629.

Oligonucleotide Array for Identification and Detection of Pythium Species†

PubMed Central

Tambong, J. T.; de Cock, A. W. A. M.; Tinker, N. A.; Lévesque, C. A.

2006-01-01

A DNA array containing 172 oligonucleotides complementary to specific diagnostic regions of internal transcribed spacers (ITS) of more than 100 species was developed for identification and detection of Pythium species. All of the species studied, with the exception of Pythium ostracodes, exhibited a positive hybridization reaction with at least one corresponding species-specific oligonucleotide. Hybridization patterns were distinct for each species. The array hybridization patterns included cluster-specific oligonucleotides that facilitated the recognition of species, including new ones, belonging to groups such as those producing filamentous or globose sporangia. BLAST analyses against 500 publicly available Pythium sequences in GenBank confirmed that species-specific oligonucleotides were unique to all of the available strains of each species, of which there were numerous economically important ones. GenBank entries of newly described species that are not putative synonyms showed no homology to sequences of the spotted species-specific oligonucleotides, but most new species did match some of the cluster-specific oligonucleotides. Further verification of the specificity of the DNA array was done with 50 additional Pythium isolates obtained by soil dilution plating. The hybridization patterns obtained were consistent with the identification of these isolates based on morphology and ITS sequence analyses. In another blind test, total DNA of the same soil samples was amplified and hybridized on the array, and the results were compared to those of 130 Pythium isolates obtained by soil dilution plating and root baiting. The 13 species detected by the DNA array corresponded to the isolates obtained by a combination of soil dilution plating and baiting, except for one new species that was not represented on the array. We conclude that the reported DNA array is a reliable tool for identification and detection of the majority of Pythium species in environmental samples. Simultaneous detection and identification of multiple species of soilborne pathogens such as Pythium species could be a major step forward for epidemiological and ecological studies. PMID:16597974

Development of a gallium-doped germanium far-infrared photoconductor direct hybrid two-dimensional array.

PubMed

Fujiwara, Mikio; Hirao, Takanori; Kawada, Mitsunobu; Shibai, Hiroshi; Matsuura, Shuji; Kaneda, Hidehiro; Patrashin, Mikhail; Nakagawa, Takao

2003-04-20

To our knowledge, we are the first to successfully report a direct hybrid two-dimensional (2D) detector array in the far-infrared region. Gallium-doped germanium (Ge:Ga) has been used extensively to produce sensitive far-infrared detectors with a cutoff wavelength of approximately equal to 110 microm (2.7 THz). It is widely used in the fields of astronomy and molecular and solid spectroscopy. However, Ge:Ga photoconductors must be cooled below 4.2 K to reduce thermal noise, and this operating condition makes it difficult to develop a large format array because of the need for a warm amplifier. Development of Ge:Ga photoconductor arrays to take 2D terahertz images is now an important target in such research fields as space astronomy. We present the design of a 20 x 3 Ge:Ga far-infrared photoconductor array directly hybridized to a Si p-type metal-oxide-semiconductor readout integrated circuit using indium-bump technology. The main obstacles in creating this 2D array were (1) fabricating a monolithic Ge:Ga 2D array with a longitudinal configuration, (2) developing a cryogenic capacitive transimpedance amplifer, and (3) developing a technology for connecting the detector to the electronics. With this technology, a prototype Ge:Ga photoconductor with a direct hybrid structure has shown a responsivity as high as 14.6 A/W and a minimum detectable power of 5.6 x 10(-17) W for an integration time of 0.14 s when it was cooled to 2.1 K. Its noise is limited by the readout circuit with 20 microV/Hz(1/2) at 1 Hz. Vibration and cooling tests demonstrated that this direct hybrid structure is strong enough for spaceborne instruments. This detector array will be installed on the Japanese infrared satellite ASTRO-F.

Array-Based Comparative Genomic Hybridization for the Genomewide Detection of Submicroscopic Chromosomal Abnormalities

PubMed Central

Vissers, Lisenka E. L. M. ; de Vries, Bert B. A. ; Osoegawa, Kazutoyo ; Janssen, Irene M. ; Feuth, Ton ; Choy, Chik On ; Straatman, Huub ; van der Vliet, Walter ; Huys, Erik H. L. P. G. ; van Rijk, Anke ; Smeets, Dominique ; van Ravenswaaij-Arts, Conny M. A. ; Knoers, Nine V. ; van der Burgt, Ineke ; de Jong, Pieter J. ; Brunner, Han G. ; van Kessel, Ad Geurts ; Schoenmakers, Eric F. P. M. ; Veltman, Joris A. 

2003-01-01

Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using ∼3,500 flourescent in situ hybridization–verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome. PMID:14628292

RUSSIAS HYBRID APPROACH: WHAT CAN NATO DO TO SHARPEN ITS SWORD AGAINST IT

DTIC Science & Technology

2016-02-16

to maintain its survival and territorial integrity. Russian President Vladimir Putin prefers to cloak his sword under an array of hybrid tools such...prefers to cloak his “sharp sword” under an array of hybrid tools such as misinformation, cyber attacks and special purpose forces intended to create...Ukraine, there are diplomatic and informational actions that NATO can employ to blunt Putin’s cloaked sword. Russia’s Struggle for Survival and

Population sequencing reveals breed and sub-species specific CNVs in cattle

USDA-ARS?s Scientific Manuscript database

Individualized copy number variation (CNV) maps have highlighted the need for population surveys of cattle to detect the rare and common variants. While SNP and comparative genomic hybridization (CGH) arrays have provided preliminary data, next-generation sequence (NGS) data analysis offers an incre...

Tips on hybridizing, washing, and scanning affymetrix microarrays.

PubMed

Ares, Manuel

2014-02-01

Starting in the late 1990s, Affymetrix, Inc. produced a commercial system for hybridizing, washing, and scanning microarrays that was designed to be easy to operate and reproducible. The system used arrays packaged in a plastic cassette or chamber in which the prefabricated array was mounted and could be filled with fluid through resealable membrane ports either by hand or by an automated "fluidics station" specially designed to handle the arrays. A special rotating hybridization oven and a specially designed scanner were also required. Primarily because of automation and standardization the Affymetrix system was and still remains popular. Here, we provide a skeleton protocol with the potential pitfalls identified. It is designed to augment the protocols provided by Affymetrix.

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.

PubMed

Haraksingh, Rajini R; Abyzov, Alexej; Urban, Alexander Eckehart

2017-04-24

High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes. Across the arrays CNV detection varied widely in number of CNV calls (4-489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0-86%). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.

Programmable Self-Assembly of DNA-Dendrimer and DNA-Fullerene Nanostructures

DTIC Science & Technology

2004-10-01

separated by high pressure liquid chromatography ( HPLC ). The resulting material was analytically pure (99%) and monodisperse. Hybridization...bacterial and viral recognition, and gene expression analysis . These major accomplishments have been disseminated by various applications including 16...designing DNA strands with specific structural properties. The direct analysis of genomic DNA and RNA in an array format without labeling or

Experimental study of surface insulated-standard hybrid tungsten planar wire array Z-pinches at “QiangGuang-I” facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Liang; Peng, Bodong; Yuan, Yuan

The experimental results of the insulated-standard hybrid wire array Z pinches carried out on “QiangGuang-I” facility at Northwest Institute of Nuclear Technology were presented and discussed. The surface insulating can impose a significant influence on the dynamics and radiation characteristics of the hybrid wire array Z pinches, especially on the early stage (t/t{sub imp} < 0.6). The expansion of insulated wires at the ablation stage is suppressed, while the streams stripped from the insulated wires move faster than that from the standard wires. The foot radiation of X-ray is enhanced by increment of the number of insulated wires, 19.6 GW, 33.6 GW, and 68.6 GWmore » for shots 14037S, 14028H, and 14039I, respectively. The surface insulation also introduces nonhomogeneity along the single wire—the streams move much faster near the electrodes. The colliding boundary of the hybrid wire array Z pinches is bias to the insulated side approximately 0.6 mm.« less

Comparison of the Roche Cobas(®) 4800 HPV assay to Digene Hybrid Capture 2, Roche Linear Array and Roche Amplicor for Detection of High-Risk Human Papillomavirus Genotypes in Women undergoing treatment for cervical dysplasia.

PubMed

Phillips, Samuel; Garland, Suzanne M; Tan, Jeffery H; Quinn, Michael A; Tabrizi, Sepehr N

2015-01-01

The recently FDA (U.S. food and drug administration) approved Roche Cobas(®) 4800 (Cobas) human papillomavirus (HPV) has limited performance data compared to current HPV detection methods for test of cure in women undergoing treatment for high grade lesions. Evaluation of Cobas HPV assay using historical samples from women undergoing treatment for cervical dysplasia. A selection of 407 samples was tested on the Cobas assay and compared to previous results from Hybrid Capture 2, HPV Amplicor and Roche Linear Array. Overall, a correlation between high-risk HPV positivity and high grade histological diagnosis was 90.6% by the Cobas, 86.1% by Hybrid Capture 2, 92.9% by HPV Amplicor and 91.8% by Roche Linear Array. The Cobas HPV assay is comparative to both the HPV Amplicor and Roche Linear Array assays and better than Hybrid capture 2 assay in the detection of High-Risk HPV in women undergoing treatment for cervical dysplasia. Copyright © 2014 Elsevier B.V. All rights reserved.

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays

PubMed Central

Cook, Michael A.; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-01-01

Background Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20–60 base) unique sequence tags, or “barcodes”, associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Methodology/Principal Findings Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5′-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. Conclusions/Significance These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis. PMID:18253494

Hybrid structures based on gold nanoparticles and semiconductor quantum dots for biosensor applications.

PubMed

Kurochkina, Margarita; Konshina, Elena; Oseev, Aleksandr; Hirsch, Soeren

2018-01-01

The luminescence amplification of semiconductor quantum dots (QD) in the presence of self-assembled gold nanoparticles (Au NPs) is one of way for creating biosensors with highly efficient transduction. The objective of this study was to fabricate the hybrid structures based on semiconductor CdSe/ZnS QDs and Au NP arrays and to use them as biosensors of protein. In this paper, the hybrid structures based on CdSe/ZnS QDs and Au NP arrays were fabricated using spin coating processes. Au NP arrays deposited on a glass wafer were investigated by optical microscopy and absorption spectroscopy depending on numbers of spin coating layers and their baking temperature. Bovine serum albumin (BSA) was used as the target protein analyte in a phosphate buffer. A confocal laser scanning microscope was used to study the luminescent properties of Au NP/QD hybrid structures and to test BSA. The dimensions of Au NP aggregates increased and the space between them decreased with increasing processing temperature. At the same time, a blue shift of the plasmon resonance peak in the absorption spectra of Au NP arrays was observed. The deposition of CdSe/ZnS QDs with a core diameter of 5 nm on the surface of the Au NP arrays caused an increase in absorption and a red shift of the plasmon peak in the spectra. The exciton-plasmon enhancement of the QDs' photoluminescence intensity has been obtained at room temperature for hybrid structures with Au NPs array pretreated at temperatures of 100°C and 150°C. It has been found that an increase in the weight content of BSA increases the photoluminescence intensity of such hybrid structures. The ability of the qualitative and quantitative determination of protein content in solution using the Au NP/QD structures as an optical biosensor has been shown experimentally.

Hybrid structures based on gold nanoparticles and semiconductor quantum dots for biosensor applications

PubMed Central

Kurochkina, Margarita; Konshina, Elena; Oseev, Aleksandr; Hirsch, Soeren

2018-01-01

Background The luminescence amplification of semiconductor quantum dots (QD) in the presence of self-assembled gold nanoparticles (Au NPs) is one of way for creating biosensors with highly efficient transduction. Aims The objective of this study was to fabricate the hybrid structures based on semiconductor CdSe/ZnS QDs and Au NP arrays and to use them as biosensors of protein. Methods In this paper, the hybrid structures based on CdSe/ZnS QDs and Au NP arrays were fabricated using spin coating processes. Au NP arrays deposited on a glass wafer were investigated by optical microscopy and absorption spectroscopy depending on numbers of spin coating layers and their baking temperature. Bovine serum albumin (BSA) was used as the target protein analyte in a phosphate buffer. A confocal laser scanning microscope was used to study the luminescent properties of Au NP/QD hybrid structures and to test BSA. Results The dimensions of Au NP aggregates increased and the space between them decreased with increasing processing temperature. At the same time, a blue shift of the plasmon resonance peak in the absorption spectra of Au NP arrays was observed. The deposition of CdSe/ZnS QDs with a core diameter of 5 nm on the surface of the Au NP arrays caused an increase in absorption and a red shift of the plasmon peak in the spectra. The exciton–plasmon enhancement of the QDs’ photoluminescence intensity has been obtained at room temperature for hybrid structures with Au NPs array pretreated at temperatures of 100°C and 150°C. It has been found that an increase in the weight content of BSA increases the photoluminescence intensity of such hybrid structures. Conclusion The ability of the qualitative and quantitative determination of protein content in solution using the Au NP/QD structures as an optical biosensor has been shown experimentally. PMID:29731613

Simplified Microarray Technique for Identifying mRNA in Rare Samples

NASA Technical Reports Server (NTRS)

Almeida, Eduardo; Kadambi, Geeta

2007-01-01

Two simplified methods of identifying messenger ribonucleic acid (mRNA), and compact, low-power apparatuses to implement the methods, are at the proof-of-concept stage of development. These methods are related to traditional methods based on hybridization of nucleic acid, but whereas the traditional methods must be practiced in laboratory settings, these methods could be practiced in field settings. Hybridization of nucleic acid is a powerful technique for detection of specific complementary nucleic acid sequences, and is increasingly being used for detection of changes in gene expression in microarrays containing thousands of gene probes. A traditional microarray study entails at least the following six steps: 1. Purification of cellular RNA, 2. Amplification of complementary deoxyribonucleic acid [cDNA] by polymerase chain reaction (PCR), 3. Labeling of cDNA with fluorophores of Cy3 (a green cyanine dye) and Cy5 (a red cyanine dye), 4. Hybridization to a microarray chip, 5. Fluorescence scanning the array(s) with dual excitation wavelengths, and 6. Analysis of the resulting images. This six-step procedure must be performed in a laboratory because it requires bulky equipment.

Nucleic acid detection methods

DOEpatents

Smith, C.L.; Yaar, R.; Szafranski, P.; Cantor, C.R.

1998-05-19

The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3{prime}-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated. 18 figs.

The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds

USDA-ARS?s Scientific Manuscript database

Individualized copy number variation (CNV) maps have highlighted the need for population surveys of cattle to detect rare and common variants. While SNP and comparative genomic hybridization (CGH) arrays have provided preliminary data, next-generation sequence (NGS) data analysis offers an increased...

Localized surface plasmon resonance properties of Ag nanorod arrays on graphene-coated Au substrate

NASA Astrophysics Data System (ADS)

Mu, Haiwei; Lv, Jingwei; Liu, Chao; Sun, Tao; Chu, Paul K.; Zhang, Jingping

2017-11-01

Localized surface plasmon resonance (LSPR) on silver nanorod (SNR) arrays deposited on a graphene-coated Au substrate is investigated by the discrete dipole approximation (DDA) method. The resonance peaks in the extinction spectra of the SNR/graphene/Au structure show significantly different profiles as SNR height, and refractive index of the surrounding medium are varied gradually. Numerical simulation reveals that the shifts in the resonance peaks arise from hybridization of multiple plasmon modes as a result of coupling between the SNR arrays and graphene-coated Au substrate. Moreover, the LSPR modes blue-shifts from 800 nm to 700 nm when the thickness of the graphene layer in the metal nanoparticle (NP) - graphene hybrid nanostructure increases from 1 nm to 5 nm, which attribute to charge transfer between the graphene layer and SNR arrays. The results provide insights into metal NP-graphene hybrid nanostructures which have potential applications in plasmonics.

Analysis of genomic alterations in neuroblastoma by multiplex ligation-dependent probe amplification and array comparative genomic hybridization: a comparison of results.

PubMed

Combaret, Valérie; Iacono, Isabelle; Bréjon, Stéphanie; Schleiermacher, Gudrun; Pierron, Gäelle; Couturier, Jérôme; Bergeron, Christophe; Blay, Jean-Yves

2012-12-01

In cases of neuroblastoma, recurring genetic alterations--losses of the 1p, 3p, 4p, and 11q and/or gains of 1q, 2p, and 17q chromosome arms--are currently used to define the therapeutic strategy in therapeutic protocols for low- and intermediate-risk patients. Different genome-wide analysis techniques, such as array comparative genomic hybridization (aCGH) or multiplex ligation-dependent probe amplification (MLPA), have been suggested for detecting chromosome segmental abnormalities. In this study, we compared the results of the two technologies in the analyses of the DNA of tumor samples from 91 neuroblastoma patients. Similar results were obtained with the two techniques for 75 samples (82%). In five cases (5.5%), the MLPA results were not interpretable. Discrepancies between the aCGH and MLPA results were observed in 11 cases (12%). Among the discrepancies, a 18q21.2-qter gain and 16p11.2 and 11q14.1-q14.3 losses were detected only by aCGH. The MLPA results showed that the 7p, 7q, and 14q chromosome arms were affected in six cases, while in two cases, 2p and 17q gains were observed; these results were confirmed by neither aCGH nor fluorescence in situ hybridization (FISH) analysis. Because of the higher sensitivity and specificity of genome-wide information, reasonable cost, and shorter time of aCGH analysis, we recommend the aCGH procedure for the analysis of genomic alterations in neuroblastoma. Copyright © 2012 Elsevier Inc. All rights reserved.

Development and application of a microarray meter tool to optimize microarray experiments

PubMed Central

Rouse, Richard JD; Field, Katrine; Lapira, Jennifer; Lee, Allen; Wick, Ivan; Eckhardt, Colleen; Bhasker, C Ramana; Soverchia, Laura; Hardiman, Gary

2008-01-01

Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control) and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization) using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray) manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a) a measure of variability in the signal intensities, b) a measure of the signal dynamic range and c) a measure of variability of the spot morphologies. PMID:18710498

A High-Efficiency Si Nanowire Array/Perovskite Hybrid Solar Cell.

PubMed

Yan, Xin; Zhang, Chen; Wang, Jiamin; Zhang, Xia; Ren, Xiaomin

2017-12-01

A low-cost Si nanowire array/perovskite hybrid solar cell is proposed and simulated. The solar cell consists of a Si p-i-n nanowire array filled with CH 3 NH 3 PbI 3 , in which both the nanowires and perovskite absorb the incident light while the nanowires act as the channels for transporting photo-generated electrons and holes. The hybrid structure has a high absorption efficiency in a broad wavelength range of 300~800 nm. A large short-circuit current density of 28.8 mA/cm 2 and remarkable conversion efficiency of 13.3% are obtained at a thin absorber thickness of 1.6 μm, which are comparable to the best results of III-V nanowire solar cells.

454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples

PubMed Central

Altimari, Annalisa; de Biase, Dario; De Maglio, Giovanna; Gruppioni, Elisa; Capizzi, Elisa; Degiovanni, Alessio; D’Errico, Antonia; Pession, Annalisa; Pizzolitto, Stefano; Fiorentino, Michelangelo; Tallini, Giovanni

2013-01-01

Detection of KRAS mutations in archival pathology samples is critical for therapeutic appropriateness of anti-EGFR monoclonal antibodies in colorectal cancer. We compared the sensitivity, specificity, and accuracy of Sanger sequencing, ARMS-Scorpion (TheraScreen®) real-time polymerase chain reaction (PCR), pyrosequencing, chip array hybridization, and 454 next-generation sequencing to assess KRAS codon 12 and 13 mutations in 60 nonconsecutive selected cases of colorectal cancer. Twenty of the 60 cases were detected as wild-type KRAS by all methods with 100% specificity. Among the 40 mutated cases, 13 were discrepant with at least one method. The sensitivity was 85%, 90%, 93%, and 92%, and the accuracy was 90%, 93%, 95%, and 95% for Sanger sequencing, TheraScreen real-time PCR, pyrosequencing, and chip array hybridization, respectively. The main limitation of Sanger sequencing was its low analytical sensitivity, whereas TheraScreen real-time PCR, pyrosequencing, and chip array hybridization showed higher sensitivity but suffered from the limitations of predesigned assays. Concordance between the methods was k = 0.79 for Sanger sequencing and k > 0.85 for the other techniques. Tumor cell enrichment correlated significantly with the abundance of KRAS-mutated deoxyribonucleic acid (DNA), evaluated as ΔCt for TheraScreen real-time PCR (P = 0.03), percentage of mutation for pyrosequencing (P = 0.001), ratio for chip array hybridization (P = 0.003), and percentage of mutation for 454 next-generation sequencing (P = 0.004). Also, 454 next-generation sequencing showed the best cross correlation for quantification of mutation abundance compared with all the other methods (P < 0.001). Our comparison showed the superiority of next-generation sequencing over the other techniques in terms of sensitivity and specificity. Next-generation sequencing will replace Sanger sequencing as the reference technique for diagnostic detection of KRAS mutation in archival tumor tissues. PMID:23950653

Biaxially stretchable supercapacitors based on the buckled hybrid fiber electrode array

NASA Astrophysics Data System (ADS)

Zhang, Nan; Zhou, Weiya; Zhang, Qiang; Luan, Pingshan; Cai, Le; Yang, Feng; Zhang, Xiao; Fan, Qingxia; Zhou, Wenbin; Xiao, Zhuojian; Gu, Xiaogang; Chen, Huiliang; Li, Kewei; Xiao, Shiqi; Wang, Yanchun; Liu, Huaping; Xie, Sishen

2015-07-01

In order to meet the growing need for smart bionic devices and epidermal electronic systems, biaxial stretchability is essential for energy storage units. Based on porous single-walled carbon nanotube/poly(3,4-ethylenedioxythiophene) (SWCNT/PEDOT) hybrid fiber, we designed and fabricated a biaxially stretchable supercapacitor, which possesses a unique configuration of the parallel buckled hybrid fiber array. Owing to the reticulate SWCNT film and the improved fabrication technique, the hybrid fiber retained its porous architecture both outwardly and inwardly, manifesting a superior capacity of 215 F g-1. H3PO4-polyvinyl alcohol gel with an optimized component ratio was introduced as both binder and stretchable electrolyte, which contributed to the regularity and stability of the buckled fiber array. The buckled structure and the quasi one-dimensional character of the fibers endow the supercapacitor with 100% stretchability along all directions. In addition, the supercapacitor exhibited good transparency, as well as excellent electrochemical properties and stability after being stretched 5000 times.In order to meet the growing need for smart bionic devices and epidermal electronic systems, biaxial stretchability is essential for energy storage units. Based on porous single-walled carbon nanotube/poly(3,4-ethylenedioxythiophene) (SWCNT/PEDOT) hybrid fiber, we designed and fabricated a biaxially stretchable supercapacitor, which possesses a unique configuration of the parallel buckled hybrid fiber array. Owing to the reticulate SWCNT film and the improved fabrication technique, the hybrid fiber retained its porous architecture both outwardly and inwardly, manifesting a superior capacity of 215 F g-1. H3PO4-polyvinyl alcohol gel with an optimized component ratio was introduced as both binder and stretchable electrolyte, which contributed to the regularity and stability of the buckled fiber array. The buckled structure and the quasi one-dimensional character of the fibers endow the supercapacitor with 100% stretchability along all directions. In addition, the supercapacitor exhibited good transparency, as well as excellent electrochemical properties and stability after being stretched 5000 times. Electronic supplementary information (ESI) available: SEM images of the twist-first hybrid fiber, TEM images of SWCNT/PEDOT hybrid bundles, Raman spectra and FTIR spectra of the hybrid electrodes, CVs of the pristine, bended and wound supercapacitor, transmittance spectra of the pristine and stretched supercapacitor, demo video of the supercapacitor. See DOI: 10.1039/c5nr03027g

Collective photonic-plasmonic resonances in noble metal - dielectric nanoparticle hybrid arrays

DOE PAGES

Hong, Yan; Reinhard, Björn M.

2014-10-27

Coherent scattering of gold and silver nanoparticles (NPs) in regular arrays can generate Surface Lattice Resonances (SLRs) with characteristically sharp spectral features. Herein, we investigate collective resonances in compositionally more complex arrays comprising NP clusters and NPs with different chemical compositions at pre-defined lattice sites. We first characterize the impact of NP clustering by exchanging individual gold NPs in the array through dimers of electromagnetically strongly coupled gold NPs. Then, we analyze hybrid arrays that contain both gold metal NP dimers and high refractive index dielectric NPs as building blocks. We demonstrate that the integration of gold NP clusters andmore » dielectric NPs into one array enhances E-field intensities not only in the vicinity of the NPs but also in the ambient medium of the entire array. In addition, this work shows that the ability to integrate multiple building blocks with different resonance conditions in one array provides new degrees of freedom for engineering optical fields in the array plane with variable amplitude and phase.« less

Development of a High-Throughput Resequencing Array for the Detection of Pathogenic Mutations in Osteogenesis Imperfecta

PubMed Central

Wang, Yao; Cui, Yazhou; Zhou, Xiaoyan; Han, Jinxiang

2015-01-01

Objective Osteogenesis imperfecta (OI) is a rare inherited skeletal disease, characterized by bone fragility and low bone density. The mutations in this disorder have been widely reported to be on various exonal hotspots of the candidate genes, including COL1A1, COL1A2, CRTAP, LEPRE1, and FKBP10, thus creating a great demand for precise genetic tests. However, large genome sizes make the process daunting and the analyses, inefficient and expensive. Therefore, we aimed at developing a fast, accurate, efficient, and cheaper sequencing platform for OI diagnosis; and to this end, use of an advanced array-based technique was proposed. Method A CustomSeq Affymetrix Resequencing Array was established for high-throughput sequencing of five genes simultaneously. Genomic DNA extraction from 13 OI patients and 85 normal controls and amplification using long-range PCR (LR-PCR) were followed by DNA fragmentation and chip hybridization, according to standard Affymetrix protocols. Hybridization signals were determined using GeneChip Sequence Analysis Software (GSEQ). To examine the feasibility, the outcome from new resequencing approach was validated by conventional capillary sequencing method. Result Overall call rates using resequencing array was 96–98% and the agreement between microarray and capillary sequencing was 99.99%. 11 out of 13 OI patients with pathogenic mutations were successfully detected by the chip analysis without adjustment, and one mutation could also be identified using manual visual inspection. Conclusion A high-throughput resequencing array was developed that detects the disease-associated mutations in OI, providing a potential tool to facilitate large-scale genetic screening for OI patients. Through this method, a novel mutation was also found. PMID:25742658

Effect of Refractive Index of Substrate on Fabrication and Optical Properties of Hybrid Au-Ag Triangular Nanoparticle Arrays

PubMed Central

Liu, Jing; Chen, Yushan; Cai, Haoyuan; Chen, Xiaoyi; Li, Changwei; Yang, Cheng-Fu

2015-01-01

In this study, the nanosphere lithography (NSL) method was used to fabricate hybrid Au-Ag triangular periodic nanoparticle arrays. The Au-Ag triangular periodic arrays were grown on different substrates, and the effect of the refractive index of substrates on fabrication and optical properties was systematically investigated. At first, the optical spectrum was simulated by the discrete dipole approximation (DDA) numerical method as a function of refractive indexes of substrates and mediums. Simulation results showed that as the substrates had the refractive indexes of 1.43 (quartz) and 1.68 (SF5 glass), the nanoparticle arrays would have better refractive index sensitivity (RIS) and figure of merit (FOM). Simulation results also showed that the peak wavelength of the extinction spectra had a red shift when the medium’s refractive index n increased. The experimental results also demonstrated that when refractive indexes of substrates were 1.43 and 1.68, the nanoparticle arrays and substrate had better adhesive ability. Meanwhile, we found the nanoparticles formed a large-scale monolayer array with the hexagonally close-packed structure. Finally, the hybrid Au-Ag triangular nanoparticle arrays were fabricated on quartz and SF5 glass substrates and their experiment extinction spectra were compared with the simulated results.

Cochlear's unique electrode portfolio now and in the future.

PubMed

von Wallenberg, E; Briggs, R

2014-05-01

To review Cochlear's electrode portfolio and discuss the merits of current and future straight and perimodiolar electrode arrays. To present an update on implant reliability. Performance and hearing preservation data from studies involving the Slim Straight (CI422), Hybrid L24 and Contour Advance electrode array were reviewed. While several studies in past found little difference in performance outcomes between subjects implanted with perimodiolar and straight arrays, recent studies demonstrated that proximity to the modiolus is correlated with better performance. Hearing threshold increase was lowest with the Hybrid L24, closely followed by the slim straight array and was largest with the Contour Advance array. The CI24RE receiver-stimulator used for the three arrays had a cumulative survival of 99% at eight years post implantation. Combining the hearing preservation benefits of slim straight arrays with perimodiolar proximity is the design objective of Cochlear's next generation electrodes.

The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

PubMed Central

2012-01-01

Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68% in Asian and 70% in Caucasian. Conclusions Our study provides an invaluable database revealing common and differential imbalance regions at specific chromosomes among Asian and Caucasian lung cancer patients. Four validation methods confirmed our database, which would help in further studies on the mechanism of lung tumorigenesis. PMID:22691236

Ultrasensitive Label-free Electronic Chip for DNA Analysis Using Carbon Nanotube Nanoelectrode Arrays

NASA Technical Reports Server (NTRS)

Li, Jun; Koehne, Jessica; Chen, Hua; Cassell, Alan; Ng, Hou Tee; Ye, Qi; Han, Jie; Meyyappan, M.

2004-01-01

There is a strong need for faster, cheaper, and simpler methods for nucleic acid analysis in today s clinical tests. Nanotechnologies can potentially provide solutions to these requirements by integrating nanomaterials with biofunctionalities. Dramatic improvement in the sensitivity and multiplexing can be achieved through the high-degree miniaturization. Here, we present our study in the development of an ultrasensitive label-free electronic chip for DNA/RNA analysis based on carbon nanotube nanoelectrode arrays. A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in a SiO2 matrix is fabricated using a bottom-up approach. Characteristic nanoelectrode behavior is observed with a low-density MWNT nanoelectrode array in measuring both the bulk and surface immobilized redox species. The open-end of MWNTs are found to present similar properties as graphite edge-plane electrodes, with a wide potential window, flexible chemical functionalities, and good biocompatibility. A BRCA1 related oligonucleotide probe with 18 bases is covalently functionalized at the open ends of the MWNTs and specifically hybridized with an oligonucleotide target as well as a PCR amplicon. The guanine bases in the target molecules are employed as the signal moieties for the electrochemical measurements. Ru(bpy)3(2+) mediator is used to further amplify the guanine oxidation signal. This technique has been employed for direct electrochemical detection of label-free PCR amplicon through specific hybridization with the BRCAl probe. The detection limit is estimated to be less than approximately 1000 DNA molecules, approaching the limit of the sensitivity by laser-based fluorescence techniques in DNA microarray. This system provides a general electronic platform for rapid molecular diagnostics in applications requiring ultrahigh sensitivity, high-degree of miniaturization, simple sample preparation, and low- cost operation.

LS-CAP: an algorithm for identifying cytogenetic aberrations in hepatocellular carcinoma using microarray data.

PubMed

He, Xianmin; Wei, Qing; Sun, Meiqian; Fu, Xuping; Fan, Sichang; Li, Yao

2006-05-01

Biological techniques such as Array-Comparative genomic hybridization (CGH), fluorescent in situ hybridization (FISH) and affymetrix single nucleotide pleomorphism (SNP) array have been used to detect cytogenetic aberrations. However, on genomic scale, these techniques are labor intensive and time consuming. Comparative genomic microarray analysis (CGMA) has been used to identify cytogenetic changes in hepatocellular carcinoma (HCC) using gene expression microarray data. However, CGMA algorithm can not give precise localization of aberrations, fails to identify small cytogenetic changes, and exhibits false negatives and positives. Locally un-weighted smoothing cytogenetic aberrations prediction (LS-CAP) based on local smoothing and binomial distribution can be expected to address these problems. LS-CAP algorithm was built and used on HCC microarray profiles. Eighteen cytogenetic abnormalities were identified, among them 5 were reported previously, and 12 were proven by CGH studies. LS-CAP effectively reduced the false negatives and positives, and precisely located small fragments with cytogenetic aberrations.

Whole Genome Amplification of Labeled Viable Single Cells Suited for Array-Comparative Genomic Hybridization.

PubMed

Kroneis, Thomas; El-Heliebi, Amin

2015-01-01

Understanding details of a complex biological system makes it necessary to dismantle it down to its components. Immunostaining techniques allow identification of several distinct cell types thereby giving an inside view of intercellular heterogeneity. Often staining reveals that the most remarkable cells are the rarest. To further characterize the target cells on a molecular level, single cell techniques are necessary. Here, we describe the immunostaining, micromanipulation, and whole genome amplification of single cells for the purpose of genomic characterization. First, we exemplify the preparation of cell suspensions from cultured cells as well as the isolation of peripheral mononucleated cells from blood. The target cell population is then subjected to immunostaining. After cytocentrifugation target cells are isolated by micromanipulation and forwarded to whole genome amplification. For whole genome amplification, we use GenomePlex(®) technology allowing downstream genomic analysis such as array-comparative genomic hybridization.

Nucleic acid in-situ hybridization detection of infectious agents

NASA Astrophysics Data System (ADS)

Thompson, Curtis T.

2000-04-01

Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

Conventional and array-based comparative genomic hybridization analysis of nasopharyngeal carcinomas from the Mediterranean area.

PubMed

Rodriguez, S; Khabir, A; Keryer, C; Perrot, C; Drira, M; Ghorbel, A; Jlidi, R; Bernheim, A; Valent, A; Busson, P

2005-03-01

Nasopharyngeal carcinoma (NPC) occurs with a high incidence in Southeast Asia and to a lesser extent in the Mediterranean area, especially in Tunisia, Algeria, and Morocco. Cellular gene alterations combined with latent Epstein-Barr virus infection are thought to be essential for NPC oncogenesis. To date, chromosome analysis with comparative genomic hybridization (CGH) has been reported exclusively for NPCs from Southeast Asia. Although NPCs from the Mediterranean area have several distinct clinical and epidemiological features, CGH investigations have been lacking. Chromosome analysis was therefore undertaken on a series of NPC xenografts and biopsies derived from patients of Mediterranean origin. Four xenografts were investigated with a combination of conventional CGH, array-based CGH, and comparative expressed sequence hybridization. In addition, 23 fresh NPC biopsies were analyzed with conventional CGH. Data obtained from xenografts and fresh biopsies were consistent, except that amplification of genes at 18p was observed only in xenografts derived from metastatic tissues. Frequent gains associated with gene overexpression were detected at 1q25 approximately qter (64%) and 12p13 (50%). Losses were noticed mainly at 11q14 approximately q23 (50%), 13q12 approximately q31 (50%), 14q24 approximately q31 (43%), and 3p13 approximately p23 (43%). Comparison with previous reports suggests that Mediterranean NPCs have higher frequencies of gains at 1q and losses at 13q than their Asian counterparts.

GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

PubMed Central

Lyng, Heidi; Lando, Malin; Brøvig, Runar S; Svendsrud, Debbie H; Johansen, Morten; Galteland, Eivind; Brustugun, Odd T; Meza-Zepeda, Leonardo A; Myklebost, Ola; Kristensen, Gunnar B; Hovig, Eivind; Stokke, Trond

2008-01-01

Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers. PMID:18500990

Design, processing and testing of LSI arrays, hybrid microelectronics task

NASA Technical Reports Server (NTRS)

Himmel, R. P.; Stuhlbarg, S. M.; Ravetti, R. G.; Zulueta, P. J.; Rothrock, C. W.

1979-01-01

Mathematical cost models previously developed for hybrid microelectronic subsystems were refined and expanded. Rework terms related to substrate fabrication, nonrecurring developmental and manufacturing operations, and prototype production are included. Sample computer programs were written to demonstrate hybrid microelectric applications of these cost models. Computer programs were generated to calculate and analyze values for the total microelectronics costs. Large scale integrated (LST) chips utilizing tape chip carrier technology were studied. The feasibility of interconnecting arrays of LSU chips utilizing tape chip carrier and semiautomatic wire bonding technology was demonstrated.

Prenatal diagnosis and molecular cytogenetic characterization of rec(10)dup(10p)inv(10)(p11.2q26.3) in a fetus associated with paternal pericentric inversion.

PubMed

Chen, Chih-Ping; Ko, Tsang-Ming; Su, Yi-Ning; Wang, Liang-Kai; Chern, Schu-Rern; Wu, Peih-Shan; Chen, Yen-Ni; Chen, Shin-Wen; Ko, Kevin; Lee, Chen-Chi; Chen, Li-Feng; Yang, Chien-Wen; Wang, Wayseen

2016-10-01

We present prenatal diagnosis and molecular cytogenetic characterization of a recombinant chromosome 10 in a fetus associated with a paternal pericentric inversion. A 35-year-old woman underwent amniocentesis at 18 weeks of gestation because of an advanced maternal age. Amniocentesis revealed a karyotype of 46,XY,der(10)del(10) (q26.3)dup(10)(p11.2p15). She underwent repeat amniocentesis at 21 weeks of gestation and array comparative genomic hybridization revealed a 31.65-Mb duplication of chromosome 10p15.3-p11.22 and a 3.07-Mb deletion of chromosome 10q26.3. Prenatal ultrasound findings were unremarkable. She was referred for genetic counseling and cytogenetic analysis revealed a karyotype of 46,XY,inv(10)(p11.2q26.3) in the father and a karyotype of 46,XX in the mother. The pregnancy was subsequently terminated, and a fetus was delivered with prominent facial dysmorphism. Postnatal cytogenetic analysis of the placenta revealed a karyotype of 46,XY, rec(10)dup(10p)inv(10)(p11.2q26.3). Fluorescence in situ hybridization analysis revealed a duplication of terminal 10p and a deletion of terminal 10q in the recombinant chromosome 10. Array comparative genomic hybridization analysis of the cord blood and umbilical cord confirmed the prenatal diagnosis. Prenatal diagnosis of a recombinant chromosome because of an advanced maternal age should alert the possibility of a paternal pericentric inversion. Copyright © 2016. Published by Elsevier B.V.

The Southern Hemisphere VLBI experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, R.A.; Meier, D.L.; Louie, A.P.

1989-07-01

Six radio telescopes were operated as the first Southern Hemisphere VLBI array in April and May 1982. Observations were made at 2.3 and 8.4 GHz. This array provided VLBI modeling and hybrid imaging of celestial radio sources in the Southern Hemisphere, high-accuracy VLBI geodesy between Southern Hemisphere sites, and subarcsecond radio astrometry of celestial sources south of declination -45 deg. The goals and implementation of the array are discussed, the methods of modeling and hybrid image production are explained, and the VLBI structure of the sources that were observed is summarized. 36 refs.

Report: Optimization study of the preparation factors for argan oil microcapsule based on hybrid-level orthogonal array design via SPSS modeling.

PubMed

Zhao, Xi; Wu, Xiaoli; Zhou, Hui; Jiang, Tao; Chen, Chun; Liu, Mingshi; Jin, Yuanbao; Yang, Dongsheng

2014-11-01

To optimize the preparation factors for argan oil microcapsule using complex coacervation of chitosan cross-linked with gelatin based on hybrid-level orthogonal array design via SPSS modeling. Eight relatively significant factors were firstly investigated and selected as calculative factors for the orthogonal array design from the total of ten factors effecting the preparation of argan oil microcapsule by utilizing the single factor variable method. The modeling of hybrid-level orthogonal array design was built in these eight factors with the relevant levels (9, 9, 9, 9, 7, 6, 2 and 2 respectively). The preparation factors for argan oil microcapsule were investigated and optimized according to the results of hybrid-level orthogonal array design. The priorities order and relevant optimum levels of preparation factors standard to base on the percentage of microcapsule with the diameter of 30~40 μm via SPSS. Experimental data showed that the optimum factors were controlling the chitosan/gelatin ratio, the systemic concentration and the core/shell ratio at 1:2, 1.5% and 1:7 respectively, presetting complex coacervation pH at 6.4, setting cross-linking time and complex coacervation at 75 min and 30 min, using the glucose-delta lactone as the type of cross-linking agent, and selecting chitosan with the molecular weight of 2000～3000.

Development of Hybrid Sensor Arrays for Sensor Arrays for Simultaneous Measurement of Pressure and Shear Stress Distribution

NASA Technical Reports Server (NTRS)

2000-01-01

This document reports on the progress in developing hybrid sensors for the simultaneous measurement of pressure and shear stress. The key feature for the success of the proposed hybrid sensor array is the ability to deposit Cu-Ni alloy with proper composition (55 - 45) on a silicon wafer to form a strain gage. This alloy strain gage replaces the normally used Si strain gages in MEMS, which are highly nonlinear and temperature dependent. The copper nickel, with proper composition (55 - 45), was successfully deposited on a silicon wafer with a few trials during this period of the project. Pictures of the Cu-Ni alloy strain gage and the x-ray spectra indicating the composition are shown. The planned tests are also reviewed.

Numerical study on refractive index sensor based on hybrid-plasmonic mode

NASA Astrophysics Data System (ADS)

Yun, Jeong-Geun; Kim, Joonsoo; Lee, Kyookeun; Lee, Yohan; Lee, Byoungho

2017-04-01

We propose a highly sensitive hybrid-plasmonic sensor based on thin-gold nanoslit arrays. The transmission characteristics of gold nanoslit arrays are analyzed as changing the thickness of gold layer. The surface plasmon polariton mode excited on the sensing medium, which is sensitive to refractive index change of the sensing medium, is strengthened by reducing the thickness of the gold layer. A design rule is suggested that steeper dispersion curve of the surface plasmon polariton mode leads to higher sensitivity. For the dispersion engineering, hybrid-plasmonic structure, which consists of thin-gold nanoslit arrays, sensing region and high refractive index dielectric space is introduced. The proposed sensor structure with period of 700 nm shows the improved sensitivity up to 1080 nm/RIU (refractive index unit), and the surface sensitivity is extremely enhanced.

Indium Hybridization of Large Format TES Bolometer Arrays to Readout Multiplexers for Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Costen, Nick; Allen, Christine

2007-01-01

The advance of new detector technologies combined with enhanced fabrication methods has resulted in an increase in development of large format arrays. The next generation of scientific instruments will utilize detectors containing hundreds to thousands of elements providing a more efficient means to conduct large area sky surveys. Some notable detectors include a 32x32 x-ray microcalorimeter for Constellation-X, an infrared bolometer called SAFIRE to fly on the airborne observatory SOFIA, and the sub-millimeter bolometer SCUBA-2 to be deployed at the JCMT which will use more than 10,000 elements for two colors, each color using four 32x40 arrays. Of these detectors, SCUBA-2 is farthest along in development and uses indium hybridization to multiplexers for readout of the large number of elements, a technology that will be required to enable the next generation of large format arrays. Our current efforts in working toward large format arrays have produced GISMO, the Goddard IRAM Superconducting 2-Millimeter observer. GISMO is a far infrared instrument to be field tested later this year at the IRAM 30 meter telescope in Spain. GISMO utilizes transition edge sensor (TES) technology in an 8x16 filled array format that allows for typical fan-out wiring and wire-bonding to four 1x32 NIST multiplexers. GISMO'S electrical wiring is routed along the tops of 30 micron walls which also serve as the mechanical framework for the array. This architecture works well for the 128 element array, but is approaching the limit for routing the necessary wires along the surface while maintaining a high fill factor. Larger format arrays will benefit greatly from making electrical connections through the wafer to the backside, where they can be hybridized to a read-out substrate tailored to handling the wiring scheme. The next generation array we are developing is a 32x40 element array on a pitch of 1135 microns that conforms to the NIST multiplexer, already developed for the SCUBA-2 instrument This architecture will utilize electrical connections that route from the TES to the support frame and through the wafer. The detector chip will then be hybridized to the NIST multiplexer via indium bump bonding. In our development scheme we are using substrates that allow for diagnostic testing of electrical continuity across the entire array and we are testing our process to minimize or eliminate any contact resistance at metal interfaces. Our goal is hybridizing a fully functional 32x40 array of TES bolometers to a NIST multiplexer. The following work presents our current progress toward enabling this technology.

Non-invasive preimplantation genetic screening using array comparative genomic hybridization on spent culture media: a proof-of-concept pilot study.

PubMed

Feichtinger, Michael; Vaccari, Enrico; Carli, Luca; Wallner, Elisabeth; Mädel, Ulrike; Figl, Katharina; Palini, Simone; Feichtinger, Wilfried

2017-06-01

The aim of this pilot study was to assess if array comparative genomic hybridization (aCGH), non-invasive preimplantation genetic screening (PGS) on blastocyst culture media is feasible. Therefore, aCGH analysis was carried out on 22 spent blastocyst culture media samples after polar body PGS because of advanced maternal age. All oocytes were fertilized by intracytoplasmic sperm injection and all embryos underwent assisted hatching. Concordance of polar body analysis and culture media genetic results was assessed. Thirteen out of 18 samples (72.2%) revealed general concordance of ploidy status (euploid or aneuploid). At least one chromosomal aberration was found concordant in 10 out of 15 embryos found to be aneuploid by both polar body and culture media analysis. Overall, 17 out of 35 (48.6%) single chromosomal aneuploidies were concordant between the culture media and polar body analysis. By analysing negative controls (oocytes with fertilization failure), notable maternal contamination was observed. Therefore, non-invasive PGS could serve as a second matrix after polar body or cleavage stage PGS; however, in euploid results, maternal contamination needs to be considered and results interpreted with caution. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

A Streamlined Protocol for Molecular Testing of the DMD Gene within a Diagnostic Laboratory: A Combination of Array Comparative Genomic Hybridization and Bidirectional Sequence Analysis

PubMed Central

Marquis-Nicholson, Renate; Lai, Daniel; Love, Jennifer M.; Love, Donald R.

2013-01-01

Purpose. The aim of this study was to develop a streamlined mutation screening protocol for the DMD gene in order to confirm a clinical diagnosis of Duchenne or Becker muscular dystrophy in affected males and to clarify the carrier status of female family members. Methods. Sequence analysis and array comparative genomic hybridization (aCGH) were used to identify mutations in the dystrophin DMD gene. We analysed genomic DNA from six individuals with a range of previously characterised mutations and from eight individuals who had not previously undergone any form of molecular analysis. Results. We successfully identified the known mutations in all six patients. A molecular diagnosis was also made in three of the four patients with a clinical diagnosis who had not undergone prior genetic screening, and testing for familial mutations was successfully completed for the remaining four patients. Conclusion. The mutation screening protocol described here meets best practice guidelines for molecular testing of the DMD gene in a diagnostic laboratory. The aCGH method is a superior alternative to more conventional assays such as multiplex ligation-dependent probe amplification (MLPA). The combination of aCGH and sequence analysis will detect mutations in 98% of patients with the Duchenne or Becker muscular dystrophy. PMID:23476807

Array CGH analysis of a cohort of Russian patients with intellectual disability.

PubMed

Kashevarova, Anna A; Nazarenko, Lyudmila P; Skryabin, Nikolay A; Salyukova, Olga A; Chechetkina, Nataliya N; Tolmacheva, Ekaterina N; Sazhenova, Elena A; Magini, Pamela; Graziano, Claudio; Romeo, Giovanni; Kučinskas, Vaidutis; Lebedev, Igor N

2014-02-15

The use of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated the identification of many new microdeletion/microduplication syndromes (MMSs). Furthermore, this method has allowed for the identification of copy number variations (CNVs) whose pathogenic role has yet to be uncovered. Here, we report on our application of array CGH for the identification of pathogenic CNVs in 79 Russian children with intellectual disability (ID). Twenty-six pathogenic or likely pathogenic changes in copy number were detected in 22 patients (28%): 8 CNVs corresponded to known MMSs, and 17 were not associated with previously described syndromes. In this report, we describe our findings and comment on genes potentially associated with ID that are located within the CNV regions. Copyright © 2013 Elsevier B.V. All rights reserved.

Faraday effect in hybrid magneto-plasmonic photonic crystals.

PubMed

Caballero, B; García-Martín, A; Cuevas, J C

2015-08-24

We present a theoretical study of the Faraday effect in hybrid magneto-plasmonic crystals that consist of Au-Co-Au perforated membranes with a periodic array of sub-wavelength holes. We show that in these hybrid systems the interplay between the extraordinary optical transmission and the magneto-optical activity leads to a resonant enhancement of the Faraday rotation, as compared to purely ferromagnetic membranes. In particular, we determine the geometrical parameters for which this enhancement is optimized and show that the inclusion of a noble metal like Au dramatically increases the Faraday rotation over a broad bandwidth. Moreover, we show that the analysis of the Faraday rotation in these periodically perforated membranes provides a further insight into the origin of the extraordinary optical transmission.

Hybrid nanostructures of well-organized arrays of colloidal quantum dots and a self-assembled monolayer of gold nanoparticles for enhanced fluorescence

NASA Astrophysics Data System (ADS)

Liu, Xiaoying; McBride, Sean P.; Jaeger, Heinrich M.; Nealey, Paul F.

2016-07-01

Hybrid nanomaterials comprised of well-organized arrays of colloidal semiconductor quantum dots (QDs) in close proximity to metal nanoparticles (NPs) represent an appealing system for high-performance, spectrum-tunable photon sources with controlled photoluminescence. Experimental realization of such materials requires well-defined QD arrays and precisely controlled QD-metal interspacing. This long-standing challenge is tackled through a strategy that synergistically combines lateral confinement and vertical stacking. Lithographically generated nanoscale patterns with tailored surface chemistry confine the QDs into well-organized arrays with high selectivity through chemical pattern directed assembly, while subsequent coating with a monolayer of close-packed Au NPs introduces the plasmonic component for fluorescence enhancement. The results show uniform fluorescence emission in large-area ordered arrays for the fabricated QD structures and demonstrate five-fold fluorescence amplification for red, yellow, and green QDs in the presence of the Au NP monolayer. Encapsulation of QDs with a silica shell is shown to extend the design space for reliable QD/metal coupling with stronger enhancement of 11 times through the tuning of QD-metal spatial separation. This approach provides new opportunities for designing hybrid nanomaterials with tailored array structures and multiple functionalities for applications such as multiplexed optical coding, color display, and quantum transduction.

Identification of flavonols in leaves of Maytenus ilicifolia and M. aquifolium (Celastraceae) by LC/UV/MS analysis.

PubMed

Tiberti, Luciana A; Yariwake, Janete H; Ndjoko, Karine; Hostettmann, Kurt

2007-02-01

A comparative analysis of the flavonoid components of the leaves of two medicinal plants known in Brazil as "espinheira santa", namely, Maytenus ilicifolia Mart. ex Reiss. and M. aquifolium Mart. (Celastraceae), and a hybrid plant, M. aquifoliumxM. ilicifolia, has been carried out using high-performance liquid chromatography coupled with photodiode array UV detection and mass spectrometry. One methoxyflavonoid glycoside and 18 flavonol-3-O-glycosides were identified in the extracts on the basis of their on-line UV spectra (measured in the absence and presence of shift reagents) and multiple stage mass spectral data. Fingerprint analysis of the flavonoid extracts revealed significant differences in the profiles of the two Maytenus species, while the hybrid plant contained flavonoids found in both parent species.

Harmonic analysis and suppression in hybrid wind & PV solar system

NASA Astrophysics Data System (ADS)

Gupta, Tripti; Namekar, Swapnil

2018-04-01

The growing demand of electricity has led to produce power through non-conventional source of energy such as solar energy, wind energy, hydro power, energy through biogas and biomass etc. Hybrid system is taken to complement the shortcoming of either sources of energy. The proposed system is grid connected hybrid wind and solar system. A 2.1 MW Doubly fed Induction Generator (DFIG) has been taken for analysis of wind farm whose rotor part is connected to two back-to-back converters. A 250 KW Photovoltaic (PV) array taken to analyze solar farm where inverter is required to convert power from DC to AC since electricity generated through solar PV is in the form of DC. Stability and reliability of the system is very important when the system is grid connected. Harmonics is the major Power quality issue which degrades the quality of power at load side. Harmonics in hybrid system arise through the use of power conversion unit. The other causes of harmonics are fluctuation in wind speed and solar irradiance. The power delivered to grid must be free from harmonics and within the limits specified by Indian grid codes. In proposed work, harmonic analysis of the hybrid system is performed in Electrical Transient Analysis program (ETAP) and single tuned harmonic filter is designed to maintain the utility grid harmonics within limits.

The dynamic process and microscopic mechanism of extraordinary terahertz transmission through perforated superconducting films

PubMed Central

Wu, J. B.; Zhang, X.; Jin, B. B.; Liu, H. T.; Chen, Y. H.; Li, Z. Y.; Zhang, C. H.; Kang, L.; Xu, W. W.; Chen, J.; Wang, H. B.; Tonouchi, M.; Wu, P. H.

2015-01-01

Superconductor is a compelling plasmonic medium at terahertz frequencies owing to its intrinsic low Ohmic loss and good tuning property. However, the microscopic physics of the interaction between terahertz wave and superconducting plasmonic structures is still unknown. In this paper, we conducted experiments of the enhanced terahertz transmission through a series of superconducting NbN subwavelength hole arrays, and employed microscopic hybrid wave model in theoretical analysis of the role of hybrid waves in the enhanced transmission. The theoretical calculation provided a good match of experimental data. In particular, we obtained the following results. When the width of the holes is far below wavelength, the enhanced transmission is mainly caused by localized resonance around individual holes. On the contrary, when the holes are large, hybrid waves scattered by the array of holes dominate the extraordinary transmission. The surface plasmon polaritions are proved to be launched on the surface of superconducting film and the excitation efficiency increases when the temperature approaches critical temperature and the working frequency goes near energy gap frequency. This work will enrich our knowledge on the microscopic physics of extraordinary optical transmission at terahertz frequencies and contribute to developing terahertz plasmonic devices. PMID:26498994

Field emission luminescence of nanodiamonds deposited on the aligned carbon nanotube array

NASA Astrophysics Data System (ADS)

Fedoseeva, Yu. V.; Bulusheva, L. G.; Okotrub, A. V.; Kanygin, M. A.; Gorodetskiy, D. V.; Asanov, I. P.; Vyalikh, D. V.; Puzyr, A. P.; Bondar, V. S.

2015-03-01

Detonation nanodiamonds (NDs) were deposited on the surface of aligned carbon nanotubes (CNTs) by immersing a CNT array in an aqueous suspension of NDs in dimethylsulfoxide (DMSO). The structure and electronic state of the obtained CNT-ND hybrid material were studied using optical and electron microscopy and Infrared, Raman, X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopy. A non-covalent interaction between NDs and CNT and preservation of vertical orientation of CNTs in the hybrid were revealed. We showed that current-voltage characteristics of the CNT-ND cathode are changed depending on the applied field; below ~3 V/µm they are similar to those of the initial CNT array and at the higher field they are close to the ND behavior. Involvement of the NDs in field emission process resulted in blue luminescence of the hybrid surface at an electric field higher than 3.5 V/µm. Photoluminescence measurements showed that the NDs emit blue-green light, while blue luminescence prevails in the CNT-ND hybrid. The quenching of green luminescence was attributed to a partial removal of oxygen-containing groups from the ND surface as the result of the hybrid synthesis.

The exposure of the hybrid detector of the Pierre Auger Observatory

NASA Astrophysics Data System (ADS)

Abreu, P.; Aglietta, M.; Ahn, E. J.; Allard, D.; Allekotte, I.; Allen, J.; Alvarez Castillo, J.; Alvarez-Muñiz, J.; Ambrosio, M.; Aminaei, A.; Anchordoqui, L.; Andringa, S.; Antičić, T.; Anzalone, A.; Aramo, C.; Arganda, E.; Arisaka, K.; Arqueros, F.; Asorey, H.; Assis, P.; Aublin, J.; Ave, M.; Avenier, M.; Avila, G.; Bäcker, T.; Badagnani, D.; Balzer, M.; Barber, K. B.; Barbosa, A. F.; Bardenet, R.; Barroso, S. L. C.; Baughman, B.; Beatty, J. J.; Becker, B. R.; Becker, K. H.; Bellétoile, A.; Bellido, J. A.; Benzvi, S.; Berat, C.; Bergmann, T.; Bertou, X.; Biermann, P. L.; Billoir, P.; Blanco, F.; Blanco, M.; Bleve, C.; Blümer, H.; Boháčová, M.; Boncioli, D.; Bonifazi, C.; Bonino, R.; Borodai, N.; Brack, J.; Brogueira, P.; Brown, W. C.; Bruijn, R.; Buchholz, P.; Bueno, A.; Burton, R. E.; Busca, N. G.; Caballero-Mora, K. S.; Caramete, L.; Caruso, R.; Castellina, A.; Catalano, O.; Cataldi, G.; Cazon, L.; Cester, R.; Chauvin, J.; Chiavassa, A.; Chinellato, J. A.; Chou, A.; Chudoba, J.; Clay, R. W.; Colombo, E.; Coluccia, M. R.; Conceição, R.; Contreras, F.; Cook, H.; Cooper, M. J.; Coppens, J.; Cordier, A.; Cotti, U.; Coutu, S.; Covault, C. E.; Creusot, A.; Criss, A.; Cronin, J.; Curutiu, A.; Dagoret-Campagne, S.; Dallier, R.; Dasso, S.; Daumiller, K.; Dawson, B. R.; de Almeida, R. M.; de Domenico, M.; de Donato, C.; de Jong, S. J.; de La Vega, G.; de Mello Junior, W. J. M.; de Mello Neto, J. R. T.; de Mitri, I.; de Souza, V.; de Vries, K. D.; Decerprit, G.; Del Peral, L.; Deligny, O.; Della Selva, A.; Dembinski, H.; Denkiewicz, A.; di Giulio, C.; Diaz, J. C.; Díaz Castro, M. L.; Diep, P. N.; Dobrigkeit, C.; D'Olivo, J. C.; Dong, P. N.; Dorofeev, A.; Dos Anjos, J. C.; Dova, M. T.; D'Urso, D.; Dutan, I.; Ebr, J.; Engel, R.; Erdmann, M.; Escobar, C. O.; Etchegoyen, A.; Facal San Luis, P.; Falcke, H.; Farrar, G.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Ferrero, A.; Fick, B.; Filevich, A.; Filipčič, A.; Fleck, I.; Fliescher, S.; Fracchiolla, C. E.; Fraenkel, E. D.; Fröhlich, U.; Fuchs, B.; Fulgione, W.; Gamarra, R. F.; Gambetta, S.; García, B.; García Gámez, D.; Garcia-Pinto, D.; Garrido, X.; Gascon, A.; Gelmini, G.; Gemmeke, H.; Gesterling, K.; Ghia, P. L.; Giaccari, U.; Giller, M.; Glass, H.; Gold, M. S.; Golup, G.; Gomez Albarracin, F.; Gómez Berisso, M.; Gonçalves, P.; Gonzalez, D.; Gonzalez, J. G.; Gookin, B.; Góra, D.; Gorgi, A.; Gouffon, P.; Gozzini, S. R.; Grashorn, E.; Grebe, S.; Grigat, M.; Grillo, A. F.; Guardincerri, Y.; Guarino, F.; Guedes, G. P.; Hague, J. D.; Hansen, P.; Harari, D.; Harmsma, S.; Harton, J. L.; Haungs, A.; Hebbeker, T.; Heck, D.; Herve, A. E.; Hojvat, C.; Holmes, V. C.; Homola, P.; Hörandel, J. R.; Horneffer, A.; Hrabovský, M.; Huege, T.; Insolia, A.; Ionita, F.; Italiano, A.; Jiraskova, S.; Kadija, K.; Kaducak, M.; Kampert, K. H.; Karhan, P.; Karova, T.; Kasper, P.; Kégl, B.; Keilhauer, B.; Keivani, A.; Kelley, J. L.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Knapp, J.; Koang, D.-H.; Kotera, K.; Krohm, N.; Krömer, O.; Kruppke-Hansen, D.; Kuehn, F.; Kuempel, D.; Kulbartz, J. K.; Kunka, N.; La Rosa, G.; Lachaud, C.; Lautridou, P.; Leão, M. S. A. B.; Lebrun, D.; Lebrun, P.; Leigui de Oliveira, M. A.; Lemiere, A.; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; López, R.; Lopez Agüera, A.; Louedec, K.; Lozano Bahilo, J.; Lucero, A.; Ludwig, M.; Lyberis, H.; Maccarone, M. C.; Macolino, C.; Maldera, S.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, V.; Maris, I. C.; Marquez Falcon, H. R.; Marsella, G.; Martello, D.; Martin, L.; Martínez Bravo, O.; Mathes, H. J.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurizio, D.; Mazur, P. O.; McEwen, M.; Medina-Tanco, G.; Melissas, M.; Melo, D.; Menichetti, E.; Menshikov, A.; Meurer, C.; Mičanović, S.; Micheletti, M. I.; Miller, W.; Miramonti, L.; Mollerach, S.; Monasor, M.; Monnier Ragaigne, D.; Montanet, F.; Morales, B.; Morello, C.; Moreno, E.; Moreno, J. C.; Morris, C.; Mostafá, M.; Mueller, S.; Muller, M. A.; Münchmeyer, M.; Mussa, R.; Navarra, G.; Navarro, J. L.; Navas, S.; Necesal, P.; Nellen, L.; Nhung, P. T.; Nierstenhoefer, N.; Nitz, D.; Nosek, D.; Nožka, L.; Nyklicek, M.; Oehlschläger, J.; Olinto, A.; Oliva, P.; Olmos-Gilbaja, V. M.; Ortiz, M.; Pacheco, N.; Pakk Selmi-Dei, D.; Palatka, M.; Pallotta, J.; Palmieri, N.; Parente, G.; Parizot, E.; Parra, A.; Parrisius, J.; Parsons, R. D.; Pastor, S.; Paul, T.; Pavlidou, V.; Payet, K.; Pech, M.; PeĶala, J.; Pelayo, R.; Pepe, I. M.; Perrone, L.; Pesce, R.; Petermann, E.; Petrera, S.; Petrinca, P.; Petrolini, A.; Petrov, Y.; Petrovic, J.; Pfendner, C.; Phan, N.; Piegaia, R.; Pierog, T.; Pimenta, M.; Pirronello, V.; Platino, M.; Ponce, V. H.; Pontz, M.; Privitera, P.; Prouza, M.; Quel, E. J.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Riggi, S.; Risse, M.; Ristori, P.; Rivera, H.; Rivière, C.; Rizi, V.; Robledo, C.; Rodriguez, G.; Rodriguez Martino, J.; Rodriguez Rojo, J.; Rodriguez-Cabo, I.; Rodríguez-Frías, M. D.; Ros, G.; Rosado, J.; Rossler, T.; Roth, M.; Rouillé-D'Orfeuil, B.; Roulet, E.; Rovero, A. C.; Salamida, F.; Salazar, H.; Salina, G.; Sánchez, F.; Santander, M.; Santo, C. E.; Santos, E.; Santos, E. M.; Sarazin, F.; Sarkar, S.; Sato, R.; Scharf, N.; Scherini, V.; Schieler, H.; Schiffer, P.; Schmidt, A.; Schmidt, F.; Schmidt, T.; Scholten, O.; Schoorlemmer, H.; Schovancova, J.; Schovánek, P.; Schroeder, F.; Schulte, S.; Schüssler, F.; Schuster, D.; Sciutto, S. J.; Scuderi, M.; Segreto, A.; Semikoz, D.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sidelnik, I.; Sigl, G.; Śmiałkowski, A.; Šmída, R.; Snow, G. R.; Sommers, P.; Sorokin, J.; Spinka, H.; Squartini, R.; Stapleton, J.; Stasielak, J.; Stephan, M.; Strazzeri, E.; Stutz, A.; Suarez, F.; Suomijärvi, T.; Supanitsky, A. D.; Šuša, T.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Tamashiro, A.; Tapia, A.; Tarutina, T.; Taşcău, O.; Tcaciuc, R.; Tcherniakhovski, D.; Tegolo, D.; Thao, N. T.; Thomas, D.; Tiffenberg, J.; Timmermans, C.; Tiwari, D. K.; Tkaczyk, W.; Todero Peixoto, C. J.; Tomé, B.; Tonachini, A.; Travnicek, P.; Tridapalli, D. B.; Tristram, G.; Trovato, E.; Tueros, M.; Ulrich, R.; Unger, M.; Urban, M.; Valdés Galicia, J. F.; Valiño, I.; Valore, L.; van den Berg, A. M.; Vargas Cárdenas, B.; Vázquez, J. R.; Vázquez, R. A.; Veberič, D.; Venters, T.; Verzi, V.; Videla, M.; Villaseñor, L.; Wahlberg, H.; Wahrlich, P.; Wainberg, O.; Warner, D.; Watson, A. A.; Weidenhaupt, K.; Weindl, A.; Westerhoff, S.; Whelan, B. J.; Wieczorek, G.; Wiencke, L.; Wilczyńska, B.; Wilczyński, H.; Will, M.; Williams, C.; Winchen, T.; Winders, L.; Winnick, M. G.; Wommer, M.; Wundheiler, B.; Yamamoto, T.; Younk, P.; Yuan, G.; Yushkov, A.; Zamorano, B.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zaw, I.; Zepeda, A.; Ziolkowski, M.; Pierre Auger Collaboration

2011-01-01

The Pierre Auger Observatory is a detector for ultra-high energy cosmic rays. It consists of a surface array to measure secondary particles at ground level and a fluorescence detector to measure the development of air showers in the atmosphere above the array. The "hybrid" detection mode combines the information from the two subsystems. We describe the determination of the hybrid exposure for events observed by the fluorescence telescopes in coincidence with at least one water-Cherenkov detector of the surface array. A detailed knowledge of the time dependence of the detection operations is crucial for an accurate evaluation of the exposure. We discuss the relevance of monitoring data collected during operations, such as the status of the fluorescence detector, background light and atmospheric conditions, that are used in both simulation and reconstruction.

The exposure of the hybrid detector of the Pierre Auger Observatory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2010-06-01

The Pierre Auger Observatory is a detector for ultra-high energy cosmic rays. It consists of a surface array to measure secondary particles at ground level and a fluorescence detector to measure the development of air showers in the atmosphere above the array. The 'hybrid' detection mode combines the information from the two subsystems. We describe the determination of the hybrid exposure for events observed by the fluorescence telescopes in coincidence with at least one water-Cherenkov detector of the surface array. A detailed knowledge of the time dependence of the detection operations is crucial for an accurate evaluation of the exposure.more » We discuss the relevance of monitoring data collected during operations, such as the status of the fluorescence detector, background light and atmospheric conditions, that are used in both simulation and reconstruction.« less

Using Hybrid Modeling to Develop Innovative Activities

ERIC Educational Resources Information Center

Lichtman, Brenda; Avans, Diana

2005-01-01

This article describes a hybrid activities model that physical educators can use with students in grades four and above to create virtually a limitless array of novel games. A brief introduction to the basic theory is followed by descriptions of some hybrid games. Hybrid games are typically the result of merging two traditional sports or other…

Photovoltaic Performance of a Nanowire/Quantum Dot Hybrid Nanostructure Array Solar Cell.

PubMed

Wu, Yao; Yan, Xin; Zhang, Xia; Ren, Xiaomin

2018-02-23

An innovative solar cell based on a nanowire/quantum dot hybrid nanostructure array is designed and analyzed. By growing multilayer InAs quantum dots on the sidewalls of GaAs nanowires, not only the absorption spectrum of GaAs nanowires is extended by quantum dots but also the light absorption of quantum dots is dramatically enhanced due to the light-trapping effect of the nanowire array. By incorporating five layers of InAs quantum dots into a 500-nm high-GaAs nanowire array, the power conversion efficiency enhancement induced by the quantum dots is six times higher than the power conversion efficiency enhancement in thin-film solar cells which contain the same amount of quantum dots, indicating that the nanowire array structure can benefit the photovoltaic performance of quantum dot solar cells.

Photovoltaic Performance of a Nanowire/Quantum Dot Hybrid Nanostructure Array Solar Cell

NASA Astrophysics Data System (ADS)

Wu, Yao; Yan, Xin; Zhang, Xia; Ren, Xiaomin

2018-02-01

An innovative solar cell based on a nanowire/quantum dot hybrid nanostructure array is designed and analyzed. By growing multilayer InAs quantum dots on the sidewalls of GaAs nanowires, not only the absorption spectrum of GaAs nanowires is extended by quantum dots but also the light absorption of quantum dots is dramatically enhanced due to the light-trapping effect of the nanowire array. By incorporating five layers of InAs quantum dots into a 500-nm high-GaAs nanowire array, the power conversion efficiency enhancement induced by the quantum dots is six times higher than the power conversion efficiency enhancement in thin-film solar cells which contain the same amount of quantum dots, indicating that the nanowire array structure can benefit the photovoltaic performance of quantum dot solar cells.

Enhanced performance of core-shell structured polyaniline at helical carbon nanotube hybrids for ammonia gas sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Xin; Wang, Qiang; Chen, Xiangnan

2014-11-17

A core-shell structured hybrid of polyaniline at helical carbon nanotubes was synthesized using in situ polymerization, which the helical carbon nanotubes were uniformly surrounded by a layer of polyaniline nanorods array. More interestingly, repeatable responses were experimentally observed that the sensitivity to ammonia gas of the as-prepared helical shaped core-shell hybrid displays an enhancement of more than two times compared to those of only polyaniline or helical carbon nanotubes sensors because of the peculiar structures with high surface area. This kind of hybrid comprising nanorod arrays of conductive polymers covering carbon nanotubes and related structures provide a potential in sensorsmore » of trace gas detection for environmental monitoring and safety forecasting.« less

[Dandy-walker syndrome and microdeletions on chromosome 7].

PubMed

Liao, Can; Fu, Fang; Li, Ru; Pan, Min; Yang, Xin; Yi, Cui-xing; Li, Jian; Li, Dong-zhi

2012-02-01

To investigate genetic etiology of Dandy-Walker syndrome with array-based comparative genomic hybridization (array-CGH). Eight fetuses with Dandy-Walker malformations but normal karyotypes by conventional cytogenetic technique were selected. DNA samples were extracted and hybridized with Affymetrix cytogenetic 2.7 M arrays by following the manufacturer's standard protocol. The data were analyzed by special software packages. By using array-CGH technique, common deletions and duplication on chromosome 7p21.3 were identified in three cases, within which were central nervous system disease associated genes NDUFA4 and PHF14. Copy number variations (CNVs) of chromosome 7p21.3 region are associated with Dandy-Walker malformations which may be due to haploinsufficiency or overexpression of NDUFA4 and PHF14 genes.

Analysis of Transient Electromagnetic Scattering from Three Dimensional Cavities

DTIC Science & Technology

2014-01-01

New York, 2002. [24] J. Jin and J. L. Volakis, A hybrid finite element method for scattering and radiation by micro strip patch antennas and arrays...applications such as the design of cavity-backed conformal antennas and the deliberate control in the form of enhancement or reduction of radar cross...electromagnetic scattering analysis, IEEE Trans. Antennas Propagat., 50 (2002), pp. 1192–1202. [22] J. Jin, Electromagnetic scattering from large, deep, and

Fabrication of heterogeneous nanomaterial array by programmable heating and chemical supply within microfluidic platform towards multiplexed gas sensing application

PubMed Central

Yang, Daejong; Kang, Kyungnam; Kim, Donghwan; Li, Zhiyong; Park, Inkyu

2015-01-01

A facile top-down/bottom-up hybrid nanofabrication process based on programmable temperature control and parallel chemical supply within microfluidic platform has been developed for the all liquid-phase synthesis of heterogeneous nanomaterial arrays. The synthesized materials and locations can be controlled by local heating with integrated microheaters and guided liquid chemical flow within microfluidic platform. As proofs-of-concept, we have demonstrated the synthesis of two types of nanomaterial arrays: (i) parallel array of TiO2 nanotubes, CuO nanospikes and ZnO nanowires, and (ii) parallel array of ZnO nanowire/CuO nanospike hybrid nanostructures, CuO nanospikes and ZnO nanowires. The laminar flow with negligible ionic diffusion between different precursor solutions as well as localized heating was verified by numerical calculation and experimental result of nanomaterial array synthesis. The devices made of heterogeneous nanomaterial array were utilized as a multiplexed sensor for toxic gases such as NO2 and CO. This method would be very useful for the facile fabrication of functional nanodevices based on highly integrated arrays of heterogeneous nanomaterials. PMID:25634814

Assessment study of infrared detector arrays for low-background astronomical research

NASA Technical Reports Server (NTRS)

Ando, K. J.

1978-01-01

The current state-of-the-art of infrared detector arrays employing charge coupled devices (CCD) or charge injection devices (CID) readout are assessed. The applicability, limitations and potentials of such arrays under the low-background astronomical observing conditions of interest for SIRFT (Shuttle Infrared Telescope Facility) are determined. The following are reviewed: (1) monolithic extrinsic arrays; (2) monolithic intrinsic arrays; (3) charge injection devices; and (4) hybrid arrays.

Development of a photodiode array biochip using a bipolar semiconductor and its application to detection of human papilloma virus.

PubMed

Baek, Taek Jin; Park, Pan Yun; Han, Kwi Nam; Kwon, Ho Taik; Seong, Gi Hun

2008-03-01

We describe a DNA microarray system using a bipolar integrated circuit photodiode array (PDA) chip as a new platform for DNA analysis. The PDA chip comprises an 8 x 6 array of photodiodes each with a diameter of 600 microm. Each photodiode element acts both as a support for an immobilizing probe DNA and as a two-dimensional photodetector. The usefulness of the PDA microarray platform is demonstrated by the detection of high-risk subtypes of human papilloma virus (HPV). The polymerase chain reaction (PCR)-amplified biotinylated HPV target DNA was hybridized with the immobilized probe DNA on the photodiode surface, and the chip was incubated in an anti-biotin antibody-conjugated gold nanoparticle solution. The silver enhancement by the gold nanoparticles bound to the biotin of the HPV target DNA precipitates silver metal particles at the chip surfaces, which block light irradiated from above. The resulting drop in output voltage depends on the amount of target DNA present in the sample solution, which allows the specific detection and the quantitative analysis of the complementary target DNA. The PDA chip showed high relative signal ratios of HPV probe DNA hybridized with complementary target DNA, indicating an excellent capability in discriminating HPV subtypes. The detection limit for the HPV target DNA analysis improved from 1.2 nM to 30 pM by changing the silver development time from 5 to 10 min. Moreover, the enhanced silver development promoted by the gold nanoparticles could be applied to a broader range of target DNA concentration by controlling the silver development time.

A Distributed Amplifier System for Bilayer Lipid Membrane (BLM) Arrays With Noise and Individual Offset Cancellation.

PubMed

Crescentini, Marco; Thei, Frederico; Bennati, Marco; Saha, Shimul; de Planque, Maurits R R; Morgan, Hywel; Tartagni, Marco

2015-06-01

Lipid bilayer membrane (BLM) arrays are required for high throughput analysis, for example drug screening or advanced DNA sequencing. Complex microfluidic devices are being developed but these are restricted in terms of array size and structure or have integrated electronic sensing with limited noise performance. We present a compact and scalable multichannel electrophysiology platform based on a hybrid approach that combines integrated state-of-the-art microelectronics with low-cost disposable fluidics providing a platform for high-quality parallel single ion channel recording. Specifically, we have developed a new integrated circuit amplifier based on a novel noise cancellation scheme that eliminates flicker noise derived from devices under test and amplifiers. The system is demonstrated through the simultaneous recording of ion channel activity from eight bilayer membranes. The platform is scalable and could be extended to much larger array sizes, limited only by electronic data decimation and communication capabilities.

Monolithically Integrated Self-Charging Power Pack Consisting of a Silicon Nanowire Array/Conductive Polymer Hybrid Solar Cell and a Laser-Scribed Graphene Supercapacitor.

PubMed

Liu, Hanhui; Li, Mengping; Kaner, Richard B; Chen, Songyan; Pei, Qibing

2018-05-09

Owing to the need for portable and sustainable energy sources and the development trend for microminiaturization and multifunctionalization in the electronic components, the study of integrated self-charging power packs has attracted increasing attention. A new self-charging power pack consisting of a silicon nanowire array/poly(3,4-ethylenedioxythiophene):polystyrenesulfonate (PEDOT:PSS) hybrid solar cell and a laser-scribed graphene (LSG) supercapacitor has been fabricated. The Si nanowire array/PEDOT:PSS hybrid solar cell structure exhibited a high power conversion efficiency (PCE) of 12.37%. The LSG demonstrated excellent energy storage capability for the power pack, with high current density, energy density, and cyclic stability when compared to other supercapacitor electrodes such as active carbon and conducting polymers. The overall efficiency of the power unit is 2.92%.

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

PubMed Central

2012-01-01

Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as limiting factors in genetic studies. We have conducted the first formal analysis of the effect of novel variants on genotyping arrays, and we have shown that these variants account for a large portion of miscalled and uncalled genotypes. Genetic studies will benefit from substantial improvements in the accuracy of their results by incorporating VINOs in their analyses. PMID:22260749

Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics

PubMed Central

2015-01-01

Controlled nucleation of nanoscale building blocks by geometrically defined seeds implanted in DNA nanoscaffolds represents a unique strategy to study and understand the dynamic processes of molecular self-assembly. Here we utilize a two-dimensional DNA origami frame with a hollow interior and selectively positioned DNA hybridization seeds to control the self-assembly of DNA tile building blocks, where the small DNA tiles are directed to fill the interior of the frame through prescribed sticky end interactions. This design facilitates the construction of DNA origami/array hybrids that adopt the overall shape and dimensions of the origami frame, forming a 2D array in the core consisting of a large number of simple repeating DNA tiles. The formation of the origami/array hybrid was characterized with atomic force microscopy, and the nucleation dynamics were monitored by serial AFM scanning and fluorescence spectroscopy, which revealed faster kinetics of growth within the frame as compared to growth without the presence of a frame. Our study provides insight into the fundamental behavior of DNA-based self-assembling systems. PMID:24575893

Comparison of array comparative genomic hybridization and quantitative real-time PCR-based aneuploidy screening of blastocyst biopsies.

PubMed

Capalbo, Antonio; Treff, Nathan R; Cimadomo, Danilo; Tao, Xin; Upham, Kathleen; Ubaldi, Filippo Maria; Rienzi, Laura; Scott, Richard T

2015-07-01

Comprehensive chromosome screening (CCS) methods are being extensively used to select chromosomally normal embryos in human assisted reproduction. Some concerns related to the stage of analysis and which aneuploidy screening method to use still remain. In this study, the reliability of blastocyst-stage aneuploidy screening and the diagnostic performance of the two mostly used CCS methods (quantitative real-time PCR (qPCR) and array comparative genome hybridization (aCGH)) has been assessed. aCGH aneuploid blastocysts were rebiopsied, blinded, and evaluated by qPCR. Discordant cases were subsequently rebiopsied, blinded, and evaluated by single-nucleotide polymorphism (SNP) array-based CCS. Although 81.7% of embryos showed the same diagnosis when comparing aCGH and qPCR-based CCS, 18.3% (22/120) of embryos gave a discordant result for at least one chromosome. SNP array reanalysis showed that a discordance was reported in ten blastocysts for aCGH, mostly due to false positives, and in four cases for qPCR. The discordant aneuploidy call rate per chromosome was significantly higher for aCGH (5.7%) compared with qPCR (0.6%; P<0.01). To corroborate these findings, 39 embryos were simultaneously biopsied for aCGH and qPCR during blastocyst-stage aneuploidy screening cycles. 35 matched including all 21 euploid embryos. Blinded SNP analysis on rebiopsies of the four embryos matched qPCR. These findings demonstrate the high reliability of diagnosis performed at the blastocyst stage with the use of different CCS methods. However, the application of aCGH can be expected to result in a higher aneuploidy rate than other contemporary methods of CCS.

Development and characterization of a microheater array device for real-time DNA mutation detection

NASA Astrophysics Data System (ADS)

Williams, Layne; Okandan, Murat; Chagovetz, Alex; Blair, Steve

2008-04-01

DNA analysis, specifically single nucleotide polymorphism (SNP) detection, is becoming increasingly important in rapid diagnostics and disease detection. Temperature is often controlled to help speed reaction rates and perform melting of hybridized oligonucleotides. The difference in melting temperatures, Tm, between wild-type and SNP sequences, respectively, to a given probe oligonucleotide, is indicative of the specificity of the reaction. We have characterized Tm's in solution and on a solid substrate of three sequences from known mutations associated with Cystic Fibrosis. Taking advantage of Tm differences, a microheater array device was designed to enable individual temperature control of up to 18 specific hybridization events. The device was fabricated at Sandia National Laboratories using surface micromachining techniques. The microheaters have been characterized using an IR camera at Sandia and show individual temperature control with minimal thermal cross talk. Development of the device as a real-time DNA detection platform, including surface chemistry and associated microfluidics, is described.

Development and characterization of a microheater array device for real-time DNA mutation detection

NASA Astrophysics Data System (ADS)

Williams, Layne; Okandan, Murat; Chagovetz, Alex; Blair, Steve

2008-02-01

DNA analysis, specifically single nucleotide polymorphism (SNP) detection, is becoming increasingly important in rapid diagnostics and disease detection. Temperature is often controlled to help speed reaction rates and perform melting of hybridized oligonucleotides. The difference in melting temperatures, Tm, between wild-type and SNP sequences, respectively, to a given probe oligonucleotide, is indicative of the specificity of the reaction. We have characterized Tm's in solution and on a solid substrate of three sequences from known mutations associated with Cystic Fibrosis. Taking advantage of Tm differences, a microheater array device was designed to enable individual temperature control of up to 18 specific hybridization events. The device was fabricated at Sandia National Laboratories using surface micromachining techniques. The microheaters have been characterized using an IR camera at Sandia and show individual temperature control with minimal thermal cross talk. Development of the device as a real-time DNA detection platform, including surface chemistry and associated microfluidics, is described.

PhylArray: phylogenetic probe design algorithm for microarray.

PubMed

Militon, Cécile; Rimour, Sébastien; Missaoui, Mohieddine; Biderre, Corinne; Barra, Vincent; Hill, David; Moné, Anne; Gagne, Geneviève; Meier, Harald; Peyretaillade, Eric; Peyret, Pierre

2007-10-01

Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.

Configuration study for a 30 GHz monolithic receive array: Technical assessment

NASA Technical Reports Server (NTRS)

Nester, W. H.; Cleaveland, B.; Edward, B.; Gotkis, S.; Hesserbacker, G.; Loh, J.; Mitchell, B.

1984-01-01

The current status of monolithic microwave integrated circuits (MMICs) in phased array feeds is discussed from the point of view of cost performance, reliability, and design considerations. Transitions to MMICs, compatible antenna radiating elements and reliability considerations are addressed. Hybrid antennas, feed array antenna technology, and offset reflectors versus phased arrays are examined.

Transcript Profiling of Common Bean (Phaseolus vulgaris) Using the GeneChip Soybean Genome Array: Optimizing Analysis by Masking Biased Probes

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common b...

Vertically aligned diamond-graphite hybrid nanorod arrays with superior field electron emission properties

NASA Astrophysics Data System (ADS)

Ramaneti, R.; Sankaran, K. J.; Korneychuk, S.; Yeh, C. J.; Degutis, G.; Leou, K. C.; Verbeeck, J.; Van Bael, M. K.; Lin, I. N.; Haenen, K.

2017-06-01

A "patterned-seeding technique" in combination with a "nanodiamond masked reactive ion etching process" is demonstrated for fabricating vertically aligned diamond-graphite hybrid (DGH) nanorod arrays. The DGH nanorod arrays possess superior field electron emission (FEE) behavior with a low turn-on field, long lifetime stability, and large field enhancement factor. Such an enhanced FEE is attributed to the nanocomposite nature of the DGH nanorods, which contain sp2-graphitic phases in the boundaries of nano-sized diamond grains. The simplicity in the nanorod fabrication process renders the DGH nanorods of greater potential for the applications as cathodes in field emission displays and microplasma display devices.

High-resolution mapping and sequence analysis of 597 cDNA clones transcribed from the 1 Mb region in human chromosome 4q16.3 containing Huntington disease gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadano, S.; Ishida, Y.; Tomiyasu, H.

1994-09-01

To complete a transcription map of the 1 Mb region in human chromosome 4p16.3 containing the Huntington disease (HD) gene, the isolation of cDNA clones are being performed throughout. Our method relies on a direct screening of the cDNA libraries probed with single copy microclones from 3 YAC clones spanning 1 Mbp of the HD gene region. AC-DNAs were isolated by a preparative pulsed-field gel electrophoresis, amplified by both a single unique primer (SUP)-PCR and a linker ligation PCR, and 6 microclone-DNA libraries were generated. Then, 8,640 microclones from these libraries were independently amplified by PCR, and arrayed onto themore » membranes. 800-900 microclones that were not cross-hybridized with total human and yeast genomic DNA, TAC vector DNA, and ribosomal cDNA on a dot hybridization (putatively carrying single copy sequences) were pooled to make 9 probe pools. A total of {approximately}1.8x10{sup 7} plaques from the human brain cDNA libraries was screened with 9 pool-probes, and then 672 positive cDNA clones were obtained. So far, 597 cDNA clones were defined and arrayed onto a map of the 1 Mbp of the HD gene region by hybridization with HD region-specific cosmid contigs and YAC clones. Further characterization including a DNA sequencing and Northern blot analysis is currently underway.« less

Rad-hard Dual-threshold High-count-rate Silicon Pixel-array Detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Adam

In this program, a Voxtel-led team demonstrates a full-format (192 x 192, 100-µm pitch, VX-810) high-dynamic-range x-ray photon-counting sensor—the Dual Photon Resolved Energy Acquisition (DUPREA) sensor. Within the Phase II program the following tasks were completed: 1) system analysis and definition of the DUPREA sensor requirements; 2) design, simulation, and fabrication of the full-format VX-810 ROIC design; 3) design, optimization, and fabrication of thick, fully depleted silicon photodiodes optimized for x-ray photon collection; 4) hybridization of the VX-810 ROIC to the photodiode array in the creation of the optically sensitive focal-plane array; 5) development of an evaluation camera; and 6)more » electrical and optical characterization of the sensor.« less

An Improved Solution for Integrated Array Optics in Quasi-Optical mm and Submm Receivers: the Hybrid Antenna

NASA Technical Reports Server (NTRS)

Buttgenbach, Thomas H.

1993-01-01

The hybrid antenna discussed here is defined as a dielectric lens-antenna as a special case of an extended hemi-spherical dielectric lens that is operated in the diffraction limited regime. It is a modified version of the planar antenna on a lens scheme developed by Rutledge. The dielectric lens-antenna is fed by a planar-structure antenna, which is mounted on the flat side of the dielectric lens-antenna using it as a substrate, and the combination is termed a hybrid antenna. Beam pattern and aperture efficiency measurements were made at millimeter and submillimeter wavelengths as a function of extension of the hemi- spherical lens and different lens sizes. An optimum extension distance is found experimentally and numerically for which excellent beam patterns and simultaneously high aperture efficiencies can be achieved. At 115 GHz the aperture efficiency was measured to be (76 4 +/- 6) % for a diffraction limited beam with sidelobes below -17 dB. Results of a single hybrid antenna with an integrated Superconductor-Insulator-Superconductor (SIS) detector and a broad-band matching structure at submillimeter wavelengths are presented. The hybrid antenna is diffraction limited, space efficient in an array due to its high aperture efficiency, and is easily mass produced, thus being well suited for focal plane heterodyne receiver arrays.

Revision of an automated microseismic location algorithm for DAS - 3C geophone hybrid array

NASA Astrophysics Data System (ADS)

Mizuno, T.; LeCalvez, J.; Raymer, D.

2017-12-01

Application of distributed acoustic sensing (DAS) has been studied in several areas in seismology. One of the areas is microseismic reservoir monitoring (e.g., Molteni et al., 2017, First Break). Considering the present limitations of DAS, which include relatively low signal-to-noise ratio (SNR) and no 3C polarization measurements, a DAS - 3C geophone hybrid array is a practical option when using a single monitoring well. Considering the large volume of data from distributed sensing, microseismic event detection and location using a source scanning type algorithm is a reasonable choice, especially for real-time monitoring. The algorithm must handle both strain rate along the borehole axis for DAS and particle velocity for 3C geophones. Only a small quantity of large SNR events will be detected throughout a large aperture encompassing the hybrid array; therefore, the aperture is to be optimized dynamically to eliminate noisy channels for a majority of events. For such hybrid array, coalescence microseismic mapping (CMM) (Drew et al., 2005, SPE) was revised. CMM forms a likelihood function of location of event and its origin time. At each receiver, a time function of event arrival likelihood is inferred using an SNR function, and it is migrated to time and space to determine hypocenter and origin time likelihood. This algorithm was revised to dynamically optimize such a hybrid array by identifying receivers where a microseismic signal is possibly detected and using only those receivers to compute the likelihood function. Currently, peak SNR is used to select receivers. To prevent false results due to small aperture, a minimum aperture threshold is employed. The algorithm refines location likelihood using 3C geophone polarization. We tested this algorithm using a ray-based synthetic dataset. Leaney (2014, PhD thesis, UBC) is used to compute particle velocity at receivers. Strain rate along the borehole axis is computed from particle velocity as DAS microseismic synthetic data. The likelihood function formed by both DAS and geophone behaves as expected with the aperture dynamically selected depending on the SNR of the event. We conclude that this algorithm can be successfully applied for such hybrid arrays to monitor microseismic activity. A study using a recently acquired dataset is planned.

'FloraArray' for screening of specific DNA probes representing the characteristics of a certain microbial community.

PubMed

Yokoi, Takahide; Kaku, Yoshiko; Suzuki, Hiroyuki; Ohta, Masayuki; Ikuta, Hajime; Isaka, Kazuichi; Sumino, Tatsuo; Wagatsuma, Masako

2007-08-01

To investigate uncharacterized microbial communities, a custom DNA microarray named 'FloraArray' was developed for screening specific probes that would represent the characteristics of a microbial community. The array was prepared by spotting 2000 plasmid DNAs from a genomic shotgun library of a sludge sample on a DNA microarray. By comparative hybridization of the array with two different samples of genomic DNA, one from the activated sludge and the other from a nonactivated sludge sample of an anaerobic ammonium oxidation (anammox) bacterial community, specific spots were visualized as a definite fluctuating profile in an MA (differential intensity ratio vs. spot intensity) plot. About 300 spots of the array accounted for the candidate probes to represent anammox reaction of the activated sludge. After sequence analysis of the probes and examination of the results of blastn searches against the reported anammox reference sequence, complete matches were found for 161 probes (58.3%) and >90% matches were found for 242 probes (87.1%). These results demonstrate that 'FloraArray' could be a useful tool for screening specific DNA molecules of unknown microbial communities.

Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm.

PubMed

Hoffmann, Thomas J; Zhan, Yiping; Kvale, Mark N; Hesselson, Stephanie E; Gollub, Jeremy; Iribarren, Carlos; Lu, Yontao; Mei, Gangwu; Purdy, Matthew M; Quesenberry, Charles; Rowell, Sarah; Shapero, Michael H; Smethurst, David; Somkin, Carol P; Van den Eeden, Stephen K; Walter, Larry; Webster, Teresa; Whitmer, Rachel A; Finn, Andrea; Schaefer, Catherine; Kwok, Pui-Yan; Risch, Neil

2011-12-01

Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East Asian array was designed using greedy pairwise SNP selection. However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging. Therefore, we developed a novel hybrid SNP selection method for the African American and Latino arrays utilizing rounds of greedy pairwise SNP selection, followed by removal from the target set of SNPs covered by imputation. The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies. Copyright © 2011 Elsevier Inc. All rights reserved.

1D Ni-Co oxide and sulfide nanoarray/carbon aerogel hybrid nanostructures for asymmetric supercapacitors with high energy density and excellent cycling stability.

PubMed

Hao, Pin; Tian, Jian; Sang, Yuanhua; Tuan, Chia-Chi; Cui, Guanwei; Shi, Xifeng; Wong, C P; Tang, Bo; Liu, Hong

2016-09-15

The fabrication of supercapacitor electrodes with high energy density and excellent cycling stability is still a great challenge. A carbon aerogel, possessing a hierarchical porous structure, high specific surface area and electrical conductivity, is an ideal backbone to support transition metal oxides and bring hope to prepare electrodes with high energy density and excellent cycling stability. Therefore, NiCo 2 S 4 nanotube array/carbon aerogel and NiCo 2 O 4 nanoneedle array/carbon aerogel hybrid supercapacitor electrode materials were synthesized by assembling Ni-Co precursor needle arrays on the surface of the channel walls of hierarchical porous carbon aerogels derived from chitosan in this study. The 1D nanostructures grow on the channel surface of the carbon aerogel vertically and tightly, contributing to the enhanced electrochemical performance with ultrahigh energy density. The energy density of NiCo 2 S 4 nanotube array/carbon aerogel and NiCo 2 O 4 nanoneedle array/carbon aerogel hybrid asymmetric supercapacitors can reach up to 55.3 Wh kg -1 and 47.5 Wh kg -1 at a power density of 400 W kg -1 , respectively. These asymmetric devices also displayed excellent cycling stability with a capacitance retention of about 96.6% and 92% over 5000 cycles.

Determination of the Pressure Equivalent Noise Signal of Vector Sensors in a Hybrid Array

DTIC Science & Technology

2012-12-01

pressure sensors for acoustic signals raises the possibility of increased sonar array performance with smaller arrays. Caulk successfully...contribution of the preamplifier in the circuit was estimated as . So the Johnson noise of the sensor wires themselves is expected to dominate

Ordered mapping of 3 alphoid DNA subsets on human chromosome 22

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antonacci, R.; Baldini, A.; Archidiacono, N.

1994-09-01

Alpha satellite DNA consists of tandemly repeated monomers of 171 bp clustered in the centromeric region of primate chromosomes. Sequence divergence between subsets located in different human chromosomes is usually high enough to ensure chromosome-specific hybridization. Alphoid probes specific for almost every human chromosome have been reported. A single chromosome can carry different subsets of alphoid DNA and some alphoid subsets can be shared by different chromosomes. We report the physical order of three alphoid DNA subsets on human chromosome 22 determined by a combination of low and high resolution cytological mapping methods. Results visually demonstrate the presence of threemore » distinct alphoid DNA domains at the centromeric region of chromosome 22. We have measured the interphase distances between the three probes in three-color FISH experiments. Statistical analysis of the results indicated the order of the subsets. Two color experiments on prometaphase chromosomes established the order of the three domains relative to the arms of chromosome 22 and confirmed the results obtained using interphase mapping. This demonstrates the applicability of interphase mapping for alpha satellite DNA orderering. However, in our experiments, interphase mapping did not provide any information about the relationship between extremities of the repeat arrays. This information was gained from extended chromatin hybridization. The extremities of two of the repeat arrays were seen to be almost overlapping whereas the third repeat array was clearly separated from the other two. Our data show the value of extended chromatin hybridization as a complement of other cytological techniques for high resolution mapping of repetitive DNA sequences.« less

Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates.

PubMed

Holden, Matthew T; Carter, Matthew C D; Wu, Cheng-Hsien; Wolfer, Jamison; Codner, Eric; Sussman, Michael R; Lynn, David M; Smith, Lloyd M

2015-11-17

The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

A Noise and Emissions Assessment of the N3-X Transport

NASA Technical Reports Server (NTRS)

Berton, Jeffrey J.; Haller, William J.

2014-01-01

Analytical predictions of certification noise and exhaust emissions for NASA's N3-X - a notional, hybrid wingbody airplane - are presented in this paper. The N3-X is a 300-passenger concept transport propelled by an array of fans distributed spanwise near the trailing edge of the wingbody. These fans are driven by electric motors deriving power from twin generators driven by turboshaft engines. Turboelectric distributed hybrid propulsion has the potential to dramatically increase the propulsive efficiency of aircraft. The noise and exhaust emission estimates presented here are generated using NASA's conceptual design systems analysis tools with several key modifications to accommodate this unconventional architecture. These tools predict certification noise and the emissions of oxides of nitrogen by leveraging data generated from a recent analysis of the N3-X propulsion system.

Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization

USDA-ARS?s Scientific Manuscript database

This study was designed to evaluate the feasibility of using a targeted array-CGH strategy for prenatal diagnosis of genomic imbalances in a clinical setting of current pregnancies. Women undergoing prenatal diagnosis were counseled and offered array-CGH (BCM V4.0) in addition to routine chromosome ...

High-resolution array comparative genomic hybridization (aCGH) identifies copy number alterations in diffuse large B-cell lymphoma that predict response to immuno-chemotherapy

PubMed Central

Kreisel, F.; Kulkarni, S.; Kerns, R. T.; Hassan, A.; Deshmukh, H.; Nagarajan, R.; Frater, J. L.; Cashen, A.

2013-01-01

Despite recent attempts at sub-categorization, including gene expression profiling into prognostically different groups of “germinal center B-cell type” and “activated B-cell type”, diffuse large B-cell lymphoma (DLBCL) remains a biologically heterogenous tumor with no clear prognostic biomarkers to guide therapy. Whole genome, high resolution array comparative genomic hybridization (aCGH) was performed on 4 cases of chemoresistant DLBCL and 4 cases of chemo-responsive DLBCL to identify genetic differences which may correlate with response to R-CHOP therapy. Array CGH analysis identified 7 DNA copy number alteration (CNA) regions exclusive to the chemoresistant group, consisting of amplifications at 1p36.13, 1q42.3, 3p21.31, 7q11.23, and 16p13.3, and loss at 9p21.3, and 14p21.31. Copy number loss of the tumor suppressor genes CDKN2A (p16, p14) and CDKN2B (p15) at 9p21.3 was validated by fluorescence in situ hybridization and immunohistochemistry as independent techniques. In the chemo-sensitive group, 12 CNAs were detected consisting of segment gains on 1p36.11, 1p36.22, 2q11.2, 8q24.3, 12p13.33, and 22q13.2 and segment loss on 6p21.32. RUNX3, a tumor suppressor gene located on 1p36.11 and MTHFR, which encodes for the enzyme methylenetetrahydrofolate reductase, located on 1p36.22 are the only known genes in this group associated with lymphoma. Whole genome aCGH analysis has detected copy number alterations exclusive to either chemoresistant or chemo-responsive DLBCL that may represent consistent clonal changes predictive for prognosis and outcome of chemotherapy. PMID:21504712

A hybrid approach to device integration on a genetic analysis platform

NASA Astrophysics Data System (ADS)

Brennan, Des; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Justice, John; Aherne, Margaret; Macek, Milan; Galvin, Paul

2012-10-01

Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization.

Ecological Success of a Group of Saccharomyces cerevisiae/Saccharomyces kudriavzevii Hybrids in the Northern European Wine-Making Environment

PubMed Central

Erny, C.; Raoult, P.; Alais, A.; Butterlin, G.; Delobel, P.; Matei-Radoi, F.; Casaregola, S.

2012-01-01

The hybrid nature of lager-brewing yeast strains has been known for 25 years; however, yeast hybrids have only recently been described in cider and wine fermentations. In this study, we characterized the hybrid genomes and the relatedness of the Eg8 industrial yeast strain and of 24 Saccharomyces cerevisiae/Saccharomyces kudriavzevii hybrid yeast strains used for wine making in France (Alsace), Germany, Hungary, and the United States. An array-based comparative genome hybridization (aCGH) profile of the Eg8 genome revealed a typical chimeric profile. Measurement of hybrids DNA content per cell by flow cytometry revealed multiple ploidy levels (2n, 3n, or 4n), and restriction fragment length polymorphism analysis of 22 genes indicated variable amounts of S. kudriavzevii genetic content in three representative strains. We developed microsatellite markers for S. kudriavzevii and used them to analyze the diversity of a population isolated from oaks in Ardèche (France). This analysis revealed new insights into the diversity of this species. We then analyzed the diversity of the wine hybrids for 12 S. cerevisiae and 7 S. kudriavzevii microsatellite loci and found that these strains are the products of multiple hybridization events between several S. cerevisiae wine yeast isolates and various S. kudriavzevii strains. The Eg8 lineage appeared remarkable, since it harbors strains found over a wide geographic area, and the interstrain divergence measured with a (δμ)2 genetic distance indicates an ancient origin. These findings reflect the specific adaptations made by S. cerevisiae/S. kudriavzevii cryophilic hybrids to winery environments in cool climates. PMID:22344648

Aleutian Array of Arrays (A-cubed) to probe a broad spectrum of fault slip under the Aleutian Islands

NASA Astrophysics Data System (ADS)

Ghosh, A.; LI, B.

2016-12-01

Alaska-Aleutian subduction zone is one of the most seismically active subduction zones in this planet. It is characterized by remarkable along-strike variations in seismic behavior, more than 50 active volcanoes, and presents a unique opportunity to serve as a natural laboratory to study subduction zone processes including fault dynamics. Yet details of the seismicity pattern, spatiotemporal distribution of slow earthquakes, nature of interaction between slow and fast earthquakes and their implication on the tectonic behavior remain unknown. We use a hybrid seismic network approach and install 3 mini seismic arrays and 5 stand-alone stations to simultaneously image subduction fault and nearby volcanic system (Makushin). The arrays and stations are strategically located in the Unalaska Island, where prolific tremor activity is detected and located by a solo pilot array in summer 2012. The hybrid network is operational between summer 2015 and 2016 in continuous mode. One of the three arrays starts in summer 2014 and provides additional data covering a longer time span. The pilot array in the Akutan Island recorded continuous seismic data for 2 months. An automatic beam-backprojection analysis detects almost daily tremor activity, with an average of more than an hour per day. We imaged two active sources separated by a tremor gap. The western source, right under the Unalaska Island shows the most prolific activity with a hint of steady migration. In addition, we are able to identify more than 10 families of low frequency earthquakes (LFEs) in this area. They are located within the tremor source area as imaged by the bean-backprojection technique. Application of a match filter technique reveals that intervals between LFE activities are shorter during tremor activity and longer during quiet time period. We expect to present new results from freshly obtained data. The experiment A-cubed is illuminating subduction zone processes under Unalaska Island in unprecedented detail.

Correction of Spatial Bias in Oligonucleotide Array Data

PubMed Central

Lemieux, Sébastien

2013-01-01

Background. Oligonucleotide microarrays allow for high-throughput gene expression profiling assays. The technology relies on the fundamental assumption that observed hybridization signal intensities (HSIs) for each intended target, on average, correlate with their target's true concentration in the sample. However, systematic, nonbiological variation from several sources undermines this hypothesis. Background hybridization signal has been previously identified as one such important source, one manifestation of which appears in the form of spatial autocorrelation. Results. We propose an algorithm, pyn, for the elimination of spatial autocorrelation in HSIs, exploiting the duality of desirable mutual information shared by probes in a common probe set and undesirable mutual information shared by spatially proximate probes. We show that this correction procedure reduces spatial autocorrelation in HSIs; increases HSI reproducibility across replicate arrays; increases differentially expressed gene detection power; and performs better than previously published methods. Conclusions. The proposed algorithm increases both precision and accuracy, while requiring virtually no changes to users' current analysis pipelines: the correction consists merely of a transformation of raw HSIs (e.g., CEL files for Affymetrix arrays). A free, open-source implementation is provided as an R package, compatible with standard Bioconductor tools. The approach may also be tailored to other platform types and other sources of bias. PMID:23573083

Characterization of a chromosome-specific chimpanzee alpha satellite subset: Evolutionary relationship to subsets on human chromosomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warburton, P.E.; Gosden, J.; Lawson, D.

1996-04-15

Alpha satellite DNA is a tandemly repeated DNA family found at the centromeres of all primate chromosomes examined. The fundamental repeat units of alpha satellite DNA are diverged 169- to 172-bp monomers, often found to be organized in chromosome-specific higher-order repeat units. The chromosomes of human (Homo sapiens (HSA)), chimpanzee (Pan troglodytes (PTR) and Pan paniscus), and gorilla (Gorilla gorilla) share a remarkable similarity and synteny. It is of interest to ask if alpha satellite arrays at centromeres of homologous chromosomes between these species are closely related (evolving in an orthologous manner) or if the evolutionary processes that homogenize andmore » spread these arrays within and between chromosomes result in nonorthologous evolution of arrays. By using PCR primers specific for human chromosome 17-specific alpha satellite DNA, we have amplified, cloned, and characterized a chromosome-specific subset from the PTR chimpanzee genome. Hybridization both on Southern blots and in situ as well as sequence analysis show that this subset is most closely related, as expected, to sequences on HSA 17. However, in situ hybridization reveals that this subset is not found on the homologous chromosome in chimpanzee (PTR 19), but instead on PTR 12, which is homologous to HSA 2p. 40 refs., 3 figs.« less

Identification of IL11RA and MELK amplification in gastric cancer by comprehensive genomic profiling of gastric cancer cell lines

PubMed Central

Calcagno, Danielle Queiroz; Takeno, Sylvia Santomi; Gigek, Carolina Oliveira; Leal, Mariana Ferreira; Wisnieski, Fernanda; Chen, Elizabeth Suchi; Araújo, Taíssa Maíra Thomaz; Lima, Eleonidas Moura; Melaragno, Maria Isabel; Demachki, Samia; Assumpção, Paulo Pimentel; Burbano, Rommel Rodriguez; Smith, Marília Cardoso

2016-01-01

AIM To identify common copy number alterations on gastric cancer cell lines. METHODS Four gastric cancer cell lines (ACP02, ACP03, AGP01 and PG100) underwent chromosomal comparative genome hybridization and array comparative genome hybridization. We also confirmed the results by fluorescence in situ hybridization analysis using the bacterial artificial chromosome clone and quantitative real time PCR analysis. RESULTS The amplification of 9p13.3 was detected in all cell lines by both methodologies. An increase in the copy number of 9p13.3 was also confirmed by fluorescence in situ hybridization analysis. Moreover, the interleukin 11 receptor alpha (IL11RA) and maternal embryonic leucine zipper kinase (MELK) genes, which are present in the 9p13.3 amplicon, revealed gains of the MELK gene in all the cell lines studied. Additionally, a gain in the copy number of IL11RA and MELK was observed in 19.1% (13/68) and 55.9% (38/68) of primary gastric adenocarcinoma samples, respectively. CONCLUSION The characterization of a small gain region at 9p13.3 in gastric cancer cell lines and primary gastric adenocarcinoma samples has revealed MELK as a candidate target gene that is possibly related to the development of gastric cancer. PMID:27920471

Operational compatibility of 30-centimeter-diameter ion thruster with integrally regulated solar array power source

NASA Technical Reports Server (NTRS)

Gooder, S. T.

1977-01-01

System tests were performed in which Integrally Regulated Solar Arrays (IRSA's) were used to directly power the beam and accelerator loads of a 30-cm-diameter, electron bombardment, mercury ion thruster. The remaining thruster loads were supplied from conventional power-processing circuits. This combination of IRSA's and conventional circuits formed a hybrid power processor. Thruster performance was evaluated at 3/4- and 1-A beam currents with both the IRSA-hybrid and conventional power processors and was found to be identical for both systems. Power processing is significantly more efficient with the hybrid system. System dynamics and IRSA response to thruster arcs are also examined.

Deterministic Coupling of Quantum Emitters in 2D Materials to Plasmonic Nanocavity Arrays.

PubMed

Tran, Toan Trong; Wang, Danqing; Xu, Zai-Quan; Yang, Ankun; Toth, Milos; Odom, Teri W; Aharonovich, Igor

2017-04-12

Quantum emitters in two-dimensional materials are promising candidates for studies of light-matter interaction and next generation, integrated on-chip quantum nanophotonics. However, the realization of integrated nanophotonic systems requires the coupling of emitters to optical cavities and resonators. In this work, we demonstrate hybrid systems in which quantum emitters in 2D hexagonal boron nitride (hBN) are deterministically coupled to high-quality plasmonic nanocavity arrays. The plasmonic nanoparticle arrays offer a high-quality, low-loss cavity in the same spectral range as the quantum emitters in hBN. The coupled emitters exhibit enhanced emission rates and reduced fluorescence lifetimes, consistent with Purcell enhancement in the weak coupling regime. Our results provide the foundation for a versatile approach for achieving scalable, integrated hybrid systems based on low-loss plasmonic nanoparticle arrays and 2D materials.

Detection limit of intragenic deletions with targeted array comparative genomic hybridization

PubMed Central

2013-01-01

Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

Ultra-Lightweight Hybrid Thin-Film Solar Cells: A Survey of Enabling Technologies for Space Power Applications

NASA Technical Reports Server (NTRS)

Hepp, Aloysius F.; McNatt, Jeremiah S.; Bailey, Sheila G.; Dickman, John E.; Raffaelle, Ryne P.; Landi, Brian J.; Anctil, Annick; DiLeo, Roberta; Jin, Michael H.-C.; Lee, Chung-Young;

A Novel Hybrid Classification Model of Genetic Algorithms, Modified k-Nearest Neighbor and Developed Backpropagation Neural Network

PubMed Central

Salari, Nader; Shohaimi, Shamarina; Najafi, Farid; Nallappan, Meenakshii; Karishnarajah, Isthrinayagy

2014-01-01

Among numerous artificial intelligence approaches, k-Nearest Neighbor algorithms, genetic algorithms, and artificial neural networks are considered as the most common and effective methods in classification problems in numerous studies. In the present study, the results of the implementation of a novel hybrid feature selection-classification model using the above mentioned methods are presented. The purpose is benefitting from the synergies obtained from combining these technologies for the development of classification models. Such a combination creates an opportunity to invest in the strength of each algorithm, and is an approach to make up for their deficiencies. To develop proposed model, with the aim of obtaining the best array of features, first, feature ranking techniques such as the Fisher's discriminant ratio and class separability criteria were used to prioritize features. Second, the obtained results that included arrays of the top-ranked features were used as the initial population of a genetic algorithm to produce optimum arrays of features. Third, using a modified k-Nearest Neighbor method as well as an improved method of backpropagation neural networks, the classification process was advanced based on optimum arrays of the features selected by genetic algorithms. The performance of the proposed model was compared with thirteen well-known classification models based on seven datasets. Furthermore, the statistical analysis was performed using the Friedman test followed by post-hoc tests. The experimental findings indicated that the novel proposed hybrid model resulted in significantly better classification performance compared with all 13 classification methods. Finally, the performance results of the proposed model was benchmarked against the best ones reported as the state-of-the-art classifiers in terms of classification accuracy for the same data sets. The substantial findings of the comprehensive comparative study revealed that performance of the proposed model in terms of classification accuracy is desirable, promising, and competitive to the existing state-of-the-art classification models. PMID:25419659

High resolution array CGH and gene expression profiling of alveolar soft part sarcoma

PubMed Central

Selvarajah, Shamini; Pyne, Saumyadipta; Chen, Eleanor; Sompallae, Ramakrishna; Ligon, Azra H.; Nielsen, Gunnlaugur P.; Dranoff, Glenn; Stack, Edward; Loda, Massimo; Flavin, Richard

2014-01-01

Purpose Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis, and little molecular evidence for its origin, initiation and progression. The aim of this study was to elucidate candidate molecular pathways involved in tumor pathogenesis. Experimental Design We employed high-throughput array comparative genomic hybridization and cDNA-Mediated Annealing, Selection, Ligation, and Extension Assay to profile the genomic and expression signatures of primary and metastatic ASPS from 17 tumors derived from 11 patients. We used an integrative bioinformatics approach to elucidate the molecular pathways associated with ASPS progression. Fluorescence in situ hybridization was performed to validate the presence of the t(X;17)(p11.2;q25) ASPL-TFE3 fusion and hence confirm the aCGH observations. Results FISH analysis identified the ASPL-TFE3 fusion in all cases. ArrayCGH revealed a higher number of numerical aberrations in metastatic tumors relative to primaries, but failed to identify consistent alterations in either group. Gene expression analysis highlighted 1,063 genes which were differentially expressed between the two groups. Gene set enrichment analysis identified 16 enriched gene sets (p < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6 was up-regulated in the primary tumors, along with several genes whose mouse orthologs have previously been implicated in Pax6-DNA binding during neural stem cell differentiation. Conclusion In addition to suggesting a tentative neural line of differentiation for ASPS, these results implicate transcriptional deregulation from fusion genes in the pathogenesis of ASPS. PMID:24493828

High Voltage Dielectrophoretic and Magnetophoretic Hybrid Integrated Circuit / Microfluidic Chip

PubMed Central

Issadore, David; Franke, Thomas; Brown, Keith A.; Hunt, Thomas P.; Westervelt, Robert M.

2010-01-01

A hybrid integrated circuit (IC) / microfluidic chip is presented that independently and simultaneously traps and moves microscopic objects suspended in fluid using both electric and magnetic fields. This hybrid chip controls the location of dielectric objects, such as living cells and drops of fluid, on a 60 × 61 array of pixels that are 30 × 38 μm2 in size, each of which can be individually addressed with a 50 V peak-to-peak, DC to 10 MHz radio frequency voltage. These high voltage pixels produce electric fields above the chip’s surface with a magnitude , resulting in strong dielectrophoresis (DEP) forces . Underneath the array of DEP pixels there is a magnetic matrix that consists of two perpendicular sets of 60 metal wires running across the chip. Each wire can be sourced with 120 mA to trap and move magnetically susceptible objects using magnetophoresis (MP). The DEP pixel array and magnetic matrix can be used simultaneously to apply forces to microscopic objects, such as living cells or lipid vesicles, that are tagged with magnetic nanoparticles. The capabilities of the hybrid IC / microfluidic chip demonstrated in this paper provide important building blocks for a platform for biological and chemical applications. PMID:20625468

High Voltage Dielectrophoretic and Magnetophoretic Hybrid Integrated Circuit / Microfluidic Chip.

PubMed

Issadore, David; Franke, Thomas; Brown, Keith A; Hunt, Thomas P; Westervelt, Robert M

2009-12-01

A hybrid integrated circuit (IC) / microfluidic chip is presented that independently and simultaneously traps and moves microscopic objects suspended in fluid using both electric and magnetic fields. This hybrid chip controls the location of dielectric objects, such as living cells and drops of fluid, on a 60 × 61 array of pixels that are 30 × 38 μm(2) in size, each of which can be individually addressed with a 50 V peak-to-peak, DC to 10 MHz radio frequency voltage. These high voltage pixels produce electric fields above the chip's surface with a magnitude , resulting in strong dielectrophoresis (DEP) forces . Underneath the array of DEP pixels there is a magnetic matrix that consists of two perpendicular sets of 60 metal wires running across the chip. Each wire can be sourced with 120 mA to trap and move magnetically susceptible objects using magnetophoresis (MP). The DEP pixel array and magnetic matrix can be used simultaneously to apply forces to microscopic objects, such as living cells or lipid vesicles, that are tagged with magnetic nanoparticles. The capabilities of the hybrid IC / microfluidic chip demonstrated in this paper provide important building blocks for a platform for biological and chemical applications.

Human minisatellite alleles detectable only after PCR amplification.

PubMed

Armour, J A; Crosier, M; Jeffreys, A J

1992-01-01

We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

A gold hybrid structure as optical coupler for quantum well infrared photodetector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Jiayi; Li, Qian; Jing, Youliang

2014-08-28

A hybrid structure consisting of a square lattice of gold disk arrays and an overlaying gold film is proposed as an optical coupler for a backside-illuminated quantum well infrared photodetector (QWIP). Finite difference time-domain method is used to numerically simulate the reflection spectra and the field distributions of the hybrid structure combined with the QWIP device. The results show that the electric field component perpendicular to the quantum well is strongly enhanced when the plasmonic resonant wavelength of the hybrid structure coincides with the response one of the quantum well infrared photodetector regardless of the polarization of the incident light.more » The effect of the diameter and thickness of an individual gold disk on the resonant wavelength is also investigated, which indicates that the localized surface plasmon also plays a role in the light coupling with the hybrid structure. The coupling efficiency can exceed 50 if the structural parameters of the gold disk arrays are well optimized.« less

Hybrid micro-scale photovoltaics for enhanced energy conversion across all irradiation conditions

NASA Astrophysics Data System (ADS)

Agrawal, Gautam

A novel hybrid photovoltaics (HPV) architecture is presented that integrates high-performance micro-optics-based concentrator photovoltaics (CPV) array technology with a 1-sun photovoltaic (PV) cell within a low-profile panel structure. The approach simultaneously captures the direct solar radiation components with arrayed high-efficiency CPV cells and the diffuse solar components with an underlying wide-area PV cell. Performance analyses predict that the hybrid approach will significantly enhance the average energy produced per unit area for the full range of diffuse/direct radiation patterns across the USA. Furthermore, cost analyses indicate that the hybrid concept may be financially attractive for a wide range of locations. Indoor and outdoor experimental evaluation of a micro-optical system designed for use in a hybrid architecture verified that a large proportion of the direct radiation component was concentrated onto emulated micro-cell regions while most of the diffuse radiation and the remaining direct radiation was collected in the 1-sun cell area.

Influence of Reinforcement Parameters and Ageing Time on Mechanical Behavior of Novel Al2024/SiC/Red Mud Composites Using Response Surface Methodology

NASA Astrophysics Data System (ADS)

Singh, Jaswinder; Chauhan, Amit

2017-12-01

This study investigates the mechanical behavior of aluminum 2024 matrix composites reinforced with silicon carbide and red mud particles. The hybrid reinforcements were successfully incorporated into the alloy matrix using the stir casting process. An orthogonal array based on Taguchi's technique was used to acquire experimental data for mechanical properties (hardness and impact energy) of the composites. The analysis of variance (ANOVA) and response surface methodology (RSM) techniques were used to evaluate the influence of test parameters (reinforcement ratio, particle size and ageing time). The morphological analysis of the surfaces (fractured during impact tests) was conducted to identify the failure mechanism. Finally, a confirmation experiment was performed to check the adequacy of the developed model. The results indicate that the ageing time is the most effective parameter as far as the hardness of the hybrid composites is concerned. It has also been revealed that red mud wt.% has maximum influence on the impact energy characteristics of the hybrid composites. The study concludes that Al2024/SiC/red mud hybrid composites possess superior mechanical performance in comparison to pure alloy under optimized conditions.

Simulation and optimum design of hybrid solar-wind and solar-wind-diesel power generation systems

NASA Astrophysics Data System (ADS)

Zhou, Wei

Solar and wind energy systems are considered as promising power generating sources due to its availability and topological advantages in local power generations. However, a drawback, common to solar and wind options, is their unpredictable nature and dependence on weather changes, both of these energy systems would have to be oversized to make them completely reliable. Fortunately, the problems caused by variable nature of these resources can be partially overcome by integrating these two resources in a proper combination to form a hybrid system. However, with the increased complexity in comparison with single energy systems, optimum design of hybrid system becomes more complicated. In order to efficiently and economically utilize the renewable energy resources, one optimal sizing method is necessary. This thesis developed an optimal sizing method to find the global optimum configuration of stand-alone hybrid (both solar-wind and solar-wind-diesel) power generation systems. By using Genetic Algorithm (GA), the optimal sizing method was developed to calculate the system optimum configuration which offers to guarantee the lowest investment with full use of the PV array, wind turbine and battery bank. For the hybrid solar-wind system, the optimal sizing method is developed based on the Loss of Power Supply Probability (LPSP) and the Annualized Cost of System (ACS) concepts. The optimization procedure aims to find the configuration that yields the best compromise between the two considered objectives: LPSP and ACS. The decision variables, which need to be optimized in the optimization process, are the PV module capacity, wind turbine capacity, battery capacity, PV module slope angle and wind turbine installation height. For the hybrid solar-wind-diesel system, minimization of the system cost is achieved not only by selecting an appropriate system configuration, but also by finding a suitable control strategy (starting and stopping point) of the diesel generator. The optimal sizing method was developed to find the system optimum configuration and settings that can achieve the custom-required Renewable Energy Fraction (fRE) of the system with minimum Annualized Cost of System (ACS). Du to the need for optimum design of the hybrid systems, an analysis of local weather conditions (solar radiation and wind speed) was carried out for the potential installation site, and mathematical simulation of the hybrid systems' components was also carried out including PV array, wind turbine and battery bank. By statistically analyzing the long-term hourly solar and wind speed data, Hong Kong area is found to have favorite solar and wind power resources compared with other areas, which validates the practical applications in Hong Kong and Guangdong area. Simulation of PV array performance includes three main parts: modeling of the maximum power output of the PV array, calculation of the total solar radiation on any tilted surface with any orientations, and PV module temperature predictions. Five parameters are introduced to account for the complex dependence of PV array performance upon solar radiation intensities and PV module temperatures. The developed simulation model was validated by using the field-measured data from one existing building-integrated photovoltaic system (BIPV) in Hong Kong, and good simulation performance of the model was achieved. Lead-acid batteries used in hybrid systems operate under very specific conditions, which often cause difficulties to predict when energy will be extracted from or supplied to the battery. In this thesis, the lead-acid battery performance is simulated by three different characteristics: battery state of charge (SOC), battery floating charge voltage and the expected battery lifetime. Good agreements were found between the predicted values and the field-measured data of a hybrid solar-wind project. At last, one 19.8kW hybrid solar-wind power generation project, designed by the optimal sizing method and set up to supply power for a telecommunication relay station on a remote island of Guangdong province, was studied. Simulation and experimental results about the operating performances and characteristics of the hybrid solar-wind project have demonstrated the feasibility and accuracy of the recommended optimal sizing method developed in this thesis.

Detector arrays for low-background space infrared astronomy

NASA Technical Reports Server (NTRS)

Mccreight, C. R.; Mckelvey, M. E.; Goebel, J. H.; Anderson, G. M.; Lee, J. H.

1986-01-01

The status of development and characterization tests of integrated infrared detector array technology for astronomy applications is described. The devices under development include intrinsic, extrinsic silicon, and extrinsic germanium detectors, with hybrid silicon multiplexers. Laboratory test results and successful astronomy imagery have established the usefulness of integrated arrays in low-background astronomy applications.

Detector arrays for low-background space infrared astronomy

NASA Technical Reports Server (NTRS)

Mccreight, C. R.; Mckelvey, M. E.; Goebel, J. H.; Anderson, G. M.; Lee, J. H.

1986-01-01

The status of development and characterization tests of integrated infrared detector array technology for astronomy applications is described. The devices under development include intrinsic, extrinsic silicon, and extrinsic germanium detectors, with hybrid silicon multiplexers. Laboratary test results and successful astronomy imagery have established the usefulness of integrated arrays in low-background astronomy applications.

Effects of silicon nanowire morphology on optical properties and hybrid solar cell performance

NASA Astrophysics Data System (ADS)

Syu, Hong-Jhang; Shiu, Shu-Chia; Hung, Yung-Jr; Lee, San-Liang; Lin, Ching-Fuh

2012-10-01

Silicon nanowire (SiNW) arrays are widespread applied on hybrid photovoltaic devices because SiNW arrays can substitute the pyramid texture and anti-reflection coating due to its strong light trapping. Also, SiNWs can be prepared through a cost-efficient process of metal-assisted chemical etching. However, though longer SiNW arrays have lower reflectance, the top of long SiNWs aggregate together to make junction synthesis difficult for SiNW/organic hybrid solar cell. To control and analyze the effect of SiNW array morphology on hybrid solar cells, here we change the metal deposition condition for metal-assisted chemical etching to obtain different SiNW array morphologies. The experiment was separated to two groups, by depositing metal, say, Ag, before etching (BE) or during etching (DE). For group BE, Ag was deposited on n-type Si (n-Si) wafers by thermal evaporation; then etched by H2O2 and HF. For group DE, n-Si was etched by Ag+ and HF directly. Ag was deposited on n-Si during etching process. Afterwards, residual Ag and SiO2 were removed by HNO3 and buffered HF, successively; then Ti and Ag were evaporated on the bottom of Si to be a cathode. Finally, SiNWs were stuck on the poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) that was spincoated on the ITO coated glass to form SiNW/organic heterojunction. The results show that group BE has reflectance lower than that in group DE in solar spectrum. However, group BE has smaller power conversion efficiency (PCE) of 8.65% and short-circuit current density (Jsc) of 24.94 mA/cm2 than group DE of PCE of 9.47% and Jsc of 26.81 mA/cm2.

Magnetic Flux Distribution of Linear Machines with Novel Three-Dimensional Hybrid Magnet Arrays

PubMed Central

Yao, Nan; Yan, Liang; Wang, Tianyi; Wang, Shaoping

2017-01-01

The objective of this paper is to propose a novel tubular linear machine with hybrid permanent magnet arrays and multiple movers, which could be employed for either actuation or sensing technology. The hybrid magnet array produces flux distribution on both sides of windings, and thus helps to increase the signal strength in the windings. The multiple movers are important for airspace technology, because they can improve the system’s redundancy and reliability. The proposed design concept is presented, and the governing equations are obtained based on source free property and Maxwell equations. The magnetic field distribution in the linear machine is thus analytically formulated by using Bessel functions and harmonic expansion of magnetization vector. Numerical simulation is then conducted to validate the analytical solutions of the magnetic flux field. It is proved that the analytical model agrees with the numerical results well. Therefore, it can be utilized for the formulation of signal or force output subsequently, depending on its particular implementation. PMID:29156577

Magnetic Flux Distribution of Linear Machines with Novel Three-Dimensional Hybrid Magnet Arrays.

PubMed

Yao, Nan; Yan, Liang; Wang, Tianyi; Wang, Shaoping

2017-11-18

The objective of this paper is to propose a novel tubular linear machine with hybrid permanent magnet arrays and multiple movers, which could be employed for either actuation or sensing technology. The hybrid magnet array produces flux distribution on both sides of windings, and thus helps to increase the signal strength in the windings. The multiple movers are important for airspace technology, because they can improve the system's redundancy and reliability. The proposed design concept is presented, and the governing equations are obtained based on source free property and Maxwell equations. The magnetic field distribution in the linear machine is thus analytically formulated by using Bessel functions and harmonic expansion of magnetization vector. Numerical simulation is then conducted to validate the analytical solutions of the magnetic flux field. It is proved that the analytical model agrees with the numerical results well. Therefore, it can be utilized for the formulation of signal or force output subsequently, depending on its particular implementation.

First data with the Hybrid Array of Gamma Ray Detector (HAGRiD)

NASA Astrophysics Data System (ADS)

Smith, K.; Baugher, T.; Burcher, S.; Carter, A. B.; Cizewski, J. A.; Chipps, K. A.; Febbraro, M.; Grzywacz, R.; Jones, K. L.; Munoz, S.; Pain, S. D.; Paulauskas, S. V.; Ratkiewicz, A.; Schmitt, K. T.; Thornsberry, C.; Toomey, R.; Walter, D.; Willoughby, H.

2018-01-01

The structure of nuclei provides insight into astrophysical reaction rates that are difficult to measure directly. These studies are often performed with transfer reactions and β-decay measurements. These experiments benefit from particle-γ coincidence measurements which provide information beyond that of particle detection alone. The Hybrid Array of Gamma Ray Detectors (HAGRiD) of LaBr3(Ce) scintillators has been designed with this purpose in mind. The design of the array permits it to be coupled with particle detector systems, such as the Oak Ridge Rutgers University Barrel Array (ORRUBA) of silicon detectors and the Versatile Array of Neutron Detectors at Low Energy (VANDLE). It is also designed to operate with the Jet Experiments in Nuclear Structure and Astrophysics (JENSA) advanced target system. HAGRiD's design avoids compromising the charged-particle angular resolution due to compact geometries which are often used to increase the γ efficiency in other systems. First experiments with HAGRiD coupled to VANDLE as well as ORRUBA and JENSA are discussed.

Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

PubMed

Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

2015-02-02

There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

Carbon Nanotube Nanoelectrode Array for Ultrasensitive DNA Detection

NASA Technical Reports Server (NTRS)

Li, Jun; Koehne, Jessica; Chen, Hua; Cassell, Alan; Ng, Hou Tee; Fan, Wendy; Ye, Qi; Han, Jie; Meyyappan, M.

2003-01-01

A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in SiO2 is used for ultrasensitive DNA detection. Characteristic nanoelectrode behavior is observed using low-density MWNT arrays for measuring both bulk and surface immobilized redox species such as K4Fe(CN)6. The open-end of MWNTs present similar properties as graphite edge-plane electrodes with wide potential window, flexible chemical functionalities, and good biocompatibility. Oligonucleotide probes are selectively functionalized at the open ends cf the nanotube array and specifically hybridized with oligonucleotide targets. The guanine groups are employed as the signal moieties in the electrochemical measurements. Ru(bpy)3(2+) mediator is used to further amplify the guanine oxidation signal. The hybridization of subattomoles of PCR amplified DNA targets is detected electrochemically by combining the MWNT nanoelectrode array with the Ru(bpy)32' amplification mechanism. This system provides a general platform of molecular diagnostics for applications requiring ultrahigh sensitivity, high-degree of miniaturization, and simple sample preparations.

Hybrid Ni/SiO2/Au dimer arrays for high-resolution refractive index sensing

NASA Astrophysics Data System (ADS)

Pourjamal, Sara; Kataja, Mikko; Maccaferri, Nicolò; Vavassori, Paolo; van Dijken, Sebastiaan

2018-05-01

We introduce a novel magnetoplasmonic sensor concept for sensitive detection of refractive index changes. The sensor consists of a periodic array of Ni/SiO2/Au dimer nanodisks. Combined effects of near-field interactions between the Ni and Au disks within the individual dimers and far-field diffractive coupling between the dimers of the array produce narrow linewidth features in the magneto-optical Faraday spectrum. We associate these features with the excitation of surface lattice resonances and show that they exhibit a spectral shift when the refractive index of the surrounding environment is varied. Because the resonances are sharp, refractive index changes are accurately detected by tracking the wavelength where the Faraday signal crosses 0. Compared to random distributions of pure Ni nanodisks or Ni/SiO2/Au dimers or periodic arrays of Ni nanodisks, the sensing figure of merit of the hybrid magnetoplasmonic array is more than one order of magnitude larger.

Toward highly stable solid-state unconventional thin-film battery-supercapacitor hybrid devices: Interfacing vertical core-shell array electrodes with a gel polymer electrolyte

NASA Astrophysics Data System (ADS)

Pandey, Gaind P.; Klankowski, Steven A.; Liu, Tao; Wu, Judy; Li, Jun

2017-02-01

A novel solid-state battery-supercapacitor hybrid device is fabricated for high-performance electrical energy storage using a Si anode and a TiO2 cathode in conjunction with a flexible, solid-like gel polymer electrolyte film as the electrolyte and separator. The electrodes were fabricated as three-dimensional nanostructured vertical arrays by sputtering active materials as conformal shells on vertically aligned carbon nanofibers (VACNFs) which serve as the current collector and structural template. Such nanostructured vertical core-shell array-electrodes enable short Li-ion diffusion path and large pseudocapacitive contribution by fast surface reactions, leading to the hybrid features of batteries and supercapacitors that can provide high specific energy over a wide range of power rates. Due to the improved mechanical stability of the infiltrated composite structure, the hybrid cell shows excellent cycling stability and is able to retain more than 95% of the original capacity after 3500 cycles. More importantly, this solid-state device can stably operate in a temperature range from -20 to 60 °C with a very low self-discharge rate and an excellent shelf life. This solid-state architecture is promising for the development of highly stable thin-film hybrid energy storage devices for unconventional applications requiring largely varied power, wider operation temperature, long shelf-life and higher safety standards.

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

PubMed Central

Euskirchen, Ghia M.; Rozowsky, Joel S.; Wei, Chia-Lin; Lee, Wah Heng; Zhang, Zhengdong D.; Hartman, Stephen; Emanuelsson, Olof; Stolc, Viktor; Weissman, Sherman; Gerstein, Mark B.; Ruan, Yijun; Snyder, Michael

2007-01-01

Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%–86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies. PMID:17568005

Development of a 1K x 1K GaAs QWIP Far IR Imaging Array

NASA Technical Reports Server (NTRS)

Jhabvala, M.; Choi, K.; Goldberg, A.; La, A.; Gunapala, S.

2003-01-01

In the on-going evolution of GaAs Quantum Well Infrared Photodetectors (QWIPs) we have developed a 1,024 x 1,024 (1K x1K), 8.4-9 microns infrared focal plane array (FPA). This 1 megapixel detector array is a hybrid using the Rockwell TCM 8050 silicon readout integrated circuit (ROIC) bump bonded to a GaAs QWIP array fabricated jointly by engineers at the Goddard Space Flight Center (GSFC) and the Army Research Laboratory (ARL). The finished hybrid is thinned at the Jet Propulsion Lab. Prior to this development the largest format array was a 512 x 640 FPA. We have integrated the 1K x 1K array into an imaging camera system and performed tests over the 40K-90K temperature range achieving BLIP performance at an operating temperature of 76K (f/2 camera system). The GaAs array is relatively easy to fabricate once the superlattice structure of the quantum wells has been defined and grown. The overall arrays costs are currently dominated by the costs associated with the silicon readout since the GaAs array fabrication is based on high yield, well-established GaAs processing capabilities. In this paper we will present the first results of our 1K x 1K QWIP array development including fabrication methodology, test data and our imaging results.

The Diagnostic Yield of Array Comparative Genomic Hybridization Is High Regardless of Severity of Intellectual Disability/Developmental Delay in Children.

PubMed

D'Arrigo, Stefano; Gavazzi, Francesco; Alfei, Enrico; Zuffardi, Orsetta; Montomoli, Cristina; Corso, Barbara; Buzzi, Erika; Sciacca, Francesca L; Bulgheroni, Sara; Riva, Daria; Pantaleoni, Chiara

2016-05-01

Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. The aim of the present study was to apply a clinical score previously designated by de Vries to 329 patients with intellectual disability/developmental disorder (intellectual disability/developmental delay) referred to our tertiary center and to see whether the clinical factors are associated with a positive outcome of aCGH analyses. Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. Our study showed that causative copy number variants are frequently found even in cases of mild intellectual disability (30.77%). We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization. © The Author(s) 2015.

Array comparative genome hybridization in patients with developmental delay: two example cases.

PubMed

Hancarova, Miroslava; Drabova, Jana; Zmitkova, Zuzana; Vlckova, Marketa; Hedvicakova, Petra; Novotna, Drahuse; Vlckova, Zdenka; Vejvalkova, Sarka; Marikova, Tatana; Sedlacek, Zdenek

2012-02-15

Developmental delay is often a predictor of mental retardation (MR) or autism, two relatively frequent developmental disorders severely affecting intellectual and social functioning. The causes of these conditions remain unknown in most patients. They have a strong genetic component, but the specific genetic defects can only be identified in a fraction of patients. Recent developments in genomics supported the establishment of the causal link between copy number variants in the genomes of some patients and their affection. One of the techniques suitable for this analysis is array comparative genome hybridization, which can be used both for detailed mapping of chromosome rearrangements identified by classical cytogenetics and for the identification of novel submicroscopic gains or losses of genetic material. We illustrate the power of this approach in two patients. Patient 1 had a cytogenetically visible deletion of chromosome X and the molecular analysis was used to specify the gene content of the deletion and the prognosis of the child. Patient 2 had a seemingly normal karyotype and the analysis revealed a small recurrent deletion of chromosome 1 likely to be responsible for his phenotype. However, the genetic dissection of MR and autism is complicated by high heterogeneity of the genetic aberrations among patients and by broad variability of phenotypic effects of individual genetic defects. Copyright © 2010 Elsevier B.V. All rights reserved.

New Hybridized Surface Wave Approach for Geotechnical Modeling of Shear Wave Velocity at Strong Motion Recording Stations

NASA Astrophysics Data System (ADS)

Kayen, R.; Carkin, B.; Minasian, D.

2006-12-01

Strong motion recording (SMR) networks often have little or no shear wave velocity measurements at stations where characterization of site amplification and site period effects is needed. Using the active Spectral Analysis of Surface Waves (SASW) method, and passive H/V microtremor method we have investigated nearly two hundred SMR sites in California, Alaska, Japan, Australia, China and Taiwan. We are conducting these studies, in part, to develop a new hybridized method of site characterization that utilizes a parallel array of harmonic-wave sources for active-source SASW, and a single long period seismometer for passive-source microtremor measurement. Surface wave methods excel in their ability to non-invasively and rapidly characterize the variation of ground stiffness properties with depth below the surface. These methods are lightweight, inexpensive to deploy, and time-efficient. They have been shown to produce accurate and deep soil stiffness profiles. By placing and wiring shakers in a large parallel circuit, either side-by-side on the ground or in a trailer-mounted array, a strong in-phase harmonic wave can be produced. The effect of arraying many sources in parallel is to increase the amplitude of waves received at far-away spaced seismometers at low frequencies so as to extend the longest wavelengths of the captured dispersion curve. The USGS system for profiling uses this concept by arraying between two and eight electro-mechanical harmonic-wave shakers. With large parallel arrays of vibrators, a dynamic force in excess of 1000 lb can be produced to vibrate the ground and produce surface waves. We adjust the harmonic wave through a swept-sine procedure to profile surface wave dispersion down to a frequency of 1 Hz and out to surface wave-wavelengths of 200-1000 meters, depending on the site stiffness. The parallel-array SASW procedure is augmented using H/V microtremor data collected with the active source turned off. Passive array microtremor data reveal the natural and resonance characteristics of the ground by capturing persistent natural vibrations. These microtremors are the result of the interaction of surface waves arriving from distant sources and the stiffness structure of the site under investigation. As such, these resonance effects are effective in constraining the layer thicknesses of the SASW shear wave velocity structure and aid in determining the depth of the deepest layer. Together, the hybridized SASW and H/V procedure provides a complete data set for modeling the geotechnical aspects of ground amplification of earthquake motions. Data from these investigations are available at http://walrus.wr.usgs.gov/geotech.

High performance hybrid magnetic structure for biotechnology applications

DOEpatents

Humphries, David E [El Cerrito, CA; Pollard, Martin J [El Cerrito, CA; Elkin, Christopher J [San Ramon, CA

2009-02-03

The present disclosure provides a high performance hybrid magnetic structure made from a combination of permanent magnets and ferromagnetic pole materials which are assembled in a predetermined array. The hybrid magnetic structure provides means for separation and other biotechnology applications involving holding, manipulation, or separation of magnetic or magnetizable molecular structures and targets. Also disclosed are further improvements to aspects of the hybrid magnetic structure, including additional elements and for adapting the use of the hybrid magnetic structure for use in biotechnology and high throughput processes.

Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization

PubMed Central

Poorman, Kelsey; Borst, Luke; Moroff, Scott; Roy, Siddharth; Labelle, Philippe; Motsinger-Reif, Alison

2017-01-01

Melanocytic lesions originating from the oral mucosa or cutaneous epithelium are common in the general dog population, with up to 100,000 diagnoses each year in the USA. Oral melanoma is the most frequent canine neoplasm of the oral cavity, exhibiting a highly aggressive course. Cutaneous melanocytomas occur frequently, but rarely develop into a malignant form. Despite the differential prognosis, it has been assumed that subtypes of melanocytic lesions represent the same disease. To address the relative paucity of information about their genomic status, molecular cytogenetic analysis was performed on the three recognized subtypes of canine melanocytic lesions. Using array comparative genomic hybridization (aCGH) analysis, highly aberrant distinct copy number status across the tumor genome for both of the malignant melanoma subtypes was revealed. The most frequent aberrations included gain of dog chromosome (CFA) 13 and 17 and loss of CFA 22. Melanocytomas possessed fewer genome wide aberrations, yet showed a recurrent gain of CFA 20q15.3–17. A distinctive copy number profile, evident only in oral melanomas, displayed a sigmoidal pattern of copy number loss followed immediately by a gain, around CFA 30q14. Moreover, when assessed by fluorescence in situ hybridization (FISH), copy number aberrations of targeted genes, such as gain of c-MYC (80 % of cases) and loss of CDKN2A (68 % of cases), were observed. This study suggests that in concordance with what is known for human melanomas, canine melanomas of the oral mucosa and cutaneous epithelium are discrete and initiated by different molecular pathways. PMID:25511566

Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

PubMed Central

Yatsenko, Svetlana A.; Shaw, Chad A.; Ou, Zhishuo; Pursley, Amber N.; Patel, Ankita; Bi, Weimin; Cheung, Sau Wai; Lupski, James R.; Chinault, A. Craig; Beaudet, Arthur L.

2009-01-01

In array-comparative genomic hybridization (array-CGH) experiments, the measurement of DNA copy number of sex chromosomal regions depends on the sex of the patient and the reference DNAs used. We evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately one-half of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. Sex-matched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs. Using sex-mismatched reference DNAs in array-CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, thus masking potential pathogenic genomic imbalances. Therefore, to optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, we suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs. PMID:19324990

High-efficient light absorption of monolayer graphene via cylindrical dielectric arrays and the sensing application

NASA Astrophysics Data System (ADS)

Zhou, Peng; Zheng, Gaige

2018-04-01

The efficiency of graphene-based optoelectronic devices is typically limited by the poor absolute absorption of light. A hybrid structure of monolayer graphene with cylindrical titanium dioxide (TiO2) array and aluminum oxide (Al2O3) spacer layer on aluminum (Al) substrate has been proposed to enhance the absorption for two-dimensional (2D) materials. By combining dielectric array with metal substrate, the structure achieves multiple absorption peaks with near unity absorbance at near-infrared wavelengths due to the resonant effect of dielectric array. Completed monolayer graphene is utilized in the design without any demand of manufacture process to form the periodic patterns. Further analysis indicates that the near-field enhancement induced by surface modes gives rise to the high absorption. This favorable field enhancement and tunability of absorption not only open up new approaches to accelerate the light-graphene interaction, but also show great potential for practical applications in high-performance optoelectronic devices, such as modulators and sensors.

Fabrication of ordered NiO coated Si nanowire array films as electrodes for a high performance lithium ion battery.

PubMed

Qiu, M C; Yang, L W; Qi, X; Li, Jun; Zhong, J X

2010-12-01

Highly ordered NiO coated Si nanowire array films are fabricated as electrodes for a high performance lithium ion battery via depositing Ni on electroless-etched Si nanowires and subsequently annealing. The structures and morphologies of as-prepared films are characterized by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. When the potential window versus lithium was controlled, the coated NiO can be selected to be electrochemically active to store and release Li+ ions, while highly conductive crystalline Si cores function as nothing more than a stable mechanical support and an efficient electrical conducting pathway. The hybrid nanowire array films exhibit superior cyclic stability and reversible capacity compared to that of NiO nanostructured films. Owing to the ease of large-scale fabrication and superior electrochemical performance, these hybrid nanowire array films will be promising anode materials for high performance lithium-ion batteries.

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Evaluation of Genomic Instability in the Abnormal Prostate

DTIC Science & Technology

2006-12-01

array CGH maps copy number aberrations relative to the genome sequence by using arrays of BAC or cDNA clones as the hybridization target instead of...data produced from these analyses complicate the interpretation of results . For these reasons, and as outlined by Davies et al., 22 it is desirable...There have been numerous studies of these abnormalities and several techniques, including 9 chromosome painting, array CGH and SNP arrays , have

Controlling the shapes and sizes of metallic nanoantennas for detection of biological molecules using hybridization phase of plasmon resonances and photonic lattice modes

NASA Astrophysics Data System (ADS)

Gutha, Rithvik R.; Sharp, Christina; Wing, Waylin J.; Sadeghi, Seyed M.

2018-02-01

Chemical sensing based on Localized Surface Plasmonic Resonances (LSPR) and the ultra-sharp optical features of surface lattice resonances (SLR) of arrays of metallic nanoantennas have attracted much attention. Recently we studied biosensing based on the transition between LSPR and SLR (hybridization phase), demonstrating significantly higher refractive index sensitivity than each of these resonances individually. In this contribution we study the impact of size and shape of the metallic nanoantennas on the hybridization process and the way they influence application of this process for biosensing, wherein miniscule variation of the refractive index of the environment leads to dramatic changes in the spectral properties of the arrays.

Miniaturized ultrasound imaging probes enabled by CMUT arrays with integrated frontend electronic circuits.

PubMed

Khuri-Yakub, B T; Oralkan, Omer; Nikoozadeh, Amin; Wygant, Ira O; Zhuang, Steve; Gencel, Mustafa; Choe, Jung Woo; Stephens, Douglas N; de la Rama, Alan; Chen, Peter; Lin, Feng; Dentinger, Aaron; Wildes, Douglas; Thomenius, Kai; Shivkumar, Kalyanam; Mahajan, Aman; Seo, Chi Hyung; O'Donnell, Matthew; Truong, Uyen; Sahn, David J

2010-01-01

Capacitive micromachined ultrasonic transducer (CMUT) arrays are conveniently integrated with frontend integrated circuits either monolithically or in a hybrid multichip form. This integration helps with reducing the number of active data processing channels for 2D arrays. This approach also preserves the signal integrity for arrays with small elements. Therefore CMUT arrays integrated with electronic circuits are most suitable to implement miniaturized probes required for many intravascular, intracardiac, and endoscopic applications. This paper presents examples of miniaturized CMUT probes utilizing 1D, 2D, and ring arrays with integrated electronics.

Low-Cost Phased Array Antenna for Sounding Rockets, Missiles, and Expendable Launch Vehicles

NASA Technical Reports Server (NTRS)

Mullinix, Daniel; Hall, Kenneth; Smith, Bruce; Corbin, Brian

2012-01-01

A low-cost beamformer phased array antenna has been developed for expendable launch vehicles, rockets, and missiles. It utilizes a conformal array antenna of ring or individual radiators (design varies depending on application) that is designed to be fed by the recently developed hybrid electrical/mechanical (vendor-supplied) phased array beamformer. The combination of these new array antennas and the hybrid beamformer results in a conformal phased array antenna that has significantly higher gain than traditional omni antennas, and costs an order of magnitude or more less than traditional phased array designs. Existing omnidirectional antennas for sounding rockets, missiles, and expendable launch vehicles (ELVs) do not have sufficient gain to support the required communication data rates via the space network. Missiles and smaller ELVs are often stabilized in flight by a fast (i.e. 4 Hz) roll rate. This fast roll rate, combined with vehicle attitude changes, greatly increases the complexity of the high-gain antenna beam-tracking problem. Phased arrays for larger ELVs with roll control are prohibitively expensive. Prior techniques involved a traditional fully electronic phased array solution, combined with highly complex and very fast inertial measurement unit phased array beamformers. The functional operation of this phased array is substantially different from traditional phased arrays in that it uses a hybrid electrical/mechanical beamformer that creates the relative time delays for steering the antenna beam via a small physical movement of variable delay lines. This movement is controlled via an innovative antenna control unit that accesses an internal measurement unit for vehicle attitude information, computes a beam-pointing angle to the target, then points the beam via a stepper motor controller. The stepper motor on the beamformer controls the beamformer variable delay lines that apply the appropriate time delays to the individual array elements to properly steer the beam. The array of phased ring radiators is unique in that it provides improved gain for a small rocket or missile that uses spin stabilization for stability. The antenna pattern created is symmetric about the roll axis (like an omnidirectional wraparound), and is thus capable of providing continuous coverage that is compatible with very fast spinning rockets. For larger ELVs with roll control, a linear array of elements can be used for the 1D scanned beamformer and phased array, or a 2D scanned beamformer can be used with an NxN element array.

Hybrid electronic tongue based on optical and electrochemical microsensors for quality control of wine.

PubMed

Gutiérrez, Manuel; Llobera, Andreu; Vila-Planas, Jordi; Capdevila, Fina; Demming, Stefanie; Büttgenbach, Stephanus; Mínguez, Santiago; Jiménez-Jorquera, Cecilia

2010-07-01

A multiparametric system able to classify red and white wines according to the grape varieties and for analysing some specific parameters is presented. The system, known as hybrid electronic tongue, consists of an array of electrochemical microsensors and a colorimetric optofluidic system. The array of electrochemical sensors is composed of six ISFETs based sensors, a conductivity sensor, a redox potential sensor and two amperometric electrodes, an Au microelectrode and a microelectrode for sensing electrochemical oxygen demand. The optofluidic system is entirely fabricated in polymer technology and comprises a hollow structure, air mirrors, microlenses and self-alignment structures. The data obtained from these sensors has been treated with multivariate advanced tools; Principal Component Analysis (PCA), for the patterning recognition and classification of wine samples, and Partial-Least Squares (PLS) regression, for quantification of several chemical and optical parameters of interest in wine quality. The results have demonstrated the utility of this system for distinguishing the samples according to the grape variety and year vintage and for quantifying several sample parameters of interest in wine quality control.

Drought-Tolerant Corn Hybrids Yield More in Drought-Stressed Environments with No Penalty in Non-stressed Environments

PubMed Central

Adee, Eric; Roozeboom, Kraig; Balboa, Guillermo R.; Schlegel, Alan; Ciampitti, Ignacio A.

2016-01-01

The potential benefit of drought-tolerant (DT) corn (Zea mays L.) hybrids may depend on drought intensity, duration, crop growth stage (timing), and the array of drought tolerance mechanisms present in selected hybrids. We hypothesized that corn hybrids containing DT traits would produce more consistent yields compared to non-DT hybrids in the presence of drought stress. The objective of this study was to define types of production environments where DT hybrids have a yield advantage compared to non-DT hybrids. Drought tolerant and non-DT hybrid pairs of similar maturity were planted in six site-years with different soil types, seasonal evapotranspiration (ET), and vapor pressure deficit (VPD), representing a range of macro-environments. Irrigation regimes and seeding rates were used to create several micro-environments within each macro-environment. Hybrid response to the range of macro and micro-environmental stresses were characterized in terms of water use efficiency, grain yield, and environmental index. Yield advantage of DT hybrids was positively correlated with environment ET and VPD. Drought tolerant hybrids yielded 5 to 7% more than non-DT hybrids in high and medium ET environments (>430 mm ET), corresponding to seasonal VPD greater than 1200 Pa. Environmental index analysis confirmed that DT hybrids were superior in stressful environments. Yield advantage for DT hybrids appeared as yield dropped below 10.8 Mg ha-1 and averaged as much as 0.6–1 Mg ha-1 at the low yield range. Hybrids with DT technology can offer a degree of buffering against drought stress by minimizing yield reduction, but also maintaining a comparable yield potential in high yielding environments. Further studies should focus on the physiological mechanisms presented in the commercially available corn drought tolerant hybrids. PMID:27790237

High throughput microcantilever detector

DOEpatents

Thundat, Thomas G.; Ferrell, Thomas L.; Hansen, Karolyn M.; Tian, Fang

2004-07-20

In an improved uncoated microcantilever detector, the sample sites are placed on a separate semi-conducting substrate and the microcantilever element detects and measures the changes before and after a chemical interaction or hybridization of the sites by sensing differences of phase angle between an alternating voltage applied to the microcantilever element and vibration of the microcantilever element. In another embodiment of the invention, multiple sample sites are on a sample array wherein an array of microcantilever elements detect and measure the change before and after chemical interactions or hybridizations of the sample sites.

Large-Format AlGaN PIN Photodiode Arrays for UV Images

NASA Technical Reports Server (NTRS)

Aslam, Shahid; Franz, David

2010-01-01

A large-format hybridized AlGaN photodiode array with an adjustable bandwidth features stray-light control, ultralow dark-current noise to reduce cooling requirements, and much higher radiation tolerance than previous technologies. This technology reduces the size, mass, power, and cost of future ultraviolet (UV) detection instruments by using lightweight, low-voltage AlGaN detectors in a hybrid detector/multiplexer configuration. The solar-blind feature eliminates the need for additional visible light rejection and reduces the sensitivity of the system to stray light that can contaminate observations.

Evaluation of the hybrid-L24 electrode using microcomputed tomography.

PubMed

Driscoll, Colin L W; Carlson, Matthew L; Fama, Anthony F; Lane, John I

2011-07-01

To compare electrode array position, and depth of insertion of the Cochlear Hybrid-L24 electrode array following traditional cochleostomy and round window (RW) insertion. Prospective cadaveric temporal bone study. Ten cadaveric temporal bones were implanted with the Hybrid-L24 electrode array; half were introduced through a RW approach, whereas the other half were inserted through a traditional scala tympani cochleostomy. A micro-CT scanner was then used to evaluate electrode position, intracochlear trauma, and depth of insertion. All electrodes were inserted into the scala tympani without significant resistance. No electrodes demonstrated tip fold-over or through-fracturing of the osseous spiral lamina, basilar membrane, or spiral ligament. The average angular depth of insertion for all 10 electrodes was 252.4°. Compared to cochleostomy insertions, electrodes inserted through the RW more commonly acquired a proximal perimodiolar orientation, followed a more predictable course, and less commonly contacted critical soft tissue structures. The results of this study demonstrate that the Hybrid-L24 electrode can be successfully inserted using a RW or traditional cochleostomy technique with minimal intracochlear trauma. Our data also suggests that with this model, RW insertions may provide particular advantages with respect to hearing preservation over the traditional cochleostomy approach. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

Rational construction of three dimensional hybrid Co3O4@NiMoO4 nanosheets array for energy storage application

NASA Astrophysics Data System (ADS)

Hong, Wei; Wang, Jinqing; Gong, Peiwei; Sun, Jinfeng; Niu, Lengyuan; Yang, Zhigang; Wang, Zhaofeng; Yang, Shengrong

2014-12-01

Electrodes with rationally designed hybrid nanostructures can offer many opportunities for the enhanced performance in electrochemical energy storage. In this work, the uniform 2D Co3O4-based building blocks have been prepared through a facile chemical etching assistant approach and a following treatment of thermal annealing. The obtained nanosheets array has been directly employed as 2D backbone for the subsequent construction of hybrid nanostructure of Co3O4@NiMoO4 by a simple hydrothermal synthesis. As a binder-free electrode, the constructed 3D hybrid nanostructures exhibit a high specific capacitance of 1526 F g-1 at a current density of 3 mA cm-2 and a capacitance retention of 72% with the increase of current density from 3 mA cm-2 to 30 mA cm-2. Moreover, an asymmetric supercapacitor based on this hybrid Co3O4@NiMoO4 and activated carbon can deliver a maximum energy density of 37.8 Wh kg-1 at a power density of 482 W kg-1. The outstanding electrochemical behaviors presented here suggest that this hybrid nanostructured material has potential applications in energy storage.

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

PubMed Central

Stolc, Viktor; Samanta, Manoj Pratim; Tongprasit, Waraporn; Sethi, Himanshu; Liang, Shoudan; Nelson, David C.; Hegeman, Adrian; Nelson, Clark; Rancour, David; Bednarek, Sebastian; Ulrich, Eldon L.; Zhao, Qin; Wrobel, Russell L.; Newman, Craig S.; Fox, Brian G.; Phillips, George N.; Markley, John L.; Sussman, Michael R.

2005-01-01

Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana. RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intron–exon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions “antisense” to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage. PMID:15755812

Resolution-Adaptive Hybrid MIMO Architectures for Millimeter Wave Communications

NASA Astrophysics Data System (ADS)

Choi, Jinseok; Evans, Brian L.; Gatherer, Alan

2017-12-01

In this paper, we propose a hybrid analog-digital beamforming architecture with resolution-adaptive ADCs for millimeter wave (mmWave) receivers with large antenna arrays. We adopt array response vectors for the analog combiners and derive ADC bit-allocation (BA) solutions in closed form. The BA solutions reveal that the optimal number of ADC bits is logarithmically proportional to the RF chain's signal-to-noise ratio raised to the 1/3 power. Using the solutions, two proposed BA algorithms minimize the mean square quantization error of received analog signals under a total ADC power constraint. Contributions of this paper include 1) ADC bit-allocation algorithms to improve communication performance of a hybrid MIMO receiver, 2) approximation of the capacity with the BA algorithm as a function of channels, and 3) a worst-case analysis of the ergodic rate of the proposed MIMO receiver that quantifies system tradeoffs and serves as the lower bound. Simulation results demonstrate that the BA algorithms outperform a fixed-ADC approach in both spectral and energy efficiency, and validate the capacity and ergodic rate formula. For a power constraint equivalent to that of fixed 4-bit ADCs, the revised BA algorithm makes the quantization error negligible while achieving 22% better energy efficiency. Having negligible quantization error allows existing state-of-the-art digital beamformers to be readily applied to the proposed system.

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

NASA Technical Reports Server (NTRS)

Stolc, Viktor; Samanta, Manoj Pratim; Tongprasit, Waraporn; Sethi, Himanshu; Liang, Shoudan; Nelson, David C.; Hegeman, Adrian; Nelson, Clark; Rancour, David; Bednarek, Sebastian;

Competitive hybridization models

NASA Astrophysics Data System (ADS)

Cherepinsky, Vera; Hashmi, Ghazala; Mishra, Bud

2010-11-01

Microarray technology, in its simplest form, allows one to gather abundance data for target DNA molecules, associated with genomes or gene-expressions, and relies on hybridizing the target to many short probe oligonucleotides arrayed on a surface. While for such multiplexed reactions conditions are optimized to make the most of each individual probe-target interaction, subsequent analysis of these experiments is based on the implicit assumption that a given experiment yields the same result regardless of whether it was conducted in isolation or in parallel with many others. It has been discussed in the literature that this assumption is frequently false, and its validity depends on the types of probes and their interactions with each other. We present a detailed physical model of hybridization as a means of understanding probe interactions in a multiplexed reaction. Ultimately, the model can be derived from a system of ordinary differential equations (ODE’s) describing kinetic mass action with conservation-of-mass equations completing the system. We examine pairwise probe interactions in detail and present a model of “competition” between the probes for the target—especially, when the target is effectively in short supply. These effects are shown to be predictable from the affinity constants for each of the four probe sequences involved, namely, the match and mismatch sequences for both probes. These affinity constants are calculated from the thermodynamic parameters such as the free energy of hybridization, which are in turn computed according to the nearest neighbor (NN) model for each probe and target sequence. Simulations based on the competitive hybridization model explain the observed variability in the signal of a given probe when measured in parallel with different groupings of other probes or individually. The results of the simulations can be used for experiment design and pooling strategies, based on which probes have been shown to have a strong effect on each other’s signal in the in silico experiment. These results are aimed at better design of multiplexed reactions on arrays used in genotyping (e.g., HLA typing, SNP, or CNV detection, etc.) and mutation analysis (e.g., cystic fibrosis, cancer, autism, etc.).

Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

PubMed Central

Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum. PMID:23409153

Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

PubMed

Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.

Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies (PISCES) for WFIRST/AFTA

NASA Technical Reports Server (NTRS)

Gong, Qian; McElwain, Michael; Greeley, Bradford; Grammer, Bryan; Marx, Catherine; Memarsadeghi, Nargess; Hilton, George; Perrin, Marshall; Sayson, Llop; Domingo, Jorge;

Array-CGH analysis in Rwandan patients presenting development delay/intellectual disability with multiple congenital anomalies.

PubMed

Uwineza, Annette; Caberg, Jean-Hubert; Hitayezu, Janvier; Hellin, Anne Cecile; Jamar, Mauricette; Dideberg, Vinciane; Rusingiza, Emmanuel K; Bours, Vincent; Mutesa, Leon

2014-07-12

Array-CGH is considered as the first-tier investigation used to identify copy number variations. Right now, there is no available data about the genetic etiology of patients with development delay/intellectual disability and congenital malformation in East Africa. Array comparative genomic hybridization was performed in 50 Rwandan patients with development delay/intellectual disability and multiple congenital abnormalities, using the Agilent's 180 K microarray platform. Fourteen patients (28%) had a global development delay whereas 36 (72%) patients presented intellectual disability. All patients presented multiple congenital abnormalities. Clinically significant copy number variations were found in 13 patients (26%). Size of CNVs ranged from 0,9 Mb to 34 Mb. Six patients had CNVs associated with known syndromes, whereas 7 patients presented rare genomic imbalances. This study showed that CNVs are present in African population and show the importance to implement genetic testing in East-African countries.

Hybrid Simulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trujillo, David J.; Sridharan, Srikesh; Weinstock, Irvin

HybSim (short for Hybrid Simulator) is a flexible, easy to use screening tool that allows the user to quanti the technical and economic benefits of installing a village hybrid generating system and simulates systems with any combination of —Diesel generator sets —Photovoltaic arrays -Wind Turbines and -Battery energy storage systems Most village systems (or small population sites such as villages, remote military bases, small communities, independent or isolated buildings or centers) depend on diesel generation systems for their source of energy. HybSim allows the user to determine other "sources" of energy that can greatly reduce the dollar to kilo-watt hourmore » ratio. Supported by the DOE, Energy Storage Program, HybSim was initially developed to help analyze the benefits of energy storage systems in Alaskan villages. Soon after its development, other sources of energy were added providing the user with a greater range of analysis opportunities and providing the village with potentially added savings. In addition to village systems, HybSim has generated interest for use from military institutions in energy provisions and USAID for international village analysis.« less

Carbon Nanotube Nanoelectrode Array as an Electronic Chip for Ultrasensitive Label-free DNA Detection

NASA Technical Reports Server (NTRS)

Li, Jun; Koehne, Jessica; Chen, Hua; Cassell, Alan; Ng, Hou Tee; Fan, Wendy; Ye, Qi; Han, Jie; Meyyappan, M.

2003-01-01

A reliable nanoelectrode array based on vertically aligned multi-walled carbon nanotubes (MWNTs) embedded in SiO2 is used for ultrasensitive DNA detection. Characteristic nanoelectrode behavior is observed using low-density MWNT arrays for measuring both bulk and surface immobilized redox species such as K4Fe(CN)6 and ferrocene derivatives. The open-end of MWNTs are found to present similar properties as graphite edge-plane electrodes with wide potential window, flexible chemical functionalities, and good biocompatibility. BRCA1 related oligonucleotide probes with 18 bp are selectively functionalized at the open ends of the nanotube array and specifically hybridized with oligonucleotide targets incorporated with a polyG tag. The guanine groups are employed as the signal moieties in the electrochemical measurements. R(bpy)(sup 2+, sub 3) mediator is used to further amplify the guanine oxidation signal. The hybridization of sub-attomoles of DNA targets is detected electrochemically by combining the MWNT nanoelectrode array with the R(bpy)(sup 2+, sub 3) amplification mechanism. This technique was employed for direct electrochemical detection of label-free PCR amplicon from a healthy donor through specific hybridization with the BRCA1 probe. The detection limit is estimated to be less than 1000 DNA molecules since abundant guanine bases in the PCR amplicon provides a large signal. This system provides a general platform for rapid molecular diagnostics in applications requiring ultrahigh sensitivity, high-degree of miniaturization, and simple sample preparation, and low-cost operation.

ArrayVigil: a methodology for statistical comparison of gene signatures using segregated-one-tailed (SOT) Wilcoxon's signed-rank test.

PubMed

Khan, Haseeb Ahmad

2005-01-28

Due to versatile diagnostic and prognostic fidelity molecular signatures or fingerprints are anticipated as the most powerful tools for cancer management in the near future. Notwithstanding the experimental advancements in microarray technology, methods for analyzing either whole arrays or gene signatures have not been firmly established. Recently, an algorithm, ArraySolver has been reported by Khan for two-group comparison of microarray gene expression data using two-tailed Wilcoxon signed-rank test. Most of the molecular signatures are composed of two sets of genes (hybrid signatures) wherein up-regulation of one set and down-regulation of the other set collectively define the purpose of a gene signature. Since the direction of a selected gene's expression (positive or negative) with respect to a particular disease condition is known, application of one-tailed statistics could be a more relevant choice. A novel method, ArrayVigil, is described for comparing hybrid signatures using segregated-one-tailed (SOT) Wilcoxon signed-rank test and the results compared with integrated-two-tailed (ITT) procedures (SPSS and ArraySolver). ArrayVigil resulted in lower P values than those obtained from ITT statistics while comparing real data from four signatures.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.

PubMed

Castle, John; Garrett-Engele, Phil; Armour, Christopher D; Duenwald, Sven J; Loerch, Patrick M; Meyer, Michael R; Schadt, Eric E; Stoughton, Roland; Parrish, Mark L; Shoemaker, Daniel D; Johnson, Jason M

2003-01-01

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing

PubMed Central

Castle, John; Garrett-Engele, Phil; Armour, Christopher D; Duenwald, Sven J; Loerch, Patrick M; Meyer, Michael R; Schadt, Eric E; Stoughton, Roland; Parrish, Mark L; Shoemaker, Daniel D; Johnson, Jason M

2003-01-01

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing. PMID:14519201

Molecular cytogenetic analysis of Xq critical regions in premature ovarian failure

PubMed Central

2013-01-01

Background One of the frequent reasons for unsuccessful conception is premature ovarian failure/primary ovarian insufficiency (POF/POI) that is defined as the loss of functional follicles below the age of 40 years. Among the genetic causes the most common one involves the X chromosome, as in Turner syndrome, partial X deletion and X-autosome translocations. Here we report a case of a 27-year-old female patient referred to genetic counselling because of premature ovarian failure. The aim of this case study to perform molecular genetic and cytogenetic analyses in order to identify the exact genetic background of the pathogenic phenotype. Results For premature ovarian failure disease diagnostics we performed the Fragile mental retardation 1 gene analysis using Southern blot technique and Repeat Primed PCR in order to identify the relationship between the Fragile mental retardation 1 gene premutation status and the premature ovarion failure disease. At this early onset, the premature ovarian failure affected patient we detected one normal allele of Fragile mental retardation 1 gene and we couldn’t verify the methylated allele, therefore we performed the cytogenetic analyses using G-banding and fluorescent in situ hybridization methods and a high resolution molecular cytogenetic method, the array comparative genomic hybridization technique. For this patient applying the G-banding, we identified a large deletion on the X chromosome at the critical region (ChrX q21.31-q28) which is associated with the premature ovarian failure phenotype. In order to detect the exact breakpoints, we used a special cytogenetic array ISCA plus CGH array and we verified a 67.355 Mb size loss at the critical region which include total 795 genes. Conclusions We conclude for this case study that the karyotyping is definitely helpful in the evaluation of premature ovarian failure patients, to identify the non submicroscopic chromosomal rearrangement, and using the array CGH technique we can contribute to the most efficient detection and mapping of exact deletion breakpoints of the deleted Xq region. PMID:24359613

Hyperbranched quasi-1D TiO2 nanostructure for hybrid organic-inorganic solar cells.

PubMed

Ghadirzadeh, Ali; Passoni, Luca; Grancini, Giulia; Terraneo, Giancarlo; Li Bassi, Andrea; Petrozza, Annamaria; Di Fonzo, Fabio

2015-04-15

The performance of hybrid solar cells is strongly affected by the device morphology. In this work, we demonstrate a poly(3-hexylthiophene-2,5-diyl)/TiO2 hybrid solar cell where the TiO2 photoanode comprises an array of tree-like hyperbranched quasi-1D nanostructures self-assembled from the gas phase. This advanced architecture enables us to increase the power conversion efficiency to over 1%, doubling the efficiency with respect to state of the art devices employing standard mesoporous titania photoanodes. This improvement is attributed to several peculiar features of this array of nanostructures: high interfacial area; increased optical density thanks to the enhanced light scattering; and enhanced crystallization of poly(3-hexylthiophene-2,5-diyl) inside the quasi-1D nanostructure.

Characterization of hybrid cells derived from spontaneous fusion events between breast epithelial cells exhibiting stem-like characteristics and breast cancer cells.

PubMed

Dittmar, Thomas; Schwitalla, Sarah; Seidel, Jeanette; Haverkampf, Sonja; Reith, Georg; Meyer-Staeckling, Sönke; Brandt, Burkhard H; Niggemann, Bernd; Zänker, Kurt S

2011-01-01

Several data of the past years clearly indicated that the fusion of tumor cells and tumor cells or tumor cells and normal cells can give rise to hybrids cells exhibited novel properties such as an increased malignancy, drug resistance, or resistance to apoptosis. In the present study we characterized hybrid cells derived from spontaneous fusion events between the breast epithelial cell line M13SV1-EGFP-Neo and two breast cancer cell lines: HS578T-Hyg and MDA-MB-435-Hyg. Short-tandem-repeat analysis revealed an overlap of parental alleles in all hybrid cells indicating that hybrid cells originated from real cell fusion events. RealTime-PCR-array gene expression data provided evidence that each hybrid cell clone exhibited a unique gene expression pattern, resulting in a specific resistance of hybrid clones towards chemotherapeutic drugs, such as doxorubicin and paclitaxel, as well as a specific migratory behavior of hybrid clones towards EGF. For instance, M13MDA435-4 hybrids showed a marked resistance towards etoposide, doxorubicin and paclitaxel, whereas hybrid clones M13MDA-435-1 and -2 were only resistant towards etoposide. Likewise, all investigated M13MDA435 hybrids responded to EGF with an increased migratory activity, whereas the migration of parental MDA-MB-435-Hyg cells was blocked by EGF, suggesting that M13MDA435 hybrids may have acquired a new motility pathway. Similar findings have been obtained for M13HS hybrids. We conclude from our data that they further support the hypothesis that cell fusion could give rise to drug resistant and migratory active tumor (hybrid) cells in cancer.

Polarization effects associated with thermal processing of HY-80 structural steel using high-power laser diode array

NASA Astrophysics Data System (ADS)

Wu, Sheldon S. Q.; Baker, Bradford W.; Rotter, Mark D.; Rubenchik, Alexander M.; Wiechec, Maxwell E.; Brown, Zachary M.; Beach, Raymond J.; Matthews, Manyalibo J.

2017-12-01

Localized heating of roughened steel surfaces using highly divergent laser light emitted from high-power laser diode arrays was experimentally demonstrated and compared with theoretical predictions. Polarization dependence was analyzed using Fresnel coefficients to understand the laser-induced temperature rise of HY-80 steel plates under 383- to 612-W laser irradiation. Laser-induced, transient temperature distributions were directly measured using bulk thermocouple probes and thermal imaging. Finite-element analysis yielded quantitative assessment of energy deposition and heat transport in HY-80 steel using absorptivity as a tuning parameter. The extracted absorptivity values ranged from 0.62 to 0.75 for S-polarized and 0.63 to 0.85 for P-polarized light, in agreement with partially oxidized iron surfaces. Microstructural analysis using electron backscatter diffraction revealed a heat affected zone for the highest temperature conditions (612 W, P-polarized) as evidence of rapid quenching and an austenite to martensite transformation. The efficient use of diode arrays for laser-assisted advanced manufacturing technologies, such as hybrid friction stir welding, is discussed.

Measurement of the proton-air cross section with Telescope Array's Middle Drum detector and surface array in hybrid mode

NASA Astrophysics Data System (ADS)

Abbasi, R. U.; Abe, M.; Abu-Zayyad, T.; Allen, M.; Azuma, R.; Barcikowski, E.; Belz, J. W.; Bergman, D. R.; Blake, S. A.; Cady, R.; Chae, M. J.; Cheon, B. G.; Chiba, J.; Chikawa, M.; Cho, W. R.; Fujii, T.; Fukushima, M.; Goto, T.; Hanlon, W.; Hayashi, Y.; Hayashida, N.; Hibino, K.; Honda, K.; Ikeda, D.; Inoue, N.; Ishii, T.; Ishimori, R.; Ito, H.; Ivanov, D.; Jui, C. C. H.; Kadota, K.; Kakimoto, F.; Kalashev, O.; Kasahara, K.; Kawai, H.; Kawakami, S.; Kawana, S.; Kawata, K.; Kido, E.; Kim, H. B.; Kim, J. H.; Kim, J. H.; Kitamura, S.; Kitamura, Y.; Kuzmin, V.; Kwon, Y. J.; Lan, J.; Lim, S. I.; Lundquist, J. P.; Machida, K.; Martens, K.; Matsuda, T.; Matsuyama, T.; Matthews, J. N.; Minamino, M.; Mukai, Y.; Myers, I.; Nagasawa, K.; Nagataki, S.; Nakamura, T.; Nonaka, T.; Nozato, A.; Ogio, S.; Ogura, J.; Ohnishi, M.; Ohoka, H.; Oki, K.; Okuda, T.; Ono, M.; Oshima, A.; Ozawa, S.; Park, I. H.; Pshirkov, M. S.; Rodriguez, D. C.; Rubtsov, G.; Ryu, D.; Sagawa, H.; Sakurai, N.; Scott, L. M.; Shah, P. D.; Shibata, F.; Shibata, T.; Shimodaira, H.; Shin, B. K.; Shin, H. S.; Smith, J. D.; Sokolsky, P.; Springer, R. W.; Stokes, B. T.; Stratton, S. R.; Stroman, T. A.; Suzawa, T.; Takamura, M.; Takeda, M.; Takeishi, R.; Taketa, A.; Takita, M.; Tameda, Y.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Thomas, S. B.; Thomson, G. B.; Tinyakov, P.; Tkachev, I.; Tokuno, H.; Tomida, T.; Troitsky, S.; Tsunesada, Y.; Tsutsumi, K.; Uchihori, Y.; Udo, S.; Urban, F.; Vasiloff, G.; Wong, T.; Yamane, R.; Yamaoka, H.; Yamazaki, K.; Yang, J.; Yashiro, K.; Yoneda, Y.; Yoshida, S.; Yoshii, H.; Zollinger, R.; Zundel, Z.; Telescope Array Collaboration

2015-08-01

In this work we are reporting on the measurement of the proton-air inelastic cross section σp-air inel using the Telescope Array detector. Based on the measurement of the σp-air inel, the proton-proton cross section σp -p value is also determined at √{s }=9 5-8+5 TeV . Detecting cosmic ray events at ultrahigh energies with the Telescope Array enables us to study this fundamental parameter that we are otherwise unable to access with particle accelerators. The data used in this report are the hybrid events observed by the Middle Drum fluorescence detector together with the surface array detector collected over five years. The value of the σp-air inel is found to be equal to 567.0 ±70.5 [Stat]-25+29[Sys] mb . The total proton-proton cross section is subsequently inferred from Glauber formalism and the Block, Halzen and Stanev QCD inspired fit and is found to be equal to 17 0-44+48[Stat]-17+19[Sys] mb .

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

PubMed Central

Haraksingh, Rajini R.; Abyzov, Alexej; Gerstein, Mark; Urban, Alexander E.; Snyder, Michael

2011-01-01

Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications. PMID:22140474

Miniaturized Ultrasound Imaging Probes Enabled by CMUT Arrays with Integrated Frontend Electronic Circuits

PubMed Central

Khuri-Yakub, B. (Pierre) T.; Oralkan, Ömer; Nikoozadeh, Amin; Wygant, Ira O.; Zhuang, Steve; Gencel, Mustafa; Choe, Jung Woo; Stephens, Douglas N.; de la Rama, Alan; Chen, Peter; Lin, Feng; Dentinger, Aaron; Wildes, Douglas; Thomenius, Kai; Shivkumar, Kalyanam; Mahajan, Aman; Seo, Chi Hyung; O’Donnell, Matthew; Truong, Uyen; Sahn, David J.

2010-01-01

Capacitive micromachined ultrasonic transducer (CMUT) arrays are conveniently integrated with frontend integrated circuits either monolithically or in a hybrid multichip form. This integration helps with reducing the number of active data processing channels for 2D arrays. This approach also preserves the signal integrity for arrays with small elements. Therefore CMUT arrays integrated with electronic circuits are most suitable to implement miniaturized probes required for many intravascular, intracardiac, and endoscopic applications. This paper presents examples of miniaturized CMUT probes utilizing 1D, 2D, and ring arrays with integrated electronics. PMID:21097106

Fiber-optic microsphere-based arrays for multiplexed biological warfare agent detection.

PubMed

Song, Linan; Ahn, Soohyoun; Walt, David R

2006-02-15

We report a multiplexed high-density DNA array capable of rapid, sensitive, and reliable identification of potential biological warfare agents. An optical fiber bundle containing 6000 individual 3.1-mum-diameter fibers was chemically etched to yield microwells and used as the substrate for the array. Eighteen different 50-mer single-stranded DNA probes were covalently attached to 3.1-mum microspheres. Probe sequences were designed for Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella melitensis, Clostridium botulinum, Vaccinia virus, and one biological warfare agent (BWA) simulant, Bacillus thuringiensis kurstaki. The microspheres were distributed into the microwells to form a randomized multiplexed high-density DNA array. A detection limit of 10 fM in a 50-microL sample volume was achieved within 30 min of hybridization for B. anthracis, Y. pestis, Vaccinia virus, and B. thuringiensis kurstaki. We used both specific responses of probes upon hybridization to complementary targets as well as response patterns of the multiplexed array to identify BWAs with high accuracy. We demonstrated the application of this multiplexed high-density DNA array for parallel identification of target BWAs in spiked sewage samples after PCR amplification. The array's miniaturized feature size, fabrication flexibility, reusability, and high reproducibility may enable this array platform to be integrated into a highly sensitive, specific, and reliable portable instrument for in situ BWA detection.

Fabricating a hybrid imaging device

NASA Technical Reports Server (NTRS)

Wadsworth, Mark (Inventor); Atlas, Gene (Inventor)

2003-01-01

A hybrid detector or imager includes two substrates fabricated under incompatible processes. An array of detectors, such as charged-coupled devices, are formed on the first substrate using a CCD fabrication process, such as a buried channel or peristaltic process. One or more charge-converting amplifiers are formed on a second substrate using a CMOS fabrication process. The two substrates are then bonded together to form a hybrid detector.

Neural system modeling and simulation using Hybrid Functional Petri Net.

PubMed

Tang, Yin; Wang, Fei

2012-02-01

The Petri net formalism has been proved to be powerful in biological modeling. It not only boasts of a most intuitive graphical presentation but also combines the methods of classical systems biology with the discrete modeling technique. Hybrid Functional Petri Net (HFPN) was proposed specially for biological system modeling. An array of well-constructed biological models using HFPN yielded very interesting results. In this paper, we propose a method to represent neural system behavior, where biochemistry and electrical chemistry are both included using the Petri net formalism. We built a model for the adrenergic system using HFPN and employed quantitative analysis. Our simulation results match the biological data well, showing that the model is very effective. Predictions made on our model further manifest the modeling power of HFPN and improve the understanding of the adrenergic system. The file of our model and more results with their analysis are available in our supplementary material.

An optical/digital processor - Hardware and applications

NASA Technical Reports Server (NTRS)

Casasent, D.; Sterling, W. M.

1975-01-01

A real-time two-dimensional hybrid processor consisting of a coherent optical system, an optical/digital interface, and a PDP-11/15 control minicomputer is described. The input electrical-to-optical transducer is an electron-beam addressed potassium dideuterium phosphate (KD2PO4) light valve. The requirements and hardware for the output optical-to-digital interface, which is constructed from modular computer building blocks, are presented. Initial experimental results demonstrating the operation of this hybrid processor in phased-array radar data processing, synthetic-aperture image correlation, and text correlation are included. The applications chosen emphasize the role of the interface in the analysis of data from an optical processor and possible extensions to the digital feedback control of an optical processor.

Hybrid III/V silicon photonic source with integrated 1D free-space beam steering.

PubMed

Doylend, J K; Heck, M J R; Bovington, J T; Peters, J D; Davenport, M L; Coldren, L A; Bowers, J E

2012-10-15

A chip-scale optical source with integrated beam steering is demonstrated. The chip was fabricated using the hybrid silicon platform and incorporates an on-chip laser, waveguide splitter, amplifiers, phase modulators, and surface gratings to comprise an optical phased array with beam steering across a 12° field of view in one axis. Tuning of the phased array is used to achieve 1.8°(steered axis)×0.6°(nonsteered axis) beam width with 7 dB background suppression for arbitrary beam direction within the field of view.

Rhabdoid glioblastoma is distinguishable from classical glioblastoma by cytogenetics and molecular genetics.

PubMed

Byeon, Sun-Ju; Cho, Hwa Jin; Baek, Hae Woon; Park, Chul-Kee; Choi, Seung-Hong; Kim, Se-Hoon; Kim, Hee Kyung; Park, Sung-Hye

2014-03-01

The clinicopathologic and molecular genetic features of 5 cases of rhabdoid glioblastoma, an extremely rare variant of glioblastoma that tends to affect patients at a young age, were investigated by immunohistochemical analysis and focused molecular genetic studies including array-based comparative genomic hybridization. All 5 cases had supratentorial tumors that immunohistochemical analysis revealed to be robustly positive for epithelial membrane antigen, vimentin, p53, and PDGFRα (platelet-derived growth factor receptor, alpha polypeptide) but only focally positive for glial fibrillary acidic protein. Although complete retention of SMARCB1 (INI1) was observed in all 5 cases, epidermal growth factor receptor (EGFR) amplification, PTEN (phosphatase and tensin homolog) loss, homozygous deletion of cyclin-dependent kinase inhibitor 2A, 1p/19q codeletion, and isocitrate dehydrogenase 1 R132/IDH2 R172 mutation were not observed in any case, although a high level of EGFR polysomy was detected in 1 recurrent tumor. Although c-MET (MET protein) expression was focal but robustly positive in 3 cases, met proto-oncogene (MET) fluorescence in situ hybridization revealed low polysomy but not MET amplification. MGMT (O-6-methylguanine-DNA methyl-40 transferase) methylation-specific polymerase chain reaction revealed MGMT methylation in only 1 case. Furthermore, array-based comparative genomic hybridization revealed gain of chromosome 7 and loss of 1p, 6, 8p, 11, 13q, and 18q but no deletion of chromosome 22. In contrast to the classical subtype of primary glioblastoma, the cases studied here were characterized by the absence of EGFR amplification, PTEN loss, and 9p homozygous deletion and overexpression of p53, PDGFRα, and c-MET, suggesting that they can be classified as the proneural or mesenchymal subtype of glioblastoma and benefit from intensive therapy that includes temozolomide. Copyright © 2014 Elsevier Inc. All rights reserved.

ALK rearrangement in a large series of consecutive non-small cell lung cancers: comparison between a new immunohistochemical approach and fluorescence in situ hybridization for the screening of patients eligible for crizotinib treatment.

PubMed

Alì, Greta; Proietti, Agnese; Pelliccioni, Serena; Niccoli, Cristina; Lupi, Cristiana; Sensi, Elisa; Giannini, Riccardo; Borrelli, Nicla; Menghi, Maura; Chella, Antonio; Ribechini, Alessandro; Cappuzzo, Federico; Melfi, Franca; Lucchi, Marco; Mussi, Alfredo; Fontanini, Gabriella

2014-11-01

Echinoderm microtubule associated proteinlike 4-anaplastic lymphoma receptor tyrosine kinase (EML4-ALK) translocation has been described in a subset of patients with non-small cell lung cancer (NSCLC) and has been shown to have oncogenic activity. Fluorescence in situ hybridization (FISH) is used to detect ALK-positive NSCLC, but it is expensive, time-consuming, and difficult for routine application. To evaluate the potential role of immunohistochemistry (IHC) as a screening tool to identify candidate cases for FISH analysis and for ALK inhibitor therapy in NSCLC. We performed FISH and IHC for ALK and mutational analysis for epidermal growth factor receptor (EGFR) and KRAS in 523 NSCLC specimens. We conducted IHC analysis with the monoclonal antibody D5F3 (Ventana Medical Systems, Tucson, Arizona) and a highly sensitive detection system. We also performed a MassARRAY-based analysis (Sequenom, San Diego, California) in a small subset of 11 samples to detect EML4-ALK rearrangement. Of the 523 NSCLC specimens, 20 (3.8%) were positive for ALK rearrangement by FISH analysis. EGFR and KRAS mutations were identified in 70 (13.4%) and 124 (23.7%) of the 523 tumor samples, respectively. ALK rearrangement and EGFR and KRAS mutations were mutually exclusive. Of 523 tumor samples analyzed, 18 (3.4%) were ALK(+) by IHC, 18 samples (3.4%) had concordant IHC and FISH results, and 2 ALK(+) cases (0.3%) by FISH failed to show ALK protein expression. In the 2 discrepant cases, we did not detect any mass peaks for the EML4-ALK variants by MassARRAY. Our results show that IHC may be a useful technique for selecting NSCLC cases to undergo ALK FISH analysis.

Value for money? Array genomic hybridization for diagnostic testing for genetic causes of intellectual disability.

PubMed

Regier, Dean A; Friedman, Jan M; Marra, Carlo A

2010-05-14

Array genomic hybridization (AGH) provides a higher detection rate than does conventional cytogenetic testing when searching for chromosomal imbalance causing intellectual disability (ID). AGH is more costly than conventional cytogenetic testing, and it remains unclear whether AGH provides good value for money. Decision analytic modeling was used to evaluate the trade-off between costs, clinical effectiveness, and benefit of an AGH testing strategy compared to a conventional testing strategy. The trade-off between cost and effectiveness was expressed via the incremental cost-effectiveness ratio. Probabilistic sensitivity analysis was performed via Monte Carlo simulation. The baseline AGH testing strategy led to an average cost increase of $217 (95% CI $172-$261) per patient and an additional 8.2 diagnoses in every 100 tested (0.082; 95% CI 0.044-0.119). The mean incremental cost per additional diagnosis was $2646 (95% CI $1619-$5296). Probabilistic sensitivity analysis demonstrated that there was a 95% probability that AGH would be cost effective if decision makers were willing to pay $4550 for an additional diagnosis. Our model suggests that using AGH instead of conventional karyotyping for most ID patients provides good value for money. Deterministic sensitivity analysis found that employing AGH after first-line cytogenetic testing had proven uninformative did not provide good value for money when compared to using AGH as first-line testing. Copyright (c) 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Detecting Biological Warfare Agents

PubMed Central

Song, Linan; Ahn, Soohyoun

2005-01-01

We developed a fiber-optic, microsphere-based, high-density array composed of 18 species-specific probe microsensors to identify biological warfare agents. We simultaneously identified multiple biological warfare agents in environmental samples by looking at specific probe responses after hybridization and response patterns of the multiplexed array. PMID:16318712

Optimization of process parameters in drilling of fibre hybrid composite using Taguchi and grey relational analysis

NASA Astrophysics Data System (ADS)

Vijaya Ramnath, B.; Sharavanan, S.; Jeykrishnan, J.

2017-03-01

Nowadays quality plays a vital role in all the products. Hence, the development in manufacturing process focuses on the fabrication of composite with high dimensional accuracy and also incurring low manufacturing cost. In this work, an investigation on machining parameters has been performed on jute-flax hybrid composite. Here, the two important responses characteristics like surface roughness and material removal rate are optimized by employing 3 machining input parameters. The input variables considered are drill bit diameter, spindle speed and feed rate. Machining is done on CNC vertical drilling machine at different levels of drilling parameters. Taguchi’s L16 orthogonal array is used for optimizing individual tool parameters. Analysis Of Variance is used to find the significance of individual parameters. The simultaneous optimization of the process parameters is done by grey relational analysis. The results of this investigation shows that, spindle speed and drill bit diameter have most effect on material removal rate and surface roughness followed by feed rate.

‘Spotted Nanoflowers’: Gold-seeded Zinc Oxide Nanohybrid for Selective Bio-capture

NASA Astrophysics Data System (ADS)

Perumal, Veeradasan; Hashim, U.; Gopinath, Subash C. B.; Haarindraprasad, R.; Foo, K. L.; Balakrishnan, S. R.; Poopalan, P.

2015-07-01

Hybrid gold nanostructures seeded into nanotextured zinc oxide (ZnO) nanoflowers (NFs) were created for novel biosensing applications. The selected ‘spotted NFs’ had a 30-nm-thick gold nanoparticle (AuNP) layer, chosen from a range of AuNP thicknesses, sputtered onto the surface. The generated nanohybrids, characterized by morphological, physical and structural analyses, were uniformly AuNP-seeded onto the ZnO NFs with an average length of 2-3 μm. Selective capture of molecular probes onto the seeded AuNPs was evidence for the specific interaction with DNA from pathogenic Leptospirosis-causing strains via hybridization and mis-match analyses. The attained detection limit was 100 fM as determined via impedance spectroscopy. High levels of stability, reproducibility and regeneration of the sensor were obtained. Selective DNA immobilization and hybridization were confirmed by nitrogen and phosphorus peaks in an X-ray photoelectron spectroscopy analysis. The created nanostructure hybrids illuminate the mechanism of generating multiple-target, high-performance detection on a single NF platform, which opens a new avenue for array-based medical diagnostics.

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array.

PubMed

Unterseer, Sandra; Bauer, Eva; Haberer, Georg; Seidel, Michael; Knaak, Carsten; Ouzunova, Milena; Meitinger, Thomas; Strom, Tim M; Fries, Ruedi; Pausch, Hubert; Bertani, Christofer; Davassi, Alessandro; Mayer, Klaus Fx; Schön, Chris-Carolin

2014-09-29

High density genotyping data are indispensable for genomic analyses of complex traits in animal and crop species. Maize is one of the most important crop plants worldwide, however a high density SNP genotyping array for analysis of its large and highly dynamic genome was not available so far. We developed a high density maize SNP array composed of 616,201 variants (SNPs and small indels). Initially, 57 M variants were discovered by sequencing 30 representative temperate maize lines and then stringently filtered for sequence quality scores and predicted conversion performance on the array resulting in the selection of 1.2 M polymorphic variants assayed on two screening arrays. To identify high-confidence variants, 285 DNA samples from a broad genetic diversity panel of worldwide maize lines including the samples used for sequencing, important founder lines for European maize breeding, hybrids, and proprietary samples with European, US, semi-tropical, and tropical origin were used for experimental validation. We selected 616 k variants according to their performance during validation, support of genotype calls through sequencing data, and physical distribution for further analysis and for the design of the commercially available Affymetrix® Axiom® Maize Genotyping Array. This array is composed of 609,442 SNPs and 6,759 indels. Among these are 116,224 variants in coding regions and 45,655 SNPs of the Illumina® MaizeSNP50 BeadChip for study comparison. In a subset of 45,974 variants, apart from the target SNP additional off-target variants are detected, which show only a minor bias towards intermediate allele frequencies. We performed principal coordinate and admixture analyses to determine the ability of the array to detect and resolve population structure and investigated the extent of LD within a worldwide validation panel. The high density Affymetrix® Axiom® Maize Genotyping Array is optimized for European and American temperate maize and was developed based on a diverse sample panel by applying stringent quality filter criteria to ensure its suitability for a broad range of applications. With 600 k variants it is the largest currently publically available genotyping array in crop species.

Hybrid TE panel test results

NASA Technical Reports Server (NTRS)

Bifano, W. J.

1972-01-01

Test results are presented for a nine couple (3 x 3 array) thermoelectric panel of hybrid thermocouples. In the hybrid couple, a hollow cylinder of p-type Si-Ge is used to encapsulate a segmented PbTe/Si-Ge n-leg. The hybrid couple is predicted to offer a 10- to 15-percent improvement in performance relative to all Si-Ge couples. The efficiency, output power, and internal resistance of the panel as well as the resistances of the individual hybrid couples are presented as a function of test time covering a period of more than 2600 hours. Initial test results indicated hybrid couple performance consistent with design predictions. Extraneous resistance ranged from 20 to 25% of the hybrid couple thermoelectric resistance.

Geiger-Mode Avalanche Photodiode Arrays Integrated to All-Digital CMOS Circuits

DTIC Science & Technology

2016-01-20

Figure 7 4×4 GMAPD array wire bonded to CMOS timing circuits Figure 8 Low‐fill‐factor APD design used in lidar sensors The APD doping...epitaxial growth and the pixels are isolated by mesa etch. 128×32 lidar image sensors were built by bump bonding the APD arrays to a CMOS timing...passive image sensor with this large a format based on hybridization of a GMAPD array to a CMOS readout. Fig. 14 shows one of the first images taken

High performance hybrid magnetic structure for biotechnology applications

DOEpatents

Humphries, David E; Pollard, Martin J; Elkin, Christopher J

2005-10-11

The present disclosure provides a high performance hybrid magnetic structure made from a combination of permanent magnets and ferromagnetic pole materials which are assembled in a predetermined array. The hybrid magnetic structure provides means for separation and other biotechnology applications involving holding, manipulation, or separation of magnetizable molecular structures and targets. Also disclosed are: a method of assembling the hybrid magnetic plates, a high throughput protocol featuring the hybrid magnetic structure, and other embodiments of the ferromagnetic pole shape, attachment and adapter interfaces for adapting the use of the hybrid magnetic structure for use with liquid handling and other robots for use in high throughput processes.

High performance hybrid magnetic structure for biotechnology applications

DOEpatents

Humphries, David E.; Pollard, Martin J.; Elkin, Christopher J.

2006-12-12

The present disclosure provides a high performance hybrid magnetic structure made from a combination of permanent magnets and ferromagnetic pole materials which are assembled in a predetermined array. The hybrid magnetic structure provides for separation and other biotechnology applications involving holding, manipulation, or separation of magnetic or magnetizable molecular structures and targets. Also disclosed are: a method of assembling the hybrid magnetic plates, a high throughput protocol featuring the hybrid magnetic structure, and other embodiments of the ferromagnetic pole shape, attachment and adapter interfaces for adapting the use of the hybrid magnetic structure for use with liquid handling and other robots for use in high throughput processes.

Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing

PubMed Central

Wiszniewska, Joanna; Bi, Weimin; Shaw, Chad; Stankiewicz, Pawel; Kang, Sung-Hae L; Pursley, Amber N; Lalani, Seema; Hixson, Patricia; Gambin, Tomasz; Tsai, Chun-hui; Bock, Hans-Georg; Descartes, Maria; Probst, Frank J; Scaglia, Fernando; Beaudet, Arthur L; Lupski, James R; Eng, Christine; Wai Cheung, Sau; Bacino, Carlos; Patel, Ankita

2014-01-01

In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner. PMID:23695279

Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure.

PubMed

Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao

2017-07-19

Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.

Engineering three-dimensional hybrid supercapacitors and microsupercapacitors for high-performance integrated energy storage

PubMed Central

El-Kady, Maher F.; Ihns, Melanie; Li, Mengping; Hwang, Jee Youn; Mousavi, Mir F.; Chaney, Lindsay; Lech, Andrew T.; Kaner, Richard B.

2015-01-01

Supercapacitors now play an important role in the progress of hybrid and electric vehicles, consumer electronics, and military and space applications. There is a growing demand in developing hybrid supercapacitor systems to overcome the energy density limitations of the current generation of carbon-based supercapacitors. Here, we demonstrate 3D high-performance hybrid supercapacitors and microsupercapacitors based on graphene and MnO2 by rationally designing the electrode microstructure and combining active materials with electrolytes that operate at high voltages. This results in hybrid electrodes with ultrahigh volumetric capacitance of over 1,100 F/cm3. This corresponds to a specific capacitance of the constituent MnO2 of 1,145 F/g, which is close to the theoretical value of 1,380 F/g. The energy density of the full device varies between 22 and 42 Wh/l depending on the device configuration, which is superior to those of commercially available double-layer supercapacitors, pseudocapacitors, lithium-ion capacitors, and hybrid supercapacitors tested under the same conditions and is comparable to that of lead acid batteries. These hybrid supercapacitors use aqueous electrolytes and are assembled in air without the need for expensive “dry rooms” required for building today’s supercapacitors. Furthermore, we demonstrate a simple technique for the fabrication of supercapacitor arrays for high-voltage applications. These arrays can be integrated with solar cells for efficient energy harvesting and storage systems. PMID:25831542

Engineering three-dimensional hybrid supercapacitors and microsupercapacitors for high-performance integrated energy storage.

PubMed

El-Kady, Maher F; Ihns, Melanie; Li, Mengping; Hwang, Jee Youn; Mousavi, Mir F; Chaney, Lindsay; Lech, Andrew T; Kaner, Richard B

2015-04-07

Supercapacitors now play an important role in the progress of hybrid and electric vehicles, consumer electronics, and military and space applications. There is a growing demand in developing hybrid supercapacitor systems to overcome the energy density limitations of the current generation of carbon-based supercapacitors. Here, we demonstrate 3D high-performance hybrid supercapacitors and microsupercapacitors based on graphene and MnO2 by rationally designing the electrode microstructure and combining active materials with electrolytes that operate at high voltages. This results in hybrid electrodes with ultrahigh volumetric capacitance of over 1,100 F/cm(3). This corresponds to a specific capacitance of the constituent MnO2 of 1,145 F/g, which is close to the theoretical value of 1,380 F/g. The energy density of the full device varies between 22 and 42 Wh/l depending on the device configuration, which is superior to those of commercially available double-layer supercapacitors, pseudocapacitors, lithium-ion capacitors, and hybrid supercapacitors tested under the same conditions and is comparable to that of lead acid batteries. These hybrid supercapacitors use aqueous electrolytes and are assembled in air without the need for expensive "dry rooms" required for building today's supercapacitors. Furthermore, we demonstrate a simple technique for the fabrication of supercapacitor arrays for high-voltage applications. These arrays can be integrated with solar cells for efficient energy harvesting and storage systems.

Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fischer, S.G.; Cayanis, E.; Boukhgalter, B.

1994-06-01

The authors have developed an efficient method for assembling ordered cosmid contigs aligned to mega-YACs and midi-YACs (average insert sizes of 1.0 and 0.35 Mb, respectively) and used this general method to initiate high-resolution physical mapping of human chromosome 13 (Chr 13). Chr 13-enriched midi-YAC (mYAC) and mega-YAC (MYAC) sublibraries were obtained from corresponding CEPH total human YAC libraries by selecting colonies with inter-Alu PCR probes derived from Chr 13 monochromosomal cell hybrid DNA. These sublibraries were arrayed on filters at high density. In this approach, the MYAC 13 sublibrary is screened by hybridization with cytogenetically assigned Chr 13 DNAmore » probes to select one or a small subset of MYACs. Inter-Alu PCR products from each mYAC are then hybridized to the MYAC and mYAC sublibraries to identify overlapping YACs and to an arrayed Chr 13-specific cosmid library to select corresponding cosmids. The set of selected cosmids, gridded on filters at high density, is hybridized with inter-Alu PCR products from each of the overlapping YACs to identify subsets of cosmids and also with riboprobes from each cosmid of the arrayed set ({open_quotes}cosmid matrix cross-hybridization{close_quotes}). From these data, cosmid contigs are assembled by a specifically designed computer program. Application of this method generates cosmid contigs spanning the length of a MYAC with few gaps. To provide a high-resolution map, ends of cosmids are sequenced at preselected sites to position densely spaced sequence-tagged sites. 33 refs., 7 figs., 1 tab.« less

Conductance based characterization of structure and hopping site density in 2D molecule-nanoparticle arrays

NASA Astrophysics Data System (ADS)

McCold, Cliff E.; Fu, Qiang; Howe, Jane Y.; Hihath, Joshua

2015-09-01

Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems.Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems. Electronic supplementary information (ESI) available: Temperature dependent measurements, activation energies, particle size distributions, void density-polydispersity relation, and DLS data. See DOI: 10.1039/c5nr04460j

Fabricating a hybrid imaging device having non-destructive sense nodes

NASA Technical Reports Server (NTRS)

Wadsworth, Mark (Inventor); Atlas, Gene (Inventor)

2001-01-01

A hybrid detector or imager includes two substrates fabricated under incompatible processes. An array of detectors, such as charged-coupled devices, are formed on the first substrate using a CCD fabrication process, such as a buried channel or peristaltic process. One or more charge-converting amplifiers are formed on a second substrate using a CMOS fabrication process. The two substrates are then bonded together to form a hybrid detector.

Syntenic conservation of HSP70 genes in cattle and humans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grosz, M.D.; Womack, J.E.; Skow, L.C.

1992-12-01

A phage library of bovine genomic DNA was screened for hybridization with a human HSP70 cDNA probe, and 21 positive plaques were identified and isolated. Restriction mapping and blot hybridization analysis of DNA from the recombinant plaques demonstrated that the cloned DNAs were derived from three different regions of the bovine genome. Ore region contains two tandemly arrayed HSP70 sequences, designated HSP70-1 and HSP70-2, separated by approximately 8 kb of DNA. Single HSP70 sequences, designated HSP70-3 and HSP70-4, were found in two other genomic regions. Locus-specific probes of unique flanking sequences from representative HSP70 clones were hybridized to restriction endonuclease-digestedmore » DNA from bovine-hamster and bovine-mouse somatic cell hybrid panels to determine the chromosomal location of the HSP70 sequences. The probe for the tandemly arrayed HSP70-1 and HSP70-2 sequences mapped to bovine chromosome 23, syntenic with glyoxalase 1, 21 steroid hydroxylase, and major histocompatibility class I loci. HSP70-3 sequences mapped to bovine chromosome 10, syntenic with nucleoside phosphorylase and murine osteosarcoma viral oncogene (v-fos), and HSP70-4 mapped to bovine syntenic group U6, syntenic with amylase 1 and phosphoglucomutase 1. On the basis of these data, the authors propose that bovine HSP70-1,2 are homologous to human HSPA1 and HSPA1L on chromosome 6p21.3, bovine HSP70-3 is the homolog of an unnamed human HSP70 gene on chromosome 14q22-q24, and bovine HSP70-4 is homologous to one of the human HSPA-6,-7 genes on chromosome 1. 34 refs., 2 figs., 1 tab.« less

A 2D/3D hybrid integral imaging display by using fast switchable hexagonal liquid crystal lens array

NASA Astrophysics Data System (ADS)

Lee, Hsin-Hsueh; Huang, Ping-Ju; Wu, Jui-Yi; Hsieh, Po-Yuan; Huang, Yi-Pai

2017-05-01

The paper proposes a new display which could switch 2D and 3D images on a monitor, and we call it as Hybrid Display. In 3D display technologies, the reduction of image resolution is still an important issue. The more angle information offer to the observer, the less spatial resolution would offer to image resolution because of the fixed panel resolution. Take it for example, in the integral photography system, the part of image without depth, like background, will reduce its resolution by transform from 2D to 3D image. Therefore, we proposed a method by using liquid crystal component to quickly switch the 2D image and 3D image. Meanwhile, the 2D image is set as a background to compensate the resolution.. In the experiment, hexagonal liquid crystal lens array would be used to take the place of fixed lens array. Moreover, in order to increase lens power of the hexagonal LC lens array, we applied high resistance (Hi-R) layer structure on the electrode. Hi-R layer would make the gradient electric field and affect the lens profile. Also, we use panel with 801 PPI to display the integral image in our system. Hence, the consequence of full resolution 2D background with the 3D depth object forms the Hybrid Display.

Improved analytical methods for microarray-based genome-composition analysis

PubMed Central

Kim, Charles C; Joyce, Elizabeth A; Chan, Kaman; Falkow, Stanley

2002-01-01

Background Whereas genome sequencing has given us high-resolution pictures of many different species of bacteria, microarrays provide a means of obtaining information on genome composition for many strains of a given species. Genome-composition analysis using microarrays, or 'genomotyping', can be used to categorize genes into 'present' and 'divergent' categories based on the level of hybridization signal. This typically involves selecting a signal value that is used as a cutoff to discriminate present (high signal) and divergent (low signal) genes. Current methodology uses empirical determination of cutoffs for classification into these categories, but this methodology is subject to several problems that can result in the misclassification of many genes. Results We describe a method that depends on the shape of the signal-ratio distribution and does not require empirical determination of a cutoff. Moreover, the cutoff is determined on an array-to-array basis, accounting for variation in strain composition and hybridization quality. The algorithm also provides an estimate of the probability that any given gene is present, which provides a measure of confidence in the categorical assignments. Conclusions Many genes previously classified as present using static methods are in fact divergent on the basis of microarray signal; this is corrected by our algorithm. We have reassigned hundreds of genes from previous genomotyping studies of Helicobacter pylori and Campylobacter jejuni strains, and expect that the algorithm should be widely applicable to genomotyping data. PMID:12429064

Vehicle antenna for the mobile satellite experiment

NASA Technical Reports Server (NTRS)

Peng, Sheng Y.; Chung, H. H.; Leggiere, D.; Foy, W.; Schaffner, G.; Nelson, J.; Pagels, W.; Vayner, M.; Faller, H. L.; Messer, L.

1988-01-01

A low profile, low cost, printed circuit, electronically steered, right hand circularly polarized phase array antenna system has been developed for the Mobile Satellite Experiment (MSAT-X) Program. The success of this antenna is based upon the development of a crossed-slot element array and detailed trade-off analyses for both the phased array and pointing system design. The optimized system provides higher gain at low elevation angles (20 degrees above the horizon) and broader frequency coverage (approximately 8 1/2 percent bandwidth) than is possible with a patch array. Detailed analysis showed that optimum performance could be achieved with a 19 element array of a triangular lattice geometry of 3.9 inch element spacing. This configuration has the effect of minimizing grating lobes at large scan angles plus it improves the intersatellite isolation. The array has an aperture 20 inches in diameter and is 0.75 inch thick overall, exclusive of the RF and power connector. The pointing system employs a hybrid approach that operates with both an external rate sensor and an internal error signal as a means of fine tuning the beam acquisition and track. Steering the beam is done electronically via 18, 3-bit diode phase shifters. A nineteenth phase shifter is not required as the center element serves as a reference only. Measured patterns and gain show that the array meets the stipulated performance specifications everywhere except at some low elevation angles.

High Temperature Superconductor/Semiconductor Hybrid Microwave Devices and Circuits

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R.; Miranda, Felix A.

1999-01-01

Contents include following: film deposition technique; laser ablation; magnetron sputtering; sequential evaporation; microwave substrates; film characterization at microwave frequencies; complex conductivity; magnetic penetration depth; surface impedance; planar single-mode filters; small antennas; antenna arrays phase noise; tunable oscillations; hybrid superconductor/semiconductor receiver front ends; and noise modeling.

Plastic-Sealed Hybrid Power Circuit Package

NASA Technical Reports Server (NTRS)

Miller, W. N.; Gray, O. E.

1983-01-01

Proposed design for hybrid high-voltage power-circuit package uses molded plastic for hermetic sealing instead of glass-to-metal seal. New package used to house high-voltage regulators and solid-state switches for applications in aircraft, electric automobiles, industrial equipment, satellites, solarcell arrays, and other equipment in extreme environments.

Expansion of CMOS array design techniques

NASA Technical Reports Server (NTRS)

Feller, A.; Ramondetta, P.

1977-01-01

The important features of the multiport (double entry) automatic placement and routing programs for standard cells are described. Measured performance and predicted performance were compared for seven CMOS/SOS array types and hybrids designed with the high speed CMOS/SOS cell family. The CMOS/SOS standard cell data sheets are listed and described.

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci.

PubMed

Milbredt, Sarah; Waldminghaus, Torsten

2017-06-07

Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci. Copyright © 2017 Milbredt and Waldminghaus.

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci

PubMed Central

Milbredt, Sarah; Waldminghaus, Torsten

2017-01-01

Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci. PMID:28450375

Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip.

PubMed

Van Nostrand, Joy D; Yin, Huaqin; Wu, Liyou; Yuan, Tong; Zhou, Jizhong

2016-01-01

Functional gene arrays, like the GeoChip, allow for the study of tens of thousands of genes in a single assay. The GeoChip array (5.0) contains probes for genes involved in geochemical cycling (N, C, S, and P), metal homeostasis, stress response, organic contaminant degradation, antibiotic resistance, secondary metabolism, and virulence factors as well as genes specific for fungi, protists, and viruses. Here, we briefly describe GeoChip design strategies (gene selection and probe design) and discuss minimum quantity and quality requirements for nucleic acids. We then provide detailed protocols for amplification, labeling, and hybridization of samples to the GeoChip.

Energy spectrum of ultra-high energy cosmic rays observed with the Telescope Array using a hybrid technique

NASA Astrophysics Data System (ADS)

Abu-Zayyad, T.; Aida, R.; Allen, M.; Anderson, R.; Azuma, R.; Barcikowski, E.; Belz, J. W.; Bergman, D. R.; Blake, S. A.; Cady, R.; Cheon, B. G.; Chiba, J.; Chikawa, M.; Cho, E. J.; Cho, W. R.; Fujii, H.; Fujii, T.; Fukuda, T.; Fukushima, M.; Hanlon, W.; Hayashi, K.; Hayashi, Y.; Hayashida, N.; Hibino, K.; Hiyama, K.; Honda, K.; Iguchi, T.; Ikeda, D.; Ikuta, K.; Inoue, N.; Ishii, T.; Ishimori, R.; Ito, H.; Ivanov, D.; Iwamoto, S.; Jui, C. C. H.; Kadota, K.; Kakimoto, F.; Kalashev, O.; Kanbe, T.; Kasahara, K.; Kawai, H.; Kawakami, S.; Kawana, S.; Kido, E.; Kim, H. B.; Kim, H. K.; Kim, J. H.; Kim, J. H.; Kitamoto, K.; Kitamura, S.; Kitamura, Y.; Kobayashi, K.; Kobayashi, Y.; Kondo, Y.; Kuramoto, K.; Kuzmin, V.; Kwon, Y. J.; Lan, J.; Lim, S. I.; Lundquist, J. P.; Machida, S.; Martens, K.; Matsuda, T.; Matsuura, T.; Matsuyama, T.; Matthews, J. N.; Minamino, M.; Miyata, K.; Murano, Y.; Myers, I.; Nagasawa, K.; Nagataki, S.; Nakamura, T.; Nam, S. W.; Nonaka, T.; Ogio, S.; Ohnishi, M.; Ohoka, H.; Oki, K.; Oku, D.; Okuda, T.; Ono, M.; Oshima, A.; Ozawa, S.; Park, I. H.; Pshirkov, M. S.; Rodriguez, D. C.; Roh, S. Y.; Rubtsov, G.; Ryu, D.; Sagawa, H.; Sakurai, N.; Sampson, A. L.; Scott, L. M.; Shah, P. D.; Shibata, F.; Shibata, T.; Shimodaira, H.; Shin, B. K.; Shin, J. I.; Shirahama, T.; Smith, J. D.; Sokolsky, P.; Springer, R. W.; Stokes, B. T.; Stratton, S. R.; Stroman, T.; Suzuki, S.; Takahashi, Y.; Takeda, M.; Taketa, A.; Takita, M.; Tameda, Y.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Thomas, S. B.; Thomson, G. B.; Tinyakov, P.; Tkachev, I.; Tokuno, H.; Tomida, T.; Troitsky, S.; Tsunesada, Y.; Tsutsumi, K.; Tsuyuguchi, Y.; Uchihori, Y.; Udo, S.; Ukai, H.; Urban, F.; Vasiloff, G.; Wada, Y.; Wong, T.; Yamakawa, Y.; Yamane, R.; Yamaoka, H.; Yamazaki, K.; Yang, J.; Yoneda, Y.; Yoshida, S.; Yoshii, H.; Zhou, X.; Zollinger, R.; Zundel, Z.

2015-02-01

We measure the spectrum of cosmic rays with energies greater than 1018.2 eV with the fluorescence detectors (FDs) and the surface detectors (SDs) of the Telescope Array Experiment using the data taken in our first 2.3-year observation from May 27, 2008 to September 7, 2010. A hybrid air shower reconstruction technique is employed to improve accuracies in determination of arrival directions and primary energies of cosmic rays using both FD and SD data. The energy spectrum presented here is in agreement with our previously published spectra and the HiRes results.

Hybridization and sequencing of nucleic acids using base pair mismatches

DOEpatents

Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

2001-01-01

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Image science team

NASA Technical Reports Server (NTRS)

Ando, K.

1982-01-01

A substantial technology base of solid state pushbroom sensors exists and is in the process of further evolution at both GSFC and JPL. Technologies being developed relate to short wave infrared (SWIR) detector arrays; HgCdTe hybrid detector arrays; InSb linear and area arrays; passive coolers; spectral beam splitters; the deposition of spectral filters on detector arrays; and the functional design of the shuttle/space platform imaging spectrometer (SIS) system. Spatial and spectral characteristics of field, aircraft and space multispectral sensors are summaried. The status, field of view, and resolution of foreign land observing systems are included.

Unstructured Adaptive Grid Computations on an Array of SMPs

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Pramanick, Ira; Sohn, Andrew; Simon, Horst D.

1996-01-01

Dynamic load balancing is necessary for parallel adaptive methods to solve unsteady CFD problems on unstructured grids. We have presented such a dynamic load balancing framework called JOVE, in this paper. Results on a four-POWERnode POWER CHALLENGEarray demonstrated that load balancing gives significant performance improvements over no load balancing for such adaptive computations. The parallel speedup of JOVE, implemented using MPI on the POWER CHALLENCEarray, was significant, being as high as 31 for 32 processors. An implementation of JOVE that exploits 'an array of SMPS' architecture was also studied; this hybrid JOVE outperformed flat JOVE by up to 28% on the meshes and adaption models tested. With large, realistic meshes and actual flow-solver and adaption phases incorporated into JOVE, hybrid JOVE can be expected to yield significant advantage over flat JOVE, especially as the number of processors is increased, thus demonstrating the scalability of an array of SMPs architecture.

A hybrid nanomemristor/transistor logic circuit capable of self-programming

PubMed Central

Borghetti, Julien; Li, Zhiyong; Straznicky, Joseph; Li, Xuema; Ohlberg, Douglas A. A.; Wu, Wei; Stewart, Duncan R.; Williams, R. Stanley

2009-01-01

Memristor crossbars were fabricated at 40 nm half-pitch, using nanoimprint lithography on the same substrate with Si metal-oxide-semiconductor field effect transistor (MOS FET) arrays to form fully integrated hybrid memory resistor (memristor)/transistor circuits. The digitally configured memristor crossbars were used to perform logic functions, to serve as a routing fabric for interconnecting the FETs and as the target for storing information. As an illustrative demonstration, the compound Boolean logic operation (A AND B) OR (C AND D) was performed with kilohertz frequency inputs, using resistor-based logic in a memristor crossbar with FET inverter/amplifier outputs. By routing the output signal of a logic operation back onto a target memristor inside the array, the crossbar was conditionally configured by setting the state of a nonvolatile switch. Such conditional programming illuminates the way for a variety of self-programmed logic arrays, and for electronic synaptic computing. PMID:19171903

A hybrid nanomemristor/transistor logic circuit capable of self-programming.

PubMed

Borghetti, Julien; Li, Zhiyong; Straznicky, Joseph; Li, Xuema; Ohlberg, Douglas A A; Wu, Wei; Stewart, Duncan R; Williams, R Stanley

2009-02-10

Memristor crossbars were fabricated at 40 nm half-pitch, using nanoimprint lithography on the same substrate with Si metal-oxide-semiconductor field effect transistor (MOS FET) arrays to form fully integrated hybrid memory resistor (memristor)/transistor circuits. The digitally configured memristor crossbars were used to perform logic functions, to serve as a routing fabric for interconnecting the FETs and as the target for storing information. As an illustrative demonstration, the compound Boolean logic operation (A AND B) OR (C AND D) was performed with kilohertz frequency inputs, using resistor-based logic in a memristor crossbar with FET inverter/amplifier outputs. By routing the output signal of a logic operation back onto a target memristor inside the array, the crossbar was conditionally configured by setting the state of a nonvolatile switch. Such conditional programming illuminates the way for a variety of self-programmed logic arrays, and for electronic synaptic computing.

MOF-5 decorated hierarchical ZnO nanorod arrays and its photoluminescence

NASA Astrophysics Data System (ADS)

Zhang, Yinmin; Lan, Ding; Wang, Yuren; Cao, He; Jiang, Heng

2011-04-01

The strategy to manipulate nanoscale materials into well-organized hierarchical architectures is very important to both material synthesis and nanodevice applications. Here, nanoscale MOF-5 crystallites were successfully fabricated onto ordered hierarchical ZnO arrays based on aqueous chemical synthesis and molecule self-assembly technology guided room temperature diffusion method, which has the advantages of energy saving and simple operation. The structures and morphologies of the samples were performed by X-ray powder diffraction and field emission scanning electronic microscopy. The MOF-5 crystallites have good quality and bind well to the hexagonal-patterned ZnO arrays. The photoluminescence spectrum shows that the emission of hybrid MOF-5-ZnO films displays a blue shift in green emission and intensity reduction in UV emission. This ordered hybrid semiconductor material is expected to exploit the great potentiality in sensors, micro/nanodevices, and screen displays.

Microfabricated Fountain Pens for High-Density DNA Arrays

PubMed Central

Reese, Matthew O.; van Dam, R. Michae; Scherer, Axel; Quake, Stephen R.

2003-01-01

We used photolithographic microfabrication techniques to create very small stainless steel fountain pens that were installed in place of conventional pens on a microarray spotter. Because of the small feature size produced by the microfabricated pens, we were able to print arrays with up to 25,000 spots/cm2, significantly higher than can be achieved by other deposition methods. This feature density is sufficiently large that a standard microscope slide can contain multiple replicates of every gene in a complex organism such as a mouse or human. We tested carryover during array printing with dye solution, labeled DNA, and hybridized DNA, and we found it to be indistinguishable from background. Hybridization also showed good sequence specificity to printed oligonucleotides. In addition to improved slide capacity, the microfabrication process offers the possibility of low-cost mass-produced pens and the flexibility to include novel pen features that cannot be machined with conventional techniques. PMID:12975313

Phased Acoustic Array Measurements of a 5.75 Percent Hybrid Wing Body Aircraft

NASA Technical Reports Server (NTRS)

Burnside, Nathan J.; Horne, William C.; Elmer, Kevin R.; Cheng, Rui; Brusniak, Leon

2016-01-01

Detailed acoustic measurements of the noise from the leading-edge Krueger flap of a 5.75 percent Hybrid Wing Body (HWB) aircraft model were recently acquired with a traversing phased microphone array in the AEDC NFAC (Arnold Engineering Development Complex, National Full Scale Aerodynamics Complex) 40- by 80-Foot Wind Tunnel at NASA Ames Research Center. The spatial resolution of the array was sufficient to distinguish between individual support brackets over the full-scale frequency range of 100 to 2875 Hertz. For conditions representative of landing and take-off configuration, the noise from the brackets dominated other sources near the leading edge. Inclusion of flight-like brackets for select conditions highlights the importance of including the correct number of leading-edge high-lift device brackets with sufficient scale and fidelity. These measurements will support the development of new predictive models.

Enteropathy-associated T-cell lymphoma--a clinicopathologic and array comparative genomic hybridization study.

PubMed

Ko, Young Hyeh; Karnan, Sivasundaram; Kim, Kyeong Mee; Park, Cheol Keun; Kang, Eun Suk; Kim, Young Ho; Kang, Won Ki; Kim, Seok Jin; Kim, Won Seog; Lee, Woo Yong; Chun, Ho Kyung; Seto, Masao

2010-09-01

According to the new World Health Organization classification system, there are 2 types of enteropathy-associated T-cell lymphoma. Type 1 is associated with celiac disease and accounts for the majority of cases in Western countries, whereas type 2 is not associated with celiac disease. To characterize enteropathy-associated T-cell lymphoma types in Korea, we carried out clinicopathologic and immunophenotypic analyses of 8 Koreans with enteropathy-associated T-cell lymphoma and investigated genomic profile using array comparative genomic hybridization. The tumors involved the small intestine in 5 patients and the colorectum in 3 patients. Two patients carried an HLA DQB10302 allele that corresponds to HLA DQ8. None of the patients had gluten-sensitive malabsorption syndrome. Intraepithelial lymphocytosis was observed in all patients. The sizes of the tumor cells were small or small-to-medium in 7 cases and medium-to-large in 1 case. The immunophenotypes of the tumor cells were CD4-CD8+CD56+ in 4 cases, CD4-CD8+CD56- in 1 case, CD4-CD8-CD56+ in 2 cases, and CD4-CD8-CD56- in 1 case. Array comparative genomic hybridization analysis showed that chromosome 9q33-q34.1 gain was present in 4 (80%) of the 5 cases examined. Other recurrent genomic alterations were gain of 6p21.1-21.31 (3/5, 60%), gain of 19q (2/5), and the loss of 3p12.1-p12.2 (2/5) and 3q26.31 (2/5). These results suggest that the most prevalent type of enteropathy-associated T-cell lymphoma in this geographic region is type 2, and the genetic changes associated with it are similar to those in Western countries. Copyright 2010 Elsevier Inc. All rights reserved.

Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies (PISCES) for WFIRST/AFTA

NASA Technical Reports Server (NTRS)

Gong, Qian; Mcelwain, Michael; Greeley, Bradford; Grammer, Bryan; Marx, Catherine; Memarsadeghi, Nargess; Stapelfeldt, Karl; Hilton, George; Sayson, Jorge Llop; Perrin, Marshall;

Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies (PISCES) for WFIRST-AFTA

NASA Technical Reports Server (NTRS)

Gong, Qian; Mcelwain, Michael; Greeley, Bradford; Grammer, Bryan; Marx, Catherine; Memarsadeghi, Nargess; Stapelfeldt, Karl; Hilton, George; Sayson, Jorge Llop; Perrin, Marshall;

Environmentally responsive optical microstructured hybrid actuator assemblies and applications thereof

DOEpatents

Aizenberg, Joanna; Aizenberg, Michael; Kim, Philseok

2016-01-05

Microstructured hybrid actuator assemblies in which microactuators carrying designed surface properties to be revealed upon actuation are embedded in a layer of responsive materials. The microactuators in a microactuator array reversibly change their configuration in response to a change in the environment without requiring an external power source to switch their optical properties.

A metallo-DNA nanowire with uninterrupted one-dimensional silver array

NASA Astrophysics Data System (ADS)

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Hattori, Yoshikazu; Saneyoshi, Hisao; Ono, Akira; Tanaka, Yoshiyuki

2017-10-01

The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal-DNA hybrid duplexes by a bottom-up approach. Here we describe a metallo-DNA nanowire—whose structure was solved by high-resolution X-ray crystallography—that consists of dodecamer duplexes held together by four different metal-mediated base pairs (the previously observed C-Ag-C, as well as G-Ag-G, G-Ag-C and T-Ag-T) and linked to each other through G overhangs involved in interduplex G-Ag-G. The resulting hybrid nanowires are 2 nm wide with a length of the order of micrometres to millimetres, and hold the silver ions in uninterrupted one-dimensional arrays along the DNA helical axis. The hybrid nanowires are further assembled into three-dimensional lattices by interactions between adenine residues, fully bulged out of the double helix.

Case for a field-programmable gate array multicore hybrid machine for an image-processing application

NASA Astrophysics Data System (ADS)

Rakvic, Ryan N.; Ives, Robert W.; Lira, Javier; Molina, Carlos

2011-01-01

General purpose computer designers have recently begun adding cores to their processors in order to increase performance. For example, Intel has adopted a homogeneous quad-core processor as a base for general purpose computing. PlayStation3 (PS3) game consoles contain a multicore heterogeneous processor known as the Cell, which is designed to perform complex image processing algorithms at a high level. Can modern image-processing algorithms utilize these additional cores? On the other hand, modern advancements in configurable hardware, most notably field-programmable gate arrays (FPGAs) have created an interesting question for general purpose computer designers. Is there a reason to combine FPGAs with multicore processors to create an FPGA multicore hybrid general purpose computer? Iris matching, a repeatedly executed portion of a modern iris-recognition algorithm, is parallelized on an Intel-based homogeneous multicore Xeon system, a heterogeneous multicore Cell system, and an FPGA multicore hybrid system. Surprisingly, the cheaper PS3 slightly outperforms the Intel-based multicore on a core-for-core basis. However, both multicore systems are beaten by the FPGA multicore hybrid system by >50%.

[Phenotype-genotype correlation analysis of 12 cases with Angelman/Prader-Willi syndrome].

PubMed

Chen, Chen; Peng, Ying; Xia, Yan; Li, Haoxian; Zhu, Huimin; Pan, Qian; Yin, Fei; Wu, Lingqian

2014-12-01

To investigate the genotype-phenotype correlation in patients with Angelman syndrome/Prader-Willi syndrome (AS/PWS) and assess the application value of high-resolution single nucleotide polymorphism microarrays (SNP array) for such diseases. Twelve AS/PWS patients were diagnosed through SNP array, fluorescence in situ hybridization (FISH) and karyotype analysis. Clinical characteristics were analyzed. Deletions ranging from 4.8 Mb to 7.0 Mb on chromosome 15q11.2-13 were detected in 11 patients. Uniparental disomy (UPD) was detected in only 1 patient. Patients with deletions could be divided into 2 groups, including 7 cases with class I and 4 with class II. The two groups however had no significant phenotypic difference. The UPD patient had relatively better development and language ability. Deletions of 6 patients were confirmed by FISH to be of de novo in origin. The risk to their sibs was determined to be less than 1%. The phenotypic differences between AS/PWS patients with class I and class II deletion need to be further studied. SNP array is useful in detecting and distinguishing of patients with deletion or UPD. This method may be applied for studying the genotype-phenotype association and the mechanism underlying AS/PWS.

Toward highly sensitive surface-enhanced Raman scattering: the design of a 3D hybrid system with monolayer graphene sandwiched between silver nanohole arrays and gold nanoparticles.

PubMed

Zhao, Yuan; Yang, Dong; Li, Xiyu; Liu, Yu; Hu, Xiang; Zhou, Dianfa; Lu, Yalin

2017-01-19

We report a novel graphene-metal hybrid system by introducing monolayer graphene between gold nanoparticles (Au NPs) and silver nanohole (Ag NH) arrays. The design incorporates three key advantages to promote the surface-enhanced Raman scattering (SERS) sensing capacity: (i) making full use of the single-atomic feature of graphene for generating uniform sub-nanometer spaces; (ii) maintaining the bottom layer of Ag nanoarrays with an ordered manner for facilitating the transfer of graphene films and assembly of the top layer of Au NPs; (iii) integrating the advantages of the strong plasmonic effect of Ag, the chemical stability of Au, as well as the mechanical flexibility and biological compatibility of graphene. In this configuration, the plasmonic properties can be fine-tuned by separately optimizing the horizontal or vertical gaps between the metal NPs. Exactly, sub-20 nm spaces between the horizontally patterned Ag tips constructed by adjacent Ag NHs, and sub-nanometer scale graphene gaps between the vertically distributed Au NP-Ag NH have been achieved. Finite element numerical simulations demonstrate that the multi-dimensional plasmonic couplings (including the Au NP-Au NP, Au NP-Ag NH and Ag NH-Ag NH couplings) promote for the hybrid platform an electric field enhancement up to 137 times. Impressively, the as-prepared 3D Au NP-graphene-Ag NH array hybrid structure manifests ultrahigh SERS sensitivity with a detection limit of 10 -13 M for R6G molecules, as well as good reproducibility and stability. This work represents a step towards high-performance SERS substrate fabrication, and opens up a new route for graphene-plasmonic hybrids in SERS applications.

Microwave performance characterization of large space antennas

NASA Technical Reports Server (NTRS)

Bathker, D. A. (Editor)

1977-01-01

Performance capabilities of large microwave space antenna configurations with apertures generally from 100 wavelengths upwards are discussed. Types of antennas considered include: phased arrays, lenses, reflectors, and hybrid combinations of phased arrays with reflectors or lenses. The performance characteristics of these broad classes of antennas are examined and compared in terms of applications.

Demonstration of 1024x1024 pixel dual-band QWIP focal plane array

NASA Astrophysics Data System (ADS)

Gunapala, S. D.; Bandara, S. V.; Liu, J. K.; Mumolo, J. M.; Ting, D. Z.; Hill, C. J.; Nguyen, J.; Rafol, S. B.

2010-04-01

QWIPs are well known for their stability, high pixel-pixel uniformity and high pixel operability which are quintessential parameters for large area imaging arrays. In this paper we report the first demonstration of the megapixel-simultaneously-readable and pixel-co-registered dual-band QWIP focal plane array (FPA). The dual-band QWIP device was developed by stacking two multi-quantum-well stacks tuned to absorb two different infrared wavelengths. The full width at half maximum (FWHM) of the mid-wave infrared (MWIR) band extends from 4.4 - 5.1 μm and FWHM of the long-wave infrared (LWIR) band extends from 7.8 - 8.8 μm. Dual-band QWIP detector arrays were hybridized with direct injection 30 μm pixel pitch megapixel dual-band simultaneously readable CMOS read out integrated circuits using the indium bump hybridization technique. The initial dual-band megapixel QWIP FPAs were cooled to 68K operating temperature. The preliminary data taken from the first megapixel QWIP FPA has shown system NE▵T of 27 and 40 mK for MWIR and LWIR bands respectively.

Multi-angle ZnO microstructures grown on Ag nanorods array for plasmon-enhanced near-UV-blue light emitter

NASA Astrophysics Data System (ADS)

Pal, Anil Kumar; Bharathi Mohan, D.

2017-10-01

Metal enhanced ultraviolet light emission has been explored in ZnO/Ag hybrid structures prepared by hydrothermal growth of multi-angled ZnO nanorods on slanted Ag nanorods array fabricated by the thermal evaporation technique. Slanted Ag nanorods are realized to be the stacking of non-spherical Ag nanoparticles, resulting in asymmetric surface plasmon resonance spectra. The surface roughness of Ag nanorod array films significantly influences the growth mechanism of ZnO nanorods, leading to the formation of multi-angled ZnO microflowers. ZnO/Ag hybrid structures facilitate the interfacial charge transfer from Ag to ZnO with the realization of negative shift in binding energy of Ag 3d orbitals by ˜0.8 eV. These high quality ZnO nanorods in ZnO/Ag hybrid nanostructures exhibit strong ultraviolet emission in the 383-396 nm region without broad deep level emission, which can be explained by a suitable band diagram. The metal enhanced photoluminescence is witnessed mainly due to interfacial charge transfer with its dependence on surface roughness of bottom layer Ag nanorods, number density of ZnO nanorods and diversity in the interfacial area between Ag and ZnO nanorods. The existence of strong ultraviolet light with minor blue light emission and appearance of CIE shade in strong violet-blue region by ZnO/Ag hybrid structures depict exciting possibilities towards near UV-blue light emitting devices.

Multi-angle ZnO microstructures grown on Ag nanorods array for plasmon-enhanced near-UV-blue light emitter.

PubMed

Pal, Anil Kumar; Mohan, D Bharathi

2017-10-13

Metal enhanced ultraviolet light emission has been explored in ZnO/Ag hybrid structures prepared by hydrothermal growth of multi-angled ZnO nanorods on slanted Ag nanorods array fabricated by the thermal evaporation technique. Slanted Ag nanorods are realized to be the stacking of non-spherical Ag nanoparticles, resulting in asymmetric surface plasmon resonance spectra. The surface roughness of Ag nanorod array films significantly influences the growth mechanism of ZnO nanorods, leading to the formation of multi-angled ZnO microflowers. ZnO/Ag hybrid structures facilitate the interfacial charge transfer from Ag to ZnO with the realization of negative shift in binding energy of Ag 3d orbitals by ∼0.8 eV. These high quality ZnO nanorods in ZnO/Ag hybrid nanostructures exhibit strong ultraviolet emission in the 383-396 nm region without broad deep level emission, which can be explained by a suitable band diagram. The metal enhanced photoluminescence is witnessed mainly due to interfacial charge transfer with its dependence on surface roughness of bottom layer Ag nanorods, number density of ZnO nanorods and diversity in the interfacial area between Ag and ZnO nanorods. The existence of strong ultraviolet light with minor blue light emission and appearance of CIE shade in strong violet-blue region by ZnO/Ag hybrid structures depict exciting possibilities towards near UV-blue light emitting devices.

Spontaneous hybrids of graphene and carbon nanotube arrays at the liquid-gas interface for Li-ion battery anodes.

PubMed

Kim, Hyeri; Kim, Jongsoon; Jeong, Hee-Sung; Kim, Hyungsub; Lee, Hoyeon; Ha, Jae-Min; Choi, Sung-Min; Kim, Tae-Ho; Nah, Yoon-Chae; Shin, Tae Joo; Bang, Joona; Satija, Sushil K; Koo, Jaseung

2018-05-17

We demonstrate that hybrid structures of graphene and single-walled carbon nanotubes (SWNTs) are precisely controlled at the liquid-gas interface. The functionalized SWNT Langmuir monolayers anchor single-layer graphene nanosheets (GNSs) suspended in water via Coulomb interaction at the interface. This GNS/SWNT hybrid multilayer electrode can be a promising anode material for Li-ion batteries, offering high specific capacity, outstanding power capability, and excellent cyclability.

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Ultrafast dynamics of metal plasmons induced by 2D semiconductor excitons in hybrid nanostructure arrays

DOE PAGES

Boulesbaa, Abdelaziz; Babicheva, Viktoriia E.; Wang, Kai; ...

2016-11-17

With the advanced progress achieved in the field of nanotechnology, localized surface plasmons resonances (LSPRs) are actively considered to improve the efficiency of metal-based photocatalysis, photodetection, and photovoltaics. Here, we report on the exchange of energy and electric charges in a hybrid composed of a two-dimensional tungsten disulfide (2D-WS 2) monolayer and an array of aluminum (Al) nanodisks. Femtosecond pump-probe spectroscopy results indicate that within ~830 fs after photoexcitation of the 2D-WS 2 semiconductor, energy transfer from the 2D-WS 2 excitons excites the plasmons of the Al array. Then, upon the radiative and/or nonradiative damping of these excited plasmons, energymore » and/or electron transfer back to the 2D-WS 2 semiconductor takes place as indicated by an increase in the reflected probe at the 2D exciton transition energies at later time-delays. This simultaneous exchange of energy and charges between the metal and the 2D-WS 2 semiconductor resulted in an extension of the average lifetime of the 2D-excitons from ~15 to ~58 ps in absence and presence of the Al array, respectively. Furthermore, the indirectly excited plasmons were found to live as long as the 2D-WS 2 excitons exist. Furthermore, the demonstrated ability to generate exciton-plasmons coupling in a hybrid nanostructure may open new opportunities for optoelectronic applications such as plasmonic-based photodetection and photocatalysis.« less

Depth of Ultra High Energy Cosmic Ray Induced Air Shower Maxima Measured by the Telescope Array Black Rock and Long Ridge FADC Fluorescence Detectors and Surface Array in Hybrid Mode

NASA Astrophysics Data System (ADS)

Abbasi, R. U.; Abe, M.; Abu-Zayyad, T.; Allen, M.; Azuma, R.; Barcikowski, E.; Belz, J. W.; Bergman, D. R.; Blake, S. A.; Cady, R.; Cheon, B. G.; Chiba, J.; Chikawa, M.; di Matteo, A.; Fujii, T.; Fujita, K.; Fukushima, M.; Furlich, G.; Goto, T.; Hanlon, W.; Hayashi, M.; Hayashi, Y.; Hayashida, N.; Hibino, K.; Honda, K.; Ikeda, D.; Inoue, N.; Ishii, T.; Ishimori, R.; Ito, H.; Ivanov, D.; Jeong, H. M.; Jeong, S. M.; Jui, C. C. H.; Kadota, K.; Kakimoto, F.; Kalashev, O.; Kasahara, K.; Kawai, H.; Kawakami, S.; Kawana, S.; Kawata, K.; Kido, E.; Kim, H. B.; Kim, J. H.; Kim, J. H.; Kishigami, S.; Kitamura, S.; Kitamura, Y.; Kuzmin, V.; Kuznetsov, M.; Kwon, Y. J.; Lee, K. H.; Lubsandorzhiev, B.; Lundquist, J. P.; Machida, K.; Martens, K.; Matsuyama, T.; Matthews, J. N.; Mayta, R.; Minamino, M.; Mukai, K.; Myers, I.; Nagasawa, K.; Nagataki, S.; Nakamura, R.; Nakamura, T.; Nonaka, T.; Oda, H.; Ogio, S.; Ogura, J.; Ohnishi, M.; Ohoka, H.; Okuda, T.; Omura, Y.; Ono, M.; Onogi, R.; Oshima, A.; Ozawa, S.; Park, I. H.; Pshirkov, M. S.; Rodriguez, D. C.; Rubtsov, G.; Ryu, D.; Sagawa, H.; Sahara, R.; Saito, K.; Saito, Y.; Sakaki, N.; Sakurai, N.; Scott, L. M.; Seki, T.; Sekino, K.; Shah, P. D.; Shibata, F.; Shibata, T.; Shimodaira, H.; Shin, B. K.; Shin, H. S.; Smith, J. D.; Sokolsky, P.; Stokes, B. T.; Stratton, S. R.; Stroman, T. A.; Suzawa, T.; Takagi, Y.; Takahashi, Y.; Takamura, M.; Takeda, M.; Takeishi, R.; Taketa, A.; Takita, M.; Tameda, Y.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Thomas, S. B.; Thomson, G. B.; Tinyakov, P.; Tkachev, I.; Tokuno, H.; Tomida, T.; Troitsky, S.; Tsunesada, Y.; Tsutsumi, K.; Uchihori, Y.; Udo, S.; Urban, F.; Wong, T.; Yamamoto, M.; Yamane, R.; Yamaoka, H.; Yamazaki, K.; Yang, J.; Yashiro, K.; Yoneda, Y.; Yoshida, S.; Yoshii, H.; Zhezher, Y.; Zundel, Z.; Telescope Array Collaboration

2018-05-01

The Telescope Array (TA) observatory utilizes fluorescence detectors and surface detectors (SDs) to observe air showers produced by ultra high energy cosmic rays in Earth’s atmosphere. Cosmic-ray events observed in this way are termed hybrid data. The depth of air shower maximum is related to the mass of the primary particle that generates the shower. This paper reports on shower maxima data collected over 8.5 yr using the Black Rock Mesa and Long Ridge fluorescence detectors in conjunction with the array of SDs. We compare the means and standard deviations of the observed {X}\\max distributions with Monte Carlo {X}\\max distributions of unmixed protons, helium, nitrogen, and iron, all generated using the QGSJet II-04 hadronic model. We also perform an unbinned maximum likelihood test of the observed data, which is subjected to variable systematic shifting of the data {X}\\max distributions to allow us to test the full distributions, and compare them to the Monte Carlo to see which elements are not compatible with the observed data. For all energy bins, QGSJet II-04 protons are found to be compatible with TA hybrid data at the 95% confidence level after some systematic {X}\\max shifting of the data. Three other QGSJet II-04 elements are found to be compatible using the same test procedure in an energy range limited to the highest energies where data statistics are sparse.

Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes

PubMed Central

Howarth, KD; Blood, KA; Ng, BL; Beavis, JC; Chua, Y; Cooke, SL; Raby, S; Ichimura, K; Collins, VP; Carter, NP; Edwards, PAW

2008-01-01

Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1Mb resolution on BAC arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Secondly, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300, and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer. PMID:18084325

In situ fabrication of Ni-Co (oxy)hydroxide nanowire-supported nanoflake arrays and their application in supercapacitors.

PubMed

Zheng, Xiaoyu; Quan, Honglin; Li, Xiaoxin; He, Hai; Ye, Qinglan; Xu, Xuetang; Wang, Fan

2016-09-29

Three-dimensional (3D) hybrid nanostructured arrays grown on a flexible substrate have recently attracted great attention owing to their potential application as supercapacitor electrodes in portable and wearable electronic devices. Here, we report an in situ conversion of Ni-Co active electrode materials for the fabrication of high-performance electrodes. Ni-Co carbonate hydroxide nanowire arrays on carbon cloth were initially synthesized via a hydrothermal method, and they were gradually converted to Ni-Co (oxy)hydroxide nanowire-supported nanoflake arrays after soaking in an alkaline solution. The evolution of the supercapacitor performance of the soaked electrode was investigated in detail. The areal capacitance increases from 281 mF cm -2 at 1 mA cm -2 to 3710 and 3900 mF cm -2 after soaking for 36 h and 48 h, respectively. More interestingly, the electrode also shows an increased capacitance with charge/discharge cycles due to the long-time soaking in KOH solution, suggesting novel cycling durability. The enhancement in capacitive performance should be related to the formation of a unique nanowire-supported nanoflake array architecture, which controls the agglomeration of nanoflakes, making them fully activated. As a result, the facile in situ fabrication of the hybrid architectural design in this study provides a new approach to fabricate high-performance Ni/Co based hydroxide nanostructure arrays for next-generation energy storage devices.

Identification of De Novo and Rare Inherited Copy Number Variants in Children with Syndromic Congenital Heart Defects.

PubMed

Hussein, Ibtessam R; Bader, Rima S; Chaudhary, Adeel G; Bassiouni, Randa; Alquaiti, Maha; Ashgan, Fai; Schulten, Hans-Juergen; Al Qahtani, Mohammad H

2018-06-01

Congenital heart defects (CHDs) are the most common birth defects in neonatal life. CHDs could be presented as isolated defects or associated with developmental delay (DD) and/or other congenital malformations. A small proportion of cardiac defects are caused by chromosomal abnormalities or single gene defects; however, in a large proportion of cases no genetic diagnosis could be achieved by clinical examination and conventional genetic analysis. The development of genome wide array-Comparative Genomic Hybridization technique (array-CGH) allowed for the detection of cryptic chromosomal imbalances and pathogenic copy number variants (CNVs) not detected by conventional techniques. We investigated 94 patients having CHDs associated with other malformations and/or DD. Clinical examination and Echocardiography was done to all patients to evaluate the type of CHD. To investigate for genome defects we applied high-density array-CGH 2 × 400K (41 patients) and CGH/SNP microarray 2 × 400K (Agilent) for 53 patients. Confirmation of results was done using Fluorescent in situ hybridization (FISH) or qPCR techniques in certain cases. Chromosomal abnormalities such as trisomy 18, 13, 21, microdeletions: del22q11.2, del7q11.23, del18 (p11.32; p11.21), tetrasomy 18p, trisomy 9p, del11q24-q25, add 15p, add(18)(q21.3), and der 9, 15 (q34.2; q11.2) were detected in 21/94 patients (22%) using both conventional cytogenetics methods and array-CGH technique. Cryptic chromosomal anomalies and pathogenic variants were detected in 15/73 (20.5%) cases. CNVs were observed in a large proportion of the studied samples (27/56) (48%). Clustering of variants was observed in chromosome 1p36, 1p21.1, 2q37, 3q29, 5p15, 7p22.3, 8p23, 11p15.5, 14q11.2, 15q11.2, 16p13.3, 16p11.2, 18p11, 21q22, and 22q11.2. CGH/SNP array could detect loss of heterozygosity (LOH) in different chromosomal loci in 10/25 patients. Array-CGH technique allowed for detection of cryptic chromosomal imbalances that could not be detected by conventional cytogenetics methods. CHDs associated with DD/congenital malformations presented with a relatively high rate of cryptic chromosomal abnormalities. Clustering of CNVs in certain genome loci needs further analysis to identify candidate genes that may provide clues for understanding the molecular pathway of cardiac development.

A Study of Phased Array Antennas for NASA's Deep Space Network

NASA Technical Reports Server (NTRS)

Jamnejad, Vahraz; Huang, John; Cesarone, Robert J.

2001-01-01

In this paper we briefly discuss various options but focus on the feasibility of the phased arrays as a viable option for this application. Of particular concern and consideration will be the cost, reliability, and performance compared to the present 70-meter antenna system, particularly the gain/noise temperature levels in the receive mode. Many alternative phased arrays including planar horizontal arrays, hybrid mechanically/electronically steered arrays, phased array of mechanically steered reflectors, multi-faceted planar arrays, phased array-fed lens antennas, and planar reflect-arrays are compared and their viability is assessed. Although they have many advantages including higher reliability, near-instantaneous beam switching or steering capability, the cost of such arrays is presently prohibitive and it is concluded that the only viable array options at the present are the arrays of a few or many small reflectors. The active planar phased arrays, however, may become feasible options in the next decade and can be considered for deployment in smaller configurations as supplementary options.

Hybrid graphene-copper UWB array sensor for brain tumor detection via scattering parameters in microwave detection system

NASA Astrophysics Data System (ADS)

Jamlos, Mohd Aminudin; Ismail, Abdul Hafiizh; Jamlos, Mohd Faizal; Narbudowicz, Adam

2017-01-01

Hybrid graphene-copper ultra-wideband array sensor applied to microwave imaging technique is successfully used in detecting and visualizing tumor inside human brain. The sensor made of graphene coated film for the patch while copper for both the transmission line and parasitic element. The hybrid sensor performance is better than fully copper sensor. Hybrid sensor recorded wider bandwidth of 2.0-10.1 GHz compared with fully copper sensor operated from 2.5 to 10.1 GHz. Higher gain of 3.8-8.5 dB is presented by hybrid sensor, while fully copper sensor stated lower gain ranging from 2.6 to 6.7 dB. Both sensors recorded excellent total efficiency averaged at 97 and 94%, respectively. The sensor used for both transmits equivalent signal and receives backscattering signal from stratified human head model in detecting tumor. Difference in the data of the scattering parameters recorded from the head model with presence and absence of tumor is used as the main data to be further processed in confocal microwave imaging algorithm in generating image. MATLAB software is utilized to analyze S-parameter signals obtained from measurement. Tumor presence is indicated by lower S-parameter values compared to higher values recorded by tumor absence.

Co(OH)2/RGO/NiO sandwich-structured nanotube arrays with special surface and synergistic effects as high-performance positive electrodes for asymmetric supercapacitors

NASA Astrophysics Data System (ADS)

Xu, Han; Zhang, Chi; Zhou, Wen; Li, Gao-Ren

2015-10-01

High power density, high energy density and excellent cycling stability are the main requirements for high-performance supercapacitors (SCs) that will be widely used for portable consumer electronics and hybrid electric vehicles. Here we investigate novel types of hybrid Co(OH)2/reduced graphene oxide (RGO)/NiO sandwich-structured nanotube arrays (SNTAs) as positive electrodes for asymmetric supercapacitors (ASCs). The synthesized Co(OH)2/RGO/NiO SNTAs exhibit a significantly improved specific capacity (~1470 F g-1 at 5 mV s-1) and excellent cycling stability with ~98% Csp retention after 10 000 cycles because of the fast transport and short diffusion paths for electroactive species, the high utilization rate of electrode materials, and special synergistic effects among Co(OH)2, RGO, and NiO. The high-performance ASCs are assembled using Co(OH)2/RGO/NiO SNTAs as positive electrodes and active carbon (AC) as negative electrodes, and they exhibit a high energy density (115 Wh kg-1), a high power density (27.5 kW kg-1) and an excellent cycling stability (less 5% Csp loss after 10 000 cycles). This study shows an important breakthrough in the design and fabrication of multi-walled hybrid nanotube arrays as positive electrodes for ASCs.High power density, high energy density and excellent cycling stability are the main requirements for high-performance supercapacitors (SCs) that will be widely used for portable consumer electronics and hybrid electric vehicles. Here we investigate novel types of hybrid Co(OH)2/reduced graphene oxide (RGO)/NiO sandwich-structured nanotube arrays (SNTAs) as positive electrodes for asymmetric supercapacitors (ASCs). The synthesized Co(OH)2/RGO/NiO SNTAs exhibit a significantly improved specific capacity (~1470 F g-1 at 5 mV s-1) and excellent cycling stability with ~98% Csp retention after 10 000 cycles because of the fast transport and short diffusion paths for electroactive species, the high utilization rate of electrode materials, and special synergistic effects among Co(OH)2, RGO, and NiO. The high-performance ASCs are assembled using Co(OH)2/RGO/NiO SNTAs as positive electrodes and active carbon (AC) as negative electrodes, and they exhibit a high energy density (115 Wh kg-1), a high power density (27.5 kW kg-1) and an excellent cycling stability (less 5% Csp loss after 10 000 cycles). This study shows an important breakthrough in the design and fabrication of multi-walled hybrid nanotube arrays as positive electrodes for ASCs. Electronic supplementary information (ESI) available: SEM images, XPS spectra, equivalent circuit, and CVs. See DOI: 10.1039/c5nr04449a

A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder

PubMed Central

Prasad, Aparna; Merico, Daniele; Thiruvahindrapuram, Bhooma; Wei, John; Lionel, Anath C.; Sato, Daisuke; Rickaby, Jessica; Lu, Chao; Szatmari, Peter; Roberts, Wendy; Fernandez, Bridget A.; Marshall, Christian R.; Hatchwell, Eli; Eis, Peggy S.; Scherer, Stephen W.

2012-01-01

The identification of rare inherited and de novo copy number variations (CNVs) in human subjects has proven a productive approach to highlight risk genes for autism spectrum disorder (ASD). A variety of microarrays are available to detect CNVs, including single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. Here, we examine a cohort of 696 unrelated ASD cases using a high-resolution one-million feature CGH microarray, the majority of which were previously genotyped with SNP arrays. Our objective was to discover new CNVs in ASD cases that were not detected by SNP microarray analysis and to delineate novel ASD risk loci via combined analysis of CGH and SNP array data sets on the ASD cohort and CGH data on an additional 1000 control samples. Of the 615 ASD cases analyzed on both SNP and CGH arrays, we found that 13,572 of 21,346 (64%) of the CNVs were exclusively detected by the CGH array. Several of the CGH-specific CNVs are rare in population frequency and impact previously reported ASD genes (e.g., NRXN1, GRM8, DPYD), as well as novel ASD candidate genes (e.g., CIB2, DAPP1, SAE1), and all were inherited except for a de novo CNV in the GPHN gene. A functional enrichment test of gene-sets in ASD cases over controls revealed nucleotide metabolism as a potential novel pathway involved in ASD, which includes several candidate genes for follow-up (e.g., DPYD, UPB1, UPP1, TYMP). Finally, this extensively phenotyped and genotyped ASD clinical cohort serves as an invaluable resource for the next step of genome sequencing for complete genetic variation detection. PMID:23275889

Evaluation of the X-Linked High-Grade Myopia Locus (MYP1) with Cone Dysfunction and Color Vision Deficiencies

PubMed Central

Metlapally, Ravikanth; Michaelides, Michel; Bulusu, Anuradha; Li, Yi-Ju; Schwartz, Marianne; Rosenberg, Thomas; Hunt, David M.; Moore, Anthony T.; Züchner, Stephan; Rickman, Catherine Bowes; Young, Terri L.

2014-01-01

Purpose X-linked high myopia with mild cone dysfunction and color vision defects has been mapped to chromosome Xq28 (MYP1 locus). CXorf2/TEX28 is a nested, intercalated gene within the red-green opsin cone pigment gene tandem array on Xq28. The authors investigated whether TEX28 gene alterations were associated with the Xq28-linked myopia phenotype. Genomic DNA from five pedigrees (with high myopia and either protanopia or deuteranopia) that mapped to Xq28 were screened for TEX28 copy number variations (CNVs) and sequence variants. Methods To examine for CNVs, ultra-high resolution array-comparative genomic hybridization (array-CGH) assays were performed comparing the subject genomic DNA with control samples (two pairs from two pedigrees). Opsin or TEX28 gene-targeted quantitative real-time gene expression assays (comparative CT method) were performed to validate the array-CGH findings. All exons of TEX28, including intron/exon boundaries, were amplified and sequenced using standard techniques. Results Array-CGH findings revealed predicted duplications in affected patient samples. Although only three copies of TEX28 were previously reported within the opsin array, quantitative real-time analysis of the TEX28 targeted assay of affected male or carrier female individuals in these pedigrees revealed either fewer (one) or more (four or five) copies than did related and control unaffected individuals. Sequence analysis of TEX28 did not reveal any variants associated with the disease status. Conclusions CNVs have been proposed to play a role in disease inheritance and susceptibility as they affect gene dosage. TEX28 gene CNVs appear to be associated with the MYP1 X-linked myopia phenotypes. PMID:19098318

Parallel gene analysis with allele-specific padlock probes and tag microarrays

PubMed Central

Banér, Johan; Isaksson, Anders; Waldenström, Erik; Jarvius, Jonas; Landegren, Ulf; Nilsson, Mats

2003-01-01

Parallel, highly specific analysis methods are required to take advantage of the extensive information about DNA sequence variation and of expressed sequences. We present a scalable laboratory technique suitable to analyze numerous target sequences in multiplexed assays. Sets of padlock probes were applied to analyze single nucleotide variation directly in total genomic DNA or cDNA for parallel genotyping or gene expression analysis. All reacted probes were then co-amplified and identified by hybridization to a standard tag oligonucleotide array. The technique was illustrated by analyzing normal and pathogenic variation within the Wilson disease-related ATP7B gene, both at the level of DNA and RNA, using allele-specific padlock probes. PMID:12930977

A novel protection scheme for a hybrid WDM/TDM PON

NASA Astrophysics Data System (ADS)

Chen, Jiajia; Wosinska, Lena; He, Sailing

2007-11-01

This paper proposes a novel protection scheme based on the cyclic property of an array waveguide grating (AWG) and neighboring connection pattern between two adjacent optical network units (ONUs) for the hybrid WDM/TDM passive optical networks (PONs). Our scheme uses 50% fewer wavelengths while offering one order of magnitude better connection availability than the existing scheme.

Discrimination of portraits using a hybrid parallel joint transform correlator system

NASA Astrophysics Data System (ADS)

Inaba, Rieko; Hashimoto, Asako; Kodate, Kashiko

1999-05-01

A hybrid parallel joint transform correlation system is demonstrated through the introduction of a five-channel binary zone plate array and is applied to the discrimination of portraits for a presumed criminal investigation. In order to improve performance, we adopt pe-processing of images with white area of 20%. Furthermore, we discuss the robustness.

Genome wide analysis in a discordant monozygotic twin with caudal appendage and multiple congenital anomalies.

PubMed

Cogulu, O; Pariltay, E; Koroglu, O A; Aykut, A; Ozyurek, R; Levent, E; Kultursay, N; Ozkinay, F

2013-01-01

Caudal appendage is a rare dysmorphic feature of which etiologic mechanisms are not well understood. Here we report monozygotic (MZ) twin brothers who are discordant for the caudal appendage and multiple congenital anomalies. Twins were the product of a 33 weeks of gestation, monochorionic-diamniotic pregnancy. On admission the proband had micrognathia, beaked nose, hypospadias, caudal appendage and juxtaductal aorta coarctation. At birth, he was small for gestational age and he had transient hypothyroidism which was detected in the newborn period. Karyotype analysis showed 46,XY. Monozygosity was shown by 15 microsatellite markers plus amelogenin (AmpFlSTR Identifiler PCR Amplification Kit, Applied Biosystems). Genome-wide copy number analysis of the twins by DNA-DNA hybridization of whole genomic DNA (NimbleGen Human CGH 385K WG-T v2.0 array) showed a significant difference at two neighboring probes with Log2 ratio: 0.72088 which are located on chromosome 3p12.3. Further analysis by high resolution of chromosome 3 array (Roche NimbleGen Human HG18 CHR3 FT Median Probe Spacing 475 bp) and quantitative PCR analysis did not confirm the deletion.

Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray.

PubMed

Boswell, Mikki G; Wells, Melissa C; Kirk, Lyndsey M; Ju, Zhenlin; Zhang, Ziping; Booth, Rachell E; Walter, Ronald B

2009-03-01

Gene expression profiling using DNA microarray technology is a useful tool for assessing gene transcript level responses after an organism is exposed to environmental stress. Herein, we detail results from studies using an 8 k medaka (Oryzias latipes) microarray to assess modulated gene expression patterns upon hypoxia exposure of the live-bearing aquaria fish, Xiphophorus maculatus. To assess the reproducibility and reliability of using the medaka array in cross-genus hybridization, a two-factor ANOVA analysis of gene expression was employed. The data show the tissue source of the RNA used for array hybridization contributed more to the observed response of modulated gene targets than did the species source of the RNA. In addition, hierarchical clustering via heat map analyses of groupings of tissues and species (Xiphophorus and medaka) suggests that hypoxia induced similar responses in the same tissues from these two diverse aquatic model organisms. Our Xiphophorus results indicate 206 brain, 37 liver, and 925 gill gene targets exhibit hypoxia induced expression changes. Analysis of the Xiphophorus data to determine those features exhibiting a significant (p<0.05)+/-3 fold change produced only two gene targets within brain tissue and 80 features within gill tissue. Of these 82 characterized features, 39 were identified via homology searching (cut-off E-value of 1 x 10(-5)) and placed into one or more biological process gene ontology groups. Among these 39 genes, metabolic energy changes and manipulation was the most affected biological pathway (13 genes).

Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization

PubMed Central

Yang, Wen-Xu; Pan, Hong; Li, Lin; Wu, Hai-Rong; Wang, Song-Tao; Bao, Xin-Hua; Jiang, Yu-Wu; Qi, Yu

2016-01-01

Background: Wolf-Hirschhorn syndrome (WHS) is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the features of Chinese WHS patients. This study aimed to characterize the clinical and molecular cytogenetic features of Chinese WHS patients using the combination of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array CGH). Methods: Clinical information was collected from ten patients with WHS. Genomic DNA was extracted from the peripheral blood of the patients. The deletions were analyzed by MLPA and array CGH. Results: All patients exhibited the core clinical symptoms of WHS, including severe growth delay, a Greek warrior helmet facial appearance, differing degrees of intellectual disability, and epilepsy or electroencephalogram anomalies. The 4p deletions ranged from 2.62 Mb to 17.25 Mb in size and included LETM1, WHSC1, and FGFR3. Conclusions: The combined use of MLPA and array CGH is an effective and specific means to diagnose WHS and allows for the precise identification of the breakpoints and sizes of deletions. The deletion of genes in the WHS candidate region is closely correlated with the core WHS phenotype. PMID:26960370

Arrays of carbon nanofibers as a platform for biosensing at the molecular level and for tissue engineering and implantation.

PubMed

Koehne, Jessica E; Chen, Hua; Cassell, Alan; Liu, Gang-yu; Li, Jun; Meyyappan, M

2009-01-01

Arrays of Carbon nanofibers (CNFs) harness the advantages of individual CNF as well the collective property of assemblies, which made them promising materials in biosensing and tissue engineering or implantation. Here, we report two studies to explore the applications of vertically aligned CNFs. First, a nanoelectrode array (NEA) based on vertically aligned CNFs embedded in SiO(2) is used for ultrasensitive DNA detection. Oligonucleotide probes are selectively functionalized at the open ends of the CNFs and specifically hybridized with oligonucleotide targets. The guanine groups are employed as the signal moieties in the electrochemical measurements. Ru(bpy)(3)(2+) mediator is used to further amplify the guanine oxidation signal. The hybridization of less than approximately 1000 molecules of PCR amplified DNA targets are detected electrochemically by combining the CNF nanoelectrode array with the Ru(bpy)(3)(2+) amplification mechanism. Second, the SiO(2) matrix was etched back to produce needle-like protruding nanoelectrode arrays to be used as cell interfacing fibers for investigating gene transfection, electrical stimulation and detection of cellular processes. Our goal is to take advantage of the nanostructure of CNFs for unconventional biomolecular studies requiring ultrahigh sensitivity, high-degree of miniaturization and selective biofunctionalization.

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform.

PubMed

Salehi, Reza; Tsoi, Stephen C M; Colazo, Marcos G; Ambrose, Divakar J; Robert, Claude; Dyck, Michael K

2017-01-30

Early embryonic loss is a large contributor to infertility in cattle. Moreover, bovine becomes an interesting model to study human preimplantation embryo development due to their similar developmental process. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. Microarray technology allows quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. One of the main decisions that have to be made when planning a microarray experiment is whether to use a one- or two-color approach. Two-color design increases technical replication, minimizes variability, improves sensitivity and accuracy as well as allows having loop designs, defining the common reference samples. Although microarray is a powerful biological tool, there are potential pitfalls that can attenuate its power. Hence, in this technical paper we demonstrate an optimized protocol for RNA extraction, amplification, labeling, hybridization of the labeled amplified RNA to the array, array scanning and data analysis using the two-color analysis strategy.

Novel SNP array analysis and exome sequencing detect a homozygous exon 7 deletion of MEGF10 causing early onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD)

PubMed Central

Pierson, Tyler Mark; Markello, Thomas; Accardi, John; Wolfe, Lynne; Adams, David; Sincan, Murat; Tarazi, Noor M.; Fajardo, Karin Fuentes; Cherukuri, Praveen F.; Bajraktari, Ilda; Meilleur, Katy G.; Donkervoort, Sandra; Jain, Mina; Hu, Ying; Lehky, Tanya J.; Cruz, Pedro; Mullikin, James C.; Bonnemann, Carsten; Gahl, William A.; Boerkoel, Cornelius F.; Tifft, Cynthia J.

2013-01-01

Early-onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD) is a myopathic disorder associated with mutations in MEGF10. By novel analysis of SNP array hybridization and exome sequence coverage, we diagnosed a 10-year old girl with EMARDD following identification of a novel homozygous deletion of exon 7 in MEGF10. In contrast to previously reported EMARDD patients, her weakness was more prominent proximally than distally, and involved her legs more than her arms. MRI of her pelvis and thighs showed muscle atrophy and fatty replacement. Ultrasound of several muscle groups revealed dense homogenous increases in echogenicity. Cloning and sequencing of the deletion breakpoint identified features suggesting the mutation arose by fork stalling and template switching. These findings constitute the first genomic deletion causing EMARDD, expand the clinical phenotype, and provide new insight into the pattern and histology of its muscular pathology. PMID:23453856

Si:Bi switched photoconducttor infrared detector array

NASA Technical Reports Server (NTRS)

Eakin, C. E.

1983-01-01

A multiplexed infrared detector array is described. The small demonstration prototype consisted of two cryogenically cooled, bismuth doped silicon, extrinsic photoconductor pixels multiplexed onto a single output channel using an on focal plane switch integration sampling technique. Noise levels of the order of 400 to 600 rms electrons per sample were demonstrated for this chip and wire hybrid version.

Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes.

PubMed

Di Gregorio, E; Riberi, E; Belligni, E F; Biamino, E; Spielmann, M; Ala, U; Calcia, A; Bagnasco, I; Carli, D; Gai, G; Giordano, M; Guala, A; Keller, R; Mandrile, G; Arduino, C; Maffè, A; Naretto, V G; Sirchia, F; Sorasio, L; Ungari, S; Zonta, A; Zacchetti, G; Talarico, F; Pappi, P; Cavalieri, S; Giorgio, E; Mancini, C; Ferrero, M; Brussino, A; Savin, E; Gandione, M; Pelle, A; Giachino, D F; De Marchi, M; Restagno, G; Provero, P; Cirillo Silengo, M; Grosso, E; Buxbaum, J D; Pasini, B; De Rubeis, S; Brusco, A; Ferrero, G B

2017-10-01

Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). Identification of genomic disorders in DD/ID. We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Solution-based analysis of multiple analytes by a sensor array: toward the development of an electronic tongue

NASA Astrophysics Data System (ADS)

Savoy, Steven M.; Lavigne, John J.; Yoo, J. S.; Wright, John; Rodriguez, Marc; Goodey, Adrian; McDoniel, Bridget; McDevitt, John T.; Anslyn, Eric V.; Shear, Jason B.; Ellington, Andrew D.; Neikirk, Dean P.

1998-12-01

A micromachined sensor array has been developed for the rapid characterization of multi-component mixtures in aqueous media. The sensor functions in a manner analogous to that of the mammalian tongue, using an array composed of individually immobilized polystyrene-polyethylene glycol composite microspheres selectively arranged in micromachined etch cavities localized o n silicon wafers. Sensing occurs via colorimetric or fluorometric changes to indicator molecules that are covalently bound to amine termination sites on the polymeric microspheres. The hybrid micromachined structure has been interfaced directly to a charged-coupled-device that is used for the simultaneous acquisition of the optical data from the individually addressable `taste bud' elements. With the miniature sensor array, acquisition of data streams composed of red, green, and blue color patterns distinctive for the analytes in the solution are rapidly acquired. The unique combination of carefully chosen reporter molecules with water permeable microspheres allows for the simultaneous detection and quantification of a variety of analytes. The fabrication of the sensor structures and the initial colorimetric and fluorescent responses for pH, Ca+2, Ce+3, and sugar are reported. Interface to microfluidic components should also be possible, producing a complete sampling/sensing system.

Evolutionary Conservation of a Coding Function for D4Z4, the Tandem DNA Repeat Mutated in Facioscapulohumeral Muscular Dystrophy

PubMed Central

Clapp, Jannine ; Mitchell, Laura M. ; Bolland, Daniel J. ; Fantes, Judy ; Corcoran, Anne E. ; Scotting, Paul J. ; Armour, John A. L. ; Hewitt, Jane E. 

2007-01-01

Facioscapulohumeral muscular dystrophy (FSHD) is caused by deletions within the polymorphic DNA tandem array D4Z4. Each D4Z4 repeat unit has an open reading frame (ORF), termed “DUX4,” containing two homeobox sequences. Because there has been no evidence of a transcript from the array, these deletions are thought to cause FSHD by a position effect on other genes. Here, we identify D4Z4 homologues in the genomes of rodents, Afrotheria (superorder of elephants and related species), and other species and show that the DUX4 ORF is conserved. Phylogenetic analysis suggests that primate and Afrotherian D4Z4 arrays are orthologous and originated from a retrotransposed copy of an intron-containing DUX gene, DUXC. Reverse-transcriptase polymerase chain reaction and RNA fluorescence and tissue in situ hybridization data indicate transcription of the mouse array. Together with the conservation of the DUX4 ORF for >100 million years, this strongly supports a coding function for D4Z4 and necessitates re-examination of current models of the FSHD disease mechanism. PMID:17668377

Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization

PubMed Central

Sabath, Daniel E.; Bender, Michael A.; Sankaran, Vijay G.; Vamos, Esther; Kentsis, Alex; Yi, Hye-Son; Greisman, Harvey A.

2017-01-01

Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most β-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volume. A small number of deletions accounts for most α-thalassemias; in contrast, there are no predominant HBB deletions causing β-thalassemia. To facilitate the identification and characterization of deletions of the HBA and HBB globin loci, we performed array-based comparative genomic hybridization using a custom oligonucleotide microarray. We accurately mapped the breakpoints of known and previously uncharacterized HBB deletions defining previously uncharacterized deletion breakpoints by PCR amplification and sequencing. The array also successfully identified the common HBA deletions --SEA and --FIL. In summary, comparative genomic hybridization can be used to characterize deletions of the HBA and HBB loci, allowing high-resolution characterization of novel deletions that are not readily detected by PCR-based methods. PMID:26612711

Sparsely-Bonded CMOS Hybrid Imager

NASA Technical Reports Server (NTRS)

Sun, Chao (Inventor); Jones, Todd J. (Inventor); Nikzad, Shouleh (Inventor); Newton, Kenneth W. (Inventor); Cunningham, Thomas J. (Inventor); Hancock, Bruce R. (Inventor); Dickie, Matthew R. (Inventor); Hoenk, Michael E. (Inventor); Wrigley, Christopher J. (Inventor); Pain, Bedabrata (Inventor)

2015-01-01

A method and device for imaging or detecting electromagnetic radiation is provided. A device structure includes a first chip interconnected with a second chip. The first chip includes a detector array, wherein the detector array comprises a plurality of light sensors and one or more transistors. The second chip includes a Read Out Integrated Circuit (ROIC) that reads out, via the transistors, a signal produced by the light sensors. A number of interconnects between the ROIC and the detector array can be less than one per light sensor or pixel.

Analog 65/130 nm CMOS 5 GHz Sub-Arrays with ROACH-2 FPGA Beamformers for Hybrid Aperture-Array Receivers

DTIC Science & Technology

2017-03-20

sub-array, which is based on all-pass filters (APFs) is realized using 130 nm CMOS technology. Approximate- discrete Fourier transform (a-DFT...fixed beams are directed at known directions [9]. The proposed approximate- discrete Fourier transform (a-DFT) based multi-beamformer [9] yields L...to digital conversion daughter board. occurs in the discrete time domain (in ROACH-2 FPGA platform) following signal digitization (see Figs. 1(d) and

Flexural analysis of palm fiber reinforced hybrid polymer matrix composite

NASA Astrophysics Data System (ADS)

Venkatachalam, G.; Gautham Shankar, A.; Raghav, Dasarath; Santhosh Kiran, R.; Mahesh, Bhargav; Kumar, Krishna

2015-07-01

Uncertainty in availability of fossil fuels in the future and global warming increased the need for more environment friendly materials. In this work, an attempt is made to fabricate a hybrid polymer matrix composite. The blend is a mixture of General Purpose Resin and Cashew Nut Shell Liquid, a natural resin extracted from cashew plant. Palm fiber, which has high strength, is used as reinforcement material. The fiber is treated with alkali (NaOH) solution to increase its strength and adhesiveness. Parametric study of flexure strength is carried out by varying alkali concentration, duration of alkali treatment and fiber volume. Taguchi L9 Orthogonal array is followed in the design of experiments procedure for simplification. With the help of ANOVA technique, regression equations are obtained which gives the level of influence of each parameter on the flexure strength of the composite.

A tubular hybrid Halbach/axially-magnetized permanent-magnet linear machine

NASA Astrophysics Data System (ADS)

Sui, Yi; Liu, Yong; Cheng, Luming; Liu, Jiaqi; Zheng, Ping

2017-05-01

A single-phase tubular permanent-magnet linear machine (PMLM) with hybrid Halbach/axially-magnetized PM arrays is proposed for free-piston Stirling power generation system. Machine topology and operating principle are elaborately illustrated. With the sinusoidal speed characteristic of the free-piston Stirling engine considered, the proposed machine is designed and calculated by finite-element analysis (FEA). The main structural parameters, such as outer radius of the mover, radial length of both the axially-magnetized PMs and ferromagnetic poles, axial length of both the middle and end radially-magnetized PMs, etc., are optimized to improve both the force capability and power density. Compared with the conventional PMLMs, the proposed machine features high mass and volume power density, and has the advantages of simple control and low converter cost. The proposed machine topology is applicable to tubular PMLMs with any phases.

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

PubMed Central

Schena, M; Shalon, D; Heller, R; Chai, A; Brown, P O; Davis, R W

1996-01-01

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855227

MECP2 duplications in six patients with complex sex chromosome rearrangements

PubMed Central

Breman, Amy M; Ramocki, Melissa B; Kang, Sung-Hae L; Williams, Misti; Freedenberg, Debra; Patel, Ankita; Bader, Patricia I; Cheung, Sau Wai

2011-01-01

Duplications of the Xq28 chromosome region resulting in functional disomy are associated with a distinct clinical phenotype characterized by infantile hypotonia, severe developmental delay, progressive neurological impairment, absent speech, and proneness to infections. Increased expression of the dosage-sensitive MECP2 gene is considered responsible for the severe neurological impairments observed in affected individuals. Although cytogenetically visible duplications of Xq28 are well documented in the published literature, recent advances using array comparative genomic hybridization (CGH) led to the detection of an increasing number of microduplications spanning MECP2. In rare cases, duplication results from intrachromosomal rearrangement between the X and Y chromosomes. We report six cases with sex chromosome rearrangements involving duplication of MECP2. Cases 1–4 are unbalanced rearrangements between X and Y, resulting in MECP2 duplication. The additional Xq material was translocated to Yp in three cases (cases 1–3), and to the heterochromatic region of Yq12 in one case (case 4). Cases 5 and 6 were identified by array CGH to have a loss in copy number at Xp and a gain in copy number at Xq28 involving the MECP2 gene. In both cases, fluorescent in situ hybridization (FISH) analysis revealed a recombinant X chromosome containing the duplicated material from Xq28 on Xp, resulting from a maternal pericentric inversion. These cases add to a growing number of MECP2 duplications that have been detected by array CGH, while demonstrating the value of confirmatory chromosome and FISH studies for the localization of the duplicated material and the identification of complex rearrangements. PMID:21119712

Microarray slide hybridization using fluorescently labeled cDNA.

PubMed

Ares, Manuel

2014-01-01

Microarray hybridization is used to determine the amount and genomic origins of RNA molecules in an experimental sample. Unlabeled probe sequences for each gene or gene region are printed in an array on the surface of a slide, and fluorescently labeled cDNA derived from the RNA target is hybridized to it. This protocol describes a blocking and hybridization protocol for microarray slides. The blocking step is particular to the chemistry of "CodeLink" slides, but it serves to remind us that almost every kind of microarray has a treatment step that occurs after printing but before hybridization. We recommend making sure of the precise treatment necessary for the particular chemistry used in the slides to be hybridized because the attachment chemistries differ significantly. Hybridization is similar to northern or Southern blots, but on a much smaller scale.

DNA hybridization detection on electrical microarrays using coulostatic pulse technique.

PubMed

Dharuman, V; Nebling, E; Grunwald, T; Albers, J; Blohm, L; Elsholz, B; Wörl, R; Hintsche, R

2006-12-15

We demonstrated a novel application of transient coulostatic pulse technique for the detection of label free DNA hybridization on nm-sized gold interdigitated ultramicroelectrode arrays (Au-IDA) made in silicon technology. The array consists of eight different positions with an Au-IDA pair at each position arranged on the Si-based Biochip. Immobilization of capture probes onto the Au-IDA was accomplished by self-assembling of thiol-modified oligonucleotides. Target hybridization was indicated by a change in the magnitude of the time dependant potential relaxation curve in presence of electroactive Fe(CN)(6)(3-) in the phosphate buffer solution. While complementary DNA hybridization showed 50% increase in the relaxation potential, the non-complementary DNA showed a negligible change. A constant behaviour was noted for all positions. The dsDNA specific intercalating molecule, methylene blue, was found to be enhancing the discrimination effect. The changes in the relaxation potential curves were further corroborated following the ELISA like experiments using ExtraAvidine alkaline phosphatase labelling and redox recycling of para-aminophenol phosphate at IDAs. The coulostatic pulse technique was shown to be useful for identifying DNA sequences from brain tumour gene CK20, human herpes simplex virus, cytomegalovirus, Epstein-Barr virus and M13 phage. Compared to the hybridization of short chain ONTs (27 mers), the hybridization of long chain M13 phage DNA showed three times higher increase in the relaxation curves. The method is fast enough to monitor hybridization interactions in milli or microsecond time scales and is well suitable for miniaturization and integration compared to the common impedance techniques for developing capacitative DNA sensors.

Molecular cytogenetics: an indispensable tool for cancer diagnosis.

PubMed

Wan, Thomas Sk; Ma, Edmond Sk

2012-01-01

Cytogenetic aberrations may escape detection or recognition in traditional karyotyping. The past decade has seen an explosion of methodological advances in molecular cytogenetics technology. These cytogenetics techniques add color to the black and white world of conventional banding. Fluorescence in-situ hybridization (FISH) study has emerged as an indispensable tool for both basic and clinical research, as well as diagnostics, in leukemia and cancers. FISH can be used to identify chromosomal abnormalities through fluorescent labeled DNA probes that target specific DNA sequences. Subsequently, FISH-based tests such as multicolor karyotyping, comparative genomic hybridization (CGH) and array CGH have been used in emerging clinical applications as they enable resolution of complex karyotypic aberrations and whole global scanning of genomic imbalances. More recently, crossspecies array CGH analysis has also been employed in cancer gene identification. The clinical impact of FISH is pivotal, especially in the diagnosis, prognosis and treatment decisions for hematological diseases, all of which facilitate the practice of personalized medicine. This review summarizes the methodology and current utilization of these FISH techniques in unraveling chromosomal changes and highlights how the field is moving away from conventional methods towards molecular cytogenetics approaches. In addition, the potential of the more recently developed FISH tests in contributing information to genetic abnormalities is illustrated.

A novel deletion in the thyrotropin Beta-subunit gene identified by array comparative genomic hybridization analysis causes central congenital hypothyroidism in a boy originating from Turkey.

PubMed

Hermanns, Pia; Couch, Robert; Leonard, Norma; Klotz, Cherise; Pohlenz, Joachim

2014-01-01

Isolated central congenital hypothyroidism (ICCH) is rare but important. Most ICCH patients are diagnosed later, which results in severe growth failure and intellectual disability. We describe a boy with ICCH due to a large homozygous TSHβ gene deletion. A 51-day-old male Turkish infant, whose parents were first cousins, was admitted for evaluation of prolonged jaundice. His clinical appearance was compatible with hypothyroidism. Venous thyrotropin (TSH) was undetectably low, with a subsequent low free T4 and a low free T3, suggestive of central hypothyroidism. Using different PCR protocols, we could not amplify both coding exons of the boy's TSHβ gene, which suggested a deletion. An array comparative genomic hybridization (aCGH) using specific probes around the TSHβ gene locus showed him to be homozygous for a 6-kb deletion spanning all exons and parts of the 5' untranslated region of the gene. Infants who are clinically suspected of having hypothyroidism should be evaluated thoroughly, even if their TSH-based screening result is normal. In cases with ICCH and undetectably low TSH serum concentrations, a TSHβ gene deletion should be considered; aCGH should be performed when gene deletions are suspected. In such cases, PCR-based sequencing techniques give negative results.

Nature-inspired optimization of quasicrystalline arrays and all-dielectric optical filters and metamaterials

NASA Astrophysics Data System (ADS)

Namin, Frank Farhad A.

Quasicrystalline solids were first observed in nature in 1980s. Their lattice geometry is devoid of translational symmetry; however it possesses long-range order as well as certain orders of rotational symmetry forbidden by translational symmetry. Mathematically, such lattices are related to aperiodic tilings. Since their discovery there has been great interest in utilizing aperiodic geometries for a wide variety of electromagnetic (EM) and optical applications. The first thrust of this dissertation addresses applications of quasicrystalline geometries for wideband antenna arrays and plasmonic nano-spherical arrays. The first application considered is the design of suitable antenna arrays for micro-UAV (unmanned aerial vehicle) swarms based on perturbation of certain types of aperiodic tilings. Due to safety reasons and to avoid possible collision between micro-UAVs it is desirable to keep the minimum separation distance between the elements several wavelengths. As a result typical periodic planar arrays are not suitable, since for periodic arrays increasing the minimum element spacing beyond one wavelength will lead to the appearance of grating lobes in the radiation pattern. It will be shown that using this method antenna arrays with very wide bandwidths and low sidelobe levels can be designed. It will also be shown that in conjunction with a phase compensation method these arrays show a large degree of versatility to positional noise. Next aperiodic aggregates of gold nano-spheres are studied. Since traditional unit cell approaches cannot be used for aperiodic geometries, we start be developing new analytical tools for aperiodic arrays. A modified version of generalized Mie theory (GMT) is developed which defines scattering coefficients for aperiodic spherical arrays. Next two specific properties of quasicrystalline gold nano-spherical arrays are considered. The optical response of these arrays can be explained in terms of the grating response of the array (photonic resonance) and the plasmonic response of the spheres (plasmonic resonance). In particular the couplings between the photonic and plasmonic modes are studied. In periodic arrays this coupling leads to the formation of a so called photonic-plasmonic hybrid mode. The formation of hybrid modes is studied in quasicrystalline arrays. Quasicrystalline structures in essence possess several periodicities which in some cases can lead to the formation of multiple hybrid modes with wider bandwidths. It is also demonstrated that the performance of these arrays can be further enhanced by employing a perturbation method. The second property considered is local field enhancements in quasicrystalline arrays of gold nanospheres. It will be shown that despite a considerably smaller filling factor quasicrystalline arrays generate larger local field enhancements which can be even further enhanced by optimally placing perturbing spheres within the prototiles that comprise the aperiodic arrays. The second thrust of research in this dissertation focuses on designing all-dielectric filters and metamaterial coatings for the optical range. In higher frequencies metals tend to have a high loss and thus they are not suitable for many applications. Hence dielectrics are used for applications in optical frequencies. In particular we focus on designing two types of structures. First a near-perfect optical mirror is designed. The design is based on optimizing a subwavelength periodic dielectric grating to obtain appropriate effective parameters that will satisfy the desired perfect mirror condition. Second, a broadband anti-reflective all-dielectric grating with wide field of view is designed. The second design is based on a new computationally efficient genetic algorithm (GA) optimization method which shapes the sidewalls of the grating based on optimizing the roots of polynomial functions.

Array-based comparative genomic hybridization analysis reveals recurrent chromosomal alterations and prognostic parameters in primary cutaneous large B-cell lymphoma.

PubMed

Dijkman, Remco; Tensen, Cornelis P; Jordanova, Ekaterina S; Knijnenburg, Jeroen; Hoefnagel, Juliette J; Mulder, Aat A; Rosenberg, Carla; Raap, Anton K; Willemze, Rein; Szuhai, Károly; Vermeer, Maarten H

2006-01-10

To evaluate the clinical relevance of genomic aberrations in primary cutaneous large B-cell lymphoma (PCLBCL). Skin biopsy samples of 31 patients with a PCLBCL classified as either primary cutaneous follicle center lymphoma (PCFCL; n = 19) or PCLBCL, leg type (n = 12), according to the WHO-European Organisation for Research and Treatment of Cancer (EORTC) classification, were investigated using array-based comparative genomic hybridization, fluorescence in situ hybridization (FISH), and examination of promoter hypermethylation. The most recurrent alterations in PCFCL were high-level DNA amplifications at 2p16.1 (63%) and deletion of chromosome 14q32.33 (68%). FISH analysis confirmed c-REL amplification in patients with gains at 2p16.1. In PCLBCL, leg type, most prominent aberrations were a high-level DNA amplification of 18q21.31-q21.33 (67%), including the BCL-2 and MALT1 genes as confirmed by FISH, and deletions of a small region within 9p21.3 containing the CDKN2A, CDKN2B, and NSG-x genes. Homozygous deletion of 9p21.3 was detected in five of 12 patients with PCLBCL, leg type, but in zero of 19 patients with PCFCL. Complete methylation of the promoter region of the CDKN2A gene was demonstrated in one PCLBCL, leg type, patient with hemizygous deletion, in one patient without deletion, but in zero of 19 patients with PCFCL. Seven of seven PCLBCL, leg type, patients with deletion of 9p21.3 and/or complete methylation of CDKN2A died as a result of their lymphoma. Our results demonstrate prominent differences in chromosomal alterations between PCFCL and PCLBCL, leg type, that support their classification as separate entities within the WHO-EORTC scheme. Inactivation of CDKN2A by either deletion or methylation of its promoter could be an important prognostic parameter for the group of PCLBCL, leg type.

Enhanced Energy Localization in Hyperthermia Treatment Based on Hybrid Electromagnetic and Ultrasonic System: Proof of Concept with Numerical Simulations.

PubMed

Nizam-Uddin, N; Elshafiey, Ibrahim

2017-01-01

This paper proposes a hybrid hyperthermia treatment system, utilizing two noninvasive modalities for treating brain tumors. The proposed system depends on focusing electromagnetic (EM) and ultrasound (US) energies. The EM hyperthermia subsystem enhances energy localization by incorporating a multichannel wideband setting and coherent-phased-array technique. A genetic algorithm based optimization tool is developed to enhance the specific absorption rate (SAR) distribution by reducing hotspots and maximizing energy deposition at tumor regions. The treatment performance is also enhanced by augmenting an ultrasonic subsystem to allow focused energy deposition into deep tumors. The therapeutic faculty of ultrasonic energy is assessed by examining the control of mechanical alignment of transducer array elements. A time reversal (TR) approach is then investigated to address challenges in energy focus in both subsystems. Simulation results of the synergetic effect of both modalities assuming a simplified model of human head phantom demonstrate the feasibility of the proposed hybrid technique as a noninvasive tool for thermal treatment of brain tumors.

Enhanced Energy Localization in Hyperthermia Treatment Based on Hybrid Electromagnetic and Ultrasonic System: Proof of Concept with Numerical Simulations

PubMed Central

Elshafiey, Ibrahim

2017-01-01

This paper proposes a hybrid hyperthermia treatment system, utilizing two noninvasive modalities for treating brain tumors. The proposed system depends on focusing electromagnetic (EM) and ultrasound (US) energies. The EM hyperthermia subsystem enhances energy localization by incorporating a multichannel wideband setting and coherent-phased-array technique. A genetic algorithm based optimization tool is developed to enhance the specific absorption rate (SAR) distribution by reducing hotspots and maximizing energy deposition at tumor regions. The treatment performance is also enhanced by augmenting an ultrasonic subsystem to allow focused energy deposition into deep tumors. The therapeutic faculty of ultrasonic energy is assessed by examining the control of mechanical alignment of transducer array elements. A time reversal (TR) approach is then investigated to address challenges in energy focus in both subsystems. Simulation results of the synergetic effect of both modalities assuming a simplified model of human head phantom demonstrate the feasibility of the proposed hybrid technique as a noninvasive tool for thermal treatment of brain tumors. PMID:28840125

Solid phase sequencing of double-stranded nucleic acids

DOEpatents

Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

2002-01-01

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

Simulation of the hybrid Tunka Advanced International Gamma-ray and Cosmic ray Astrophysics (TAIGA)

NASA Astrophysics Data System (ADS)

Kunnas, M.; Astapov, I.; Barbashina, N.; Beregnev, S.; Bogdanov, A.; Bogorodskii, D.; Boreyko, V.; Brückner, M.; Budnev, N.; Chiavassa, A.; Chvalaev, O.; Dyachok, A.; Epimakhov, S.; Eremin, T.; Gafarov, A.; Gorbunov, N.; Grebenyuk, V.; Gress, O.; Gress, T.; Grinyuk, A.; Grishin, O.; Horns, D.; Ivanova, A.; Karpov, N.; Kalmykov, N.; Kazarina, Y.; Kindin, V.; Kirichkov, N.; Kiryuhin, S.; Kokoulin, R.; Kompaniets, K.; Konstantinov, E.; Korobchenko, A.; Korosteleva, E.; Kozhin, V.; Kuzmichev, L.; Lenok, V.; Lubsandorzhiev, B.; Lubsandorzhiev, N.; Mirgazov, R.; Mirzoyan, R.; Monkhoev, R.; Nachtigall, R.; Pakhorukov, A.; Panasyuk, M.; Pankov, L.; Perevalov, A.; Petrukhin, A.; Platonov, V.; Poleschuk, V.; Popescu, M.; Popova, E.; Porelli, A.; Porokhovoy, S.; Prosin, V.; Ptuskin, V.; Romanov, V.; Rubtsov, G. I.; Müger; Rybov, E.; Samoliga, V.; Satunin, P.; Saunkin, A.; Savinov, V.; Semeney, Yu; Shaibonov (junior, B.; Silaev, A.; Silaev (junior, A.; Skurikhin, A.; Slunecka, M.; Spiering, C.; Sveshnikova, L.; Tabolenko, V.; Tkachenko, A.; Tkachev, L.; Tluczykont, M.; Veslopopov, A.; Veslopopova, E.; Voronov, D.; Wischnewski, R.; Yashin, I.; Yurin, K.; Zagorodnikov, A.; Zirakashvili, V.; Zurbanov, V.

2015-08-01

Up to several 10s of TeV, Imaging Air Cherenkov Telescopes (IACTs) have proven to be the instruments of choice for GeV/TeV gamma-ray astronomy due to their good reconstrucion quality and gamma-hadron separation power. However, sensitive observations at and above 100 TeV require very large effective areas (10 km2 and more), which is difficult and expensive to achieve. The alternative to IACTs are shower front sampling arrays (non-imaging technique or timing-arrays) with a large area and a wide field of view. Such experiments provide good core position, energy and angular resolution, but only poor gamma-hadron separation. Combining both experimental approaches, using the strengths of both techniques, could optimize the sensitivity to the highest energies. The TAIGA project plans to combine the non-imaging HiSCORE [8] array with small (∼10m2) imaging telescopes. This paper covers simulation results of this hybrid approach.

Comparative genomic hybridization.

PubMed

Pinkel, Daniel; Albertson, Donna G

2005-01-01

Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

Quantitative PCR high-resolution melting (qPCR-HRM) curve analysis, a new approach to simultaneously screen point mutations and large rearrangements: application to MLH1 germline mutations in Lynch syndrome.

PubMed

Rouleau, Etienne; Lefol, Cédrick; Bourdon, Violaine; Coulet, Florence; Noguchi, Tetsuro; Soubrier, Florent; Bièche, Ivan; Olschwang, Sylviane; Sobol, Hagay; Lidereau, Rosette

2009-06-01

Several techniques have been developed to screen mismatch repair (MMR) genes for deleterious mutations. Until now, two different techniques were required to screen for both point mutations and large rearrangements. For the first time, we propose a new approach, called "quantitative PCR (qPCR) high-resolution melting (HRM) curve analysis (qPCR-HRM)," which combines qPCR and HRM to obtain a rapid and cost-effective method suitable for testing a large series of samples. We designed PCR amplicons to scan the MLH1 gene using qPCR HRM. Seventy-six patients were fully scanned in replicate, including 14 wild-type patients and 62 patients with known mutations (57 point mutations and five rearrangements). To validate the detected mutations, we used sequencing and/or hybridization on a dedicated MLH1 array-comparative genomic hybridization (array-CGH). All point mutations and rearrangements detected by denaturing high-performance liquid chromatography (dHPLC)+multiplex ligation-dependent probe amplification (MLPA) were successfully detected by qPCR HRM. Three large rearrangements were characterized with the dedicated MLH1 array-CGH. One variant was detected with qPCR HRM in a wild-type patient and was located within the reverse primer. One variant was not detected with qPCR HRM or with dHPLC due to its proximity to a T-stretch. With qPCR HRM, prescreening for point mutations and large rearrangements are performed in one tube and in one step with a single machine, without the need for any automated sequencer in the prescreening process. In replicate, its reagent cost, sensitivity, and specificity are comparable to those of dHPLC+MLPA techniques. However, qPCR HRM outperformed the other techniques in terms of its rapidity and amount of data provided.

Mild Intellectual Disability Associated with a Progeny of Father-Daughter Incest: Genetic and Environmental Considerations

ERIC Educational Resources Information Center

Ansermet, Francois; Lespinasse, James; Gimelli, Stefania; Bena, Frederique; Paoloni-Giacobino, Ariane

2010-01-01

We report the case of a 34-year-old female resulting from a father-daughter sexual abuse and presenting a phenotype of mild intellectual disability with minor dysmorphic features. Karyotyping showed a normal 46, XX constitution. Array-based comparative genomic hybridization (array-CGH) revealed a heterozygote 320kb 6p22.3 microdeletion in the…

A Novel 6.14 Mb Duplication of Chromosome 8p21 in a Patient with Autism and Self Mutilation

ERIC Educational Resources Information Center

Ozgen, Heval M.; Staal, Wouter G.; Barber, John C.; de Jonge, Maretha V.; Eleveld, Marc J.; Beemer, Frits A.; Hochstenbach, Ron; Poot, Martin

2009-01-01

Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders with a strong genetic etiology. Cytogenetic abnormalities have been detected in 5-10% of the patients with autism. In this study, we present the clinical, cytogenetic and array-comparative genomic hybridization (array-CGH) evaluation of a 13-year-old male with severe…

Customization and design of directed self-assembly using hybrid prepatterns

NASA Astrophysics Data System (ADS)

Cheng, Joy; Doerk, Gregory S.; Rettner, Charles T.; Singh, Gurpreet; Tjio, Melia; Truong, Hoa; Arellano, Noel; Balakrishnan, Srinivasan; Brink, Markus; Tsai, Hsinyu; Liu, Chi-Chun; Guillorn, Michael; Sanders, Daniel P.

2015-03-01

Diminishing error tolerance renders the customization of patterns created through directed self-assembly (DSA) extremely challenging at tighter pitch. A self-aligned customization scheme can be achieved using a hybrid prepattern comprising both organic and inorganic regions that serves as a guiding prepattern to direct the self-assembly of the block copolymers as well as a cut mask pattern for the DSA arrays aligned to it. In this paper, chemoepitaxy-based self-aligned customization is demonstrated using two types of organic-inorganic prepatterns. CHEETAH prepattern for "CHemoepitaxy Etch Trim using a self-Aligned Hardmask" of preferential hydrogen silsesquioxane (HSQ, inorganic resist), non-preferential organic underlayer is fabricated using electron beam lithography. Customized trench or hole arrays can be achieved through co-transfer of DSA-formed arrays and CHEETAH prepattern. Herein, we also introduce a tone-reversed version called reverse-CHEETAH (or rCHEETAH) in which customized line segments can be achieved through co-transfer of DSA-formed arrays formed on a prepattern wherein the inorganic HSQ regions are nonpreferential and the organic regions are PMMA preferential. Examples of two-dimensional self-aligned customization including 25nm pitch fin structures and an 8-bar "IBM" illustrate the versatility of this customization scheme using rCHEETAH.

Plasmonic Biosensor Based on Vertical Arrays of Gold Nanoantennas.

PubMed

Klinghammer, Stephanie; Uhlig, Tino; Patrovsky, Fabian; Böhm, Matthias; Schütt, Julian; Pütz, Nils; Baraban, Larysa; Eng, Lukas M; Cuniberti, Gianaurelio

2018-06-25

Implementing large arrays of gold nanowires as functional elements of a plasmonic biosensor is an important task for future medical diagnostic applications. Here we present a microfluidic-channel-integrated sensor for the label-free detection of biomolecules, relying on localized surface plasmon resonances. Large arrays (∼1 cm 2 ) of vertically aligned and densely packed gold nanorods to receive, locally confine, and amplify the external optical signal are used to allow for reliable biosensing. We accomplish this by monitoring the change of the optical nanostructure resonance in the presence of biomolecules within the tight focus area above the nanoantennas, combined with a surface treatment of the nanowires for a specific binding of the target molecules. As a first application, we detect the binding kinetics of two distinct DNA strands as well as the following hybridization of two complementary strands (cDNA) with different lengths (25 and 100 bp). Upon immobilization, a redshift of 1 nm was detected; further backfilling and hybridization led to a peak shift of additional 2 and 5 nm for 25 and 100 bp, respectively. We believe that this work gives deeper insight into the functional understanding and technical implementation of a large array of gold nanowires for future medical applications.

Development of digital sideband separating down-conversion for Yuan-Tseh Lee Array

NASA Astrophysics Data System (ADS)

Li, Chao-Te; Kubo, Derek; Cheng, Jen-Chieh; Kuroda, John; Srinivasan, Ranjani; Ho, Solomon; Guzzino, Kim; Chen, Ming-Tang

2016-07-01

This report presents a down-conversion method involving digital sideband separation for the Yuan-Tseh Lee Array (YTLA) to double the processing bandwidth. The receiver consists of a MMIC HEMT LNA front end operating at a wavelength of 3 mm, and sub-harmonic mixers that output signals at intermediate frequencies (IFs) of 2-18 GHz. The sideband separation scheme involves an analog 90° hybrid followed by two mixers that provide down-conversion of the IF signal to a pair of in-phase (I) and quadrature (Q) signals in baseband. The I and Q baseband signals are digitized using 5 Giga sample per second (Gsps) analog-to-digital converters (ADCs). A second hybrid is digitally implemented using field-programmable gate arrays (FPGAs) to produce two sidebands, each with a bandwidth of 1.6 GHz. The 2 x 1.6 GHz band can be tuned to cover any 3.6 GHz window within the aforementioned IF range of the array. Sideband rejection ratios (SRRs) above 20 dB can be obtained across the 3.6 GHz bandwidth by equalizing the power and delay between the I and Q baseband signals. Furthermore, SRRs above 30 dB can be achieved when calibration is applied.

Dry Process for Manufacturing Hybridized Boron Fiber/Carbon Fiber Thermoplastic Composite Materials from a Solution Coated Precursor

NASA Technical Reports Server (NTRS)

Belvin, Harry L. (Inventor); Cano, Roberto J. (Inventor)

2003-01-01

An apparatus for producing a hybrid boron reinforced polymer matrix composite from precursor tape and a linear array of boron fibers. The boron fibers are applied onto the precursor tapes and the precursor tape processed within a processing component having an impregnation bar assembly. After passing through variable-dimension forming nip-rollers, the precursor tape with the boron fibers becomes a hybrid boron reinforced polymer matrix composite. A driving mechanism is used to pulled the precursor tape through the method and a take-up spool is used to collect the formed hybrid boron reinforced polymer matrix composite.

Design of hybrid two-dimensional and three-dimensional nanostructured arrays for electronic and sensing applications

NASA Astrophysics Data System (ADS)

Ko, Hyunhyub

This dissertation presents the design of organic/inorganic hybrid 2D and 3D nanostructured arrays via controlled assembly of nanoscale building blocks. Two representative nanoscale building blocks such as carbon nanotubes (one-dimension) and metal nanoparticles (zero-dimension) are the core materials for the study of solution-based assembly of nanostructured arrays. The electrical, mechanical, and optical properties of the assembled nanostructure arrays have been investigated for future device applications. We successfully demonstrated the prospective use of assembled nanostructure arrays for electronic and sensing applications by designing flexible carbon nanotube nanomembranes as mechanical sensors, highly-oriented carbon nanotubes arrays for thin-film transistors, and gold nanoparticle arrays for SERS chemical sensors. In first section, we fabricated highly ordered carbon nanotube (CNT) arrays by tilted drop-casting or dip-coating of CNT solution on silicon substrates functionalized with micropatterned self-assembled monolayers. We further exploited the electronic performance of thin-film transistors based on highly-oriented, densely packed CNT micropatterns and showed that the carrier mobility is largely improved compared to randomly oriented CNTs. The prospective use of Raman-active CNTs for potential mechanical sensors has been investigated by studying the mechano-optical properties of flexible carbon nanotube nanomembranes, which contain freely-suspended carbon nanotube array encapsulated into ultrathin (<50 nm) layer-by-layer (LbL) polymer multilayers. In second section, we fabricated 3D nano-canal arrays of porous alumina membranes decorated with gold nanoparticles for prospective SERS sensors. We showed extraordinary SERS enhancement and suggested that the high performance is associated with the combined effects of Raman-active hot spots of nanoparticle aggregates and the optical waveguide properties of nano-canals. We demonstrated the ability of this SERS substrate for trace level sensing of nitroaromatic explosives by detecting down to 100 zeptogram (˜330 molecules) of DNT.

Genotype-phenotype relationships in human red/green color-vision defects: Molecular and psychophysical studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deeb, S.S.; Motulsky, A.G.; Lindsey, D.T.

1992-10-01

The relationship between the molecular structure of the X-linked red and green visual pigment genes and color-vision phenotype as ascertained by anomaloscopy was studied in 64 color-defective males. The great majority of red-green defects were associated with either the deletion of the green-pigment gene or the formation of 5[prime] red-green hybrid genes or 5[prime] green-red hybrid genes. A rapid PCR-based method allowed detection of hybrid genes, including those undetectable by Southern blot analysis, as well as more precise localization of the fusion points in hybrid genes. Protan color-vision defects appeared always associated with 5[prime] red-green hybrid genes. Carriers of singlemore » red-green hybrid genes with fusion in introns 1-4 were protanopes. However, carriers of hybrid genes with red-green fusions in introns 2, 3, or 4 in the presence of additional normal green genes manifested as either protanopes or protanomalous trichromats, with the majority being protanomalous. Deutan defects were associated with green-pigment gene deletions, with 5[prime] green-red hybrid genes, or, rarely, with 5[prime] green-red-green hybrid genes. Complete green-pigment gene deletions or green-red fusions in intron 1 were usually associated with deuteranopia, although the authors unexpectedly found three carriers of a single red-pigment gene without any green-pigment genes to be deuteranomalous trichromats. All but one of the other deuteranomalous subjects had green-red hybrid genes with intron 1, 2, 3, or 4 fusions, as well as several normal green-pigment genes. The one exception had a grossly normal gene array, presumably with a more subtle mutation. Amino acid differences in exon 5 largely determine whether a hybrid gene will be more redlike or more greenlike in phenotype. Various discrepancies as to severity (dichromacy or trichromacy) remain unexplained but may arise because of variability of expression, postreceptoral variation, or both.« less

Research on illumination uniformity of high-power LED array light source

NASA Astrophysics Data System (ADS)

Yu, Xiaolong; Wei, Xueye; Zhang, Ou; Zhang, Xinwei

2018-06-01

Uniform illumination is one of the most important problem that must be solved in the application of high-power LED array. A numerical optimization algorithm, is applied to obtain the best LED array typesetting so that the light intensity of the target surface is evenly distributed. An evaluation function is set up through the standard deviation of the illuminance function, then the particle swarm optimization algorithm is utilized to optimize different arrays. Furthermore, the light intensity distribution is obtained by optical ray tracing method. Finally, a hybrid array is designed and the optical ray tracing method is applied to simulate the array. The simulation results, which is consistent with the traditional theoretical calculation, show that the algorithm introduced in this paper is reasonable and effective.

Solar-to-vehicle (S2V) systems for powering commuters of the future

NASA Astrophysics Data System (ADS)

Birnie, Dunbar P.

Hybrid electric vehicles are growing in popularity and significance in our marketplace as gasoline prices continue to rise. Consumers are also increasingly aware of their carbon "footprint" and seek ways of lowering their carbon dioxide output. Plug-in hybrid and electric vehicles appear to be the next wave in helping transition from a gasoline-based transportation infrastructure to an electric-grid-sourced mode, though most plug-in scenarios ultimately rely on having the electric utilities converted from fossil sources to renewable generation in the long run. At present, one of the key advantages of plug-in hybrid/electric vehicles is that they can be charged at home, at night, when lower off-peak rates could apply. The present analysis considers a further advancement: the impact of daytime recharging using solar arrays located at commuters' work sites. This would convert large parking areas into solar recharge stations for commuters. The solar power would be large enough to supply many commuters' needs. The implications for electric car design in relation to commuter range are discussed in detail.

Unified synchronization criteria in an array of coupled neural networks with hybrid impulses.

PubMed

Wang, Nan; Li, Xuechen; Lu, Jianquan; Alsaadi, Fuad E

2018-05-01

This paper investigates the problem of globally exponential synchronization of coupled neural networks with hybrid impulses. Two new concepts on average impulsive interval and average impulsive gain are proposed to deal with the difficulties coming from hybrid impulses. By employing the Lyapunov method combined with some mathematical analysis, some efficient unified criteria are obtained to guarantee the globally exponential synchronization of impulsive networks. Our method and criteria are proved to be effective for impulsively coupled neural networks simultaneously with synchronizing impulses and desynchronizing impulses, and we do not need to discuss these two kinds of impulses separately. Moreover, by using our average impulsive interval method, we can obtain an interesting and valuable result for the case of average impulsive interval T a =∞. For some sparse impulsive sequences with T a =∞, the impulses can happen for infinite number of times, but they do not have essential influence on the synchronization property of networks. Finally, numerical examples including scale-free networks are exploited to illustrate our theoretical results. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genotype-phenotype relationships in human red/green color-vision defects: molecular and psychophysical studies.

PubMed Central

Deeb, S S; Lindsey, D T; Hibiya, Y; Sanocki, E; Winderickx, J; Teller, D Y; Motulsky, A G

1992-01-01

The relationship between the molecular structure of the X-linked red and green visual pigment genes and color-vision phenotype as ascertained by anomaloscopy was studied in 64 color-defective males. The great majority of red-green defects were associated with either the deletion of the green-pigment gene or the formation of 5' red-green hybrid genes or 5' green-red hybrid genes. A rapid PCR-based method allowed detection of hybrid genes, including those undetectable by Southern blot analysis, as well as more precise localization of the fusion points in hybrid genes. Protan color-vision defects appeared always associated with 5' red-green hybrid genes. Carriers of single red-green hybrid genes with fusion in introns 1-4 were protanopes. However, carriers of hybrid genes with red-green fusions in introns 2, 3, or 4 in the presence of additional normal green genes manifested as either protanopes or protanomalous trichromats, with the majority being protanomalous. Deutan defects were associated with green-pigment gene deletions, with 5' green-red hybrid genes, or, rarely, with 5' green-red-green hybrid genes. Complete green-pigment gene deletions or green-red fusions in intron 1 were usually associated with deuteranopia, although we unexpectedly found three carriers of a single red-pigment gene without any green-pigment genes to be deuteranomalous trichromats. All but one of the other deuteranomalous subjects had green-red hybrid genes with intron 1, 2, 3, or 4 fusions, as well as several normal green-pigment genes. The one exception had a grossly normal gene array, presumably with a more subtle mutation. Amino acid differences in exon 5 largely determine whether a hybrid gene will be more redlike or more greenlike in phenotype. Various discrepancies as to severity (dichromacy or trichromacy) remain unexplained but may arise because of variability of expression, postreceptoral variation, or both. When phenotypic color-vision defects exist, the kind of defect (protan or deutan) can be predicted by molecular analysis. Red-green hybrid genes are probably always associated with protan color-vision defects, while the presence of green-red hybrid genes may not always manifest phenotypically with color-vision defects. Four subjects who were found to have 5' green-red hybrid genes in addition to normal red- and green-pigment genes had normal color vision as determined by anomaloscopy. These were discovered among a group of 129 Caucasian males who had been recruited as volunteers for a vision study.(ABSTRACT TRUNCATED AT 400 WORDS) Images Figure 3 PMID:1415215

Microarray-based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances.

PubMed

Emy Dorfman, Luiza; Leite, Júlio César L; Giugliani, Roberto; Riegel, Mariluce

2015-01-01

To identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array-CGH) in DNA samples of neonates with congenital anomalies of unknown cause from a birth defects monitoring program at a public maternity hospital. A blind genomic analysis was performed retrospectively in 35 stored DNA samples of neonates born between July of 2011 and December of 2012. All potential DNA copy number variations detected (CNVs) were matched with those reported in public genomic databases, and their clinical significance was evaluated. Out of a total of 35 samples tested, 13 genomic imbalances were detected in 12/35 cases (34.3%). In 4/35 cases (11.4%), chromosomal imbalances could be defined as pathogenic; in 5/35 (14.3%) cases, DNA CNVs of uncertain clinical significance were identified; and in 4/35 cases (11.4%), normal variants were detected. Among the four cases with results considered causally related to the clinical findings, two of the four (50%) showed causative alterations already associated with well-defined microdeletion syndromes. In two of the four samples (50%), the chromosomal imbalances found, although predicted as pathogenic, had not been previously associated with recognized clinical entities. Array-CGH analysis allowed for a higher rate of detection of chromosomal anomalies, and this determination is especially valuable in neonates with congenital anomalies of unknown etiology, or in cases in which karyotype results cannot be obtained. Moreover, although the interpretation of the results must be refined, this method is a robust and precise tool that can be used in the first-line investigation of congenital anomalies, and should be considered for prospective/retrospective analyses of DNA samples by birth defect monitoring programs. Copyright © 2014 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Colloidal silica films for high-capacity DNA arrays

NASA Astrophysics Data System (ADS)

Glazer, Marc Irving

The human genome project has greatly expanded the amount of genetic information available to researchers, but before this vast new source of data can be fully utilized, techniques for rapid, large-scale analysis of DNA and RNA must continue to develop. DNA arrays have emerged as a powerful new technology for analyzing genomic samples in a highly parallel format. The detection sensitivity of these arrays is dependent on the quantity and density of immobilized probe molecules. We have investigated substrates with a porous, "three-dimensional" surface layer as a means of increasing the surface area available for the synthesis of oligonucleotide probes, thereby increasing the number of available probes and the amount of detectable bound target. Porous colloidal silica films were created by two techniques. In the first approach, films were deposited by spin-coating silica colloid suspensions onto flat glass substrates, with the pores being formed by the natural voids between the solid particles (typically 23nm pores, 35% porosity). In the second approach, latex particles were co-deposited with the silica and then pyrolyzed, creating films with larger pores (36 nm), higher porosity (65%), and higher surface area. For 0.3 mum films, enhancements of eight to ten-fold and 12- to 14-fold were achieved with the pure silica films and the films "templated" with polymer latex, respectively. In gene expression assays for up to 7,000 genes using complex biological samples, the high-capacity films provided enhanced signals and performed equivalently or better than planar glass on all other functional measures, confirming that colloidal silica films are a promising platform for high-capacity DNA arrays. We have also investigated the kinetics of hybridization on planar glass and high-capacity substrates. Adsorption on planar arrays is similar to ideal Langmuir-type adsorption, although with an "overshoot" at high solution concentration. Hybridization on high-capacity films is controlled by traditional adsorption (ka) and desorption (kd) coefficients, as well as morphology factors and transient binding interactions between the target and probes. The strength of the transient probe/target binding interactions are on the order of 5--7 DNA base pairs, which suggests the formation of nucleation or other metastable complexes, rather than fully-zippered duplexes.

High performance architecture design for large scale fibre-optic sensor arrays using distributed EDFAs and hybrid TDM/DWDM

NASA Astrophysics Data System (ADS)

Liao, Yi; Austin, Ed; Nash, Philip J.; Kingsley, Stuart A.; Richardson, David J.

2013-09-01

A distributed amplified dense wavelength division multiplexing (DWDM) array architecture is presented for interferometric fibre-optic sensor array systems. This architecture employs a distributed erbium-doped fibre amplifier (EDFA) scheme to decrease the array insertion loss, and employs time division multiplexing (TDM) at each wavelength to increase the number of sensors that can be supported. The first experimental demonstration of this system is reported including results which show the potential for multiplexing and interrogating up to 4096 sensors using a single telemetry fibre pair with good system performance. The number can be increased to 8192 by using dual pump sources.

Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme.

PubMed

Cowell, John K; Matsui, Sei-Ichi; Wang, Yong D; LaDuca, Jeffrey; Conroy, Jeffrey; McQuaid, Devin; Nowak, Norma J

2004-05-01

Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.

Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer

PubMed Central

Han, Wonshik; Han, Mi-Ryung; Kang, Jason Jongho; Bae, Ji-Yeon; Lee, Ji Hyun; Bae, Young Ju; Lee, Jeong Eon; Shin, Hyuk-Jae; Hwang, Ki-Tae; Hwang, Sung-Eun; Kim, Sung-Won; Noh, Dong-Young

2006-01-01

Background A considerable proportion of estrogen receptor (ER)-positive breast cancer recurs despite tamoxifen treatment, which is a serious problem commonly encountered in clinical practice. We tried to find novel prognostic markers in this subtype of breast cancer. Methods We performed array comparative genomic hybridization (CGH) with 1,440 human bacterial artificial chromosome (BAC) clones to assess copy number changes in 28 fresh-frozen ER-positive breast cancer tissues. All of the patients included had received at least 1 year of tamoxifen treatment. Nine patients had distant recurrence within 5 years (Recurrence group) of diagnosis and 19 patients were alive without disease at least 5 years after diagnosis (Non-recurrence group). Results Potential prognostic variables were comparable between the two groups. In an unsupervised clustering analysis, samples from each group were well separated. The most common regions of gain in all samples were 1q32.1, 17q23.3, 8q24.11, 17q12-q21.1, and 8p11.21, and the most common regions of loss were 6q14.1-q16.3, 11q21-q24.3, and 13q13.2-q14.3, as called by CGH-Explorer software. The average frequency of copy number changes was similar between the two groups. The most significant chromosomal alterations found more often in the Recurrence group using two different statistical methods were loss of 11p15.5-p15.4, 1p36.33, 11q13.1, and 11p11.2 (adjusted p values <0.001). In subgroup analysis according to lymph node status, loss of 11p15 and 1p36 were found more often in Recurrence group with borderline significance within the lymph node positive patients (adjusted p = 0.052). Conclusion Our array CGH analysis with BAC clones could detect various genomic alterations in ER-positive breast cancers, and Recurrence group samples showed a significantly different pattern of DNA copy number changes than did Non-recurrence group samples. PMID:16608533

Simultaneous monitoring of multiple contrast agents using a hybrid MR-DOT system

NASA Astrophysics Data System (ADS)

Gulsen, Gultekin; Unlu, Mehmet Burcin; Birgul, Ozlem; Nalcioglu, Orhan

2007-02-01

Frequency domain diffuse optical tomography (DOT) is a recently emerging technique that uses arrays of sources and detectors to obtain spatially dependent optical parameters of tissue. Here, we describe the design of a hybrid MR-DOT system for dynamic imaging cancer. The combined system acquires both MR and optical data simultaneously. The performance of the system is tested with phantom and in-vivo studies. Gd-DTPA and ICG was used for this purpose and the enhancement kinetics of both agents are recorded using the hybrid system.

A MEMS Based Hybrid Preconcentrator/Chemiresistor Chemical Sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

HUGHES,ROBERT C.; PATEL,SANJAY V.; MANGINELL,RONALD P.

2000-06-12

A hybrid of a microfabricated planar preconcentrator and a four element chemiresistor array chip has been fabricated and the performance as a chemical sensor system has been demonstrated. The close proximity of the chemiresistor sensor to the preconcentrator absorbent layer allows for fast transfer of the preconcentrated molecules during the heating and resorption step. The hybrid can be used in a conventional flow sampling system for detection of low concentrations of analyte molecules or in a pumpless/valveless mode with a grooved lid to confine the desorption plume from the preconcentrator during heating.

Measurement of horizontal air showers with the Auger Engineering Radio Array

NASA Astrophysics Data System (ADS)

Kambeitz, Olga

2017-03-01

The Auger Engineering Radio Array (AERA), at the Pierre Auger Observatory in Argentina, measures the radio emission of extensive air showers in the 30-80 MHz frequency range. AERA consists of more than 150 antenna stations distributed over 17 km2. Together with the Auger surface detector, the fluorescence detector and the underground muon detector (AMIGA), AERA is able to measure cosmic rays with energies above 1017 eV in a hybrid detection mode. AERA is optimized for the detection of air showers up to 60° zenith angle, however, using the reconstruction of horizontal air showers with the Auger surface array, very inclined showers can also be measured. In this contribution an analysis of the AERA data in the zenith angle range from 62° to 80° will be presented. CoREAS simulations predict radio emission footprints of several km2 for horizontal air showers, which are now confirmed by AERA measurements. This can lead to radio-based composition measurements and energy determination of horizontal showers in the future and the radio detection of neutrino induced showers is possible.

Dose-response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol.

PubMed

Hook, Sharon E; Skillman, Ann D; Small, Jack A; Schultz, Irvin R

2006-07-01

Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss,were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as "expression signatures". Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that different doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose.

Generic Synthesis of Carbon Nanotube Branches on Metal Oxide Arrays Exhibiting Stable High-Rate and Long-Cycle Sodium-Ion Storage.

PubMed

Xia, Xinhui; Chao, Dongliang; Zhang, Yongqi; Zhan, Jiye; Zhong, Yu; Wang, Xiuli; Wang, Yadong; Shen, Ze Xiang; Tu, Jiangping; Fan, Hong Jin

2016-06-01

A new and generic strategy to construct interwoven carbon nanotube (CNT) branches on various metal oxide nanostructure arrays (exemplified by V2 O3 nanoflakes, Co3 O4 nanowires, Co3 O4 -CoTiO3 composite nanotubes, and ZnO microrods), in order to enhance their electrochemical performance, is demonstrated for the first time. In the second part, the V2 O3 /CNTs core/branch composite arrays as the host for Na(+) storage are investigated in detail. This V2 O3 /CNTs hybrid electrode achieves a reversible charge storage capacity of 612 mAh g(-1) at 0.1 A g(-1) and outstanding high-rate cycling stability (a capacity retention of 100% after 6000 cycles at 2 A g(-1) , and 70% after 10 000 cycles at 10 A g(-1) ). Kinetics analysis reveals that the Na(+) storage is a pseudocapacitive dominating process and the CNTs improve the levels of pseudocapacitive energy by providing a conductive network. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

No evidence for mosaic pathogenic copy number variations in cardiac tissue from patients with congenital heart malformations.

PubMed

Winberg, Johanna; Berggren, Håkan; Malm, Torsten; Johansson, Sune; Johansson Ramgren, Jens; Nilsson, Boris; Liedén, Agne; Nordenskjöld, Agneta; Gustavsson, Peter; Nordgren, Ann

2015-03-01

The aim of this study was to investigate if pathogenic copy number variations (CNVs) are present in mosaic form in patients with congenital heart malformations. We have collected cardiac tissue and blood samples from 23 patients with congenital heart malformations that underwent cardiac surgery and screened for mosaic gene dose alterations restricted to cardiac tissue using array comparative genomic hybridization (array CGH). We did not find evidence of CNVs in mosaic form after array CGH analysis. Pathogenic CNVs that were present in both cardiac tissue and blood were detected in 2/23 patients (9%), and in addition we found several constitutional CNVs of unclear clinical significance. This is the first study investigating mosaicism for CNVs in heart tissue compared to peripheral blood and the results do not indicate that pathogenic mosaic copy number changes are common in patients with heart malformations. Importantly, in line with previous studies, our results show that constitutional pathogenic CNVs are important factors contributing to congenital heart malformations. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

A proposed metric for assessing the measurement quality of individual microarrays

PubMed Central

Kim, Kyoungmi; Page, Grier P; Beasley, T Mark; Barnes, Stephen; Scheirer, Katherine E; Allison, David B

2006-01-01

Background High-density microarray technology is increasingly applied to study gene expression levels on a large scale. Microarray experiments rely on several critical steps that may introduce error and uncertainty in analyses. These steps include mRNA sample extraction, amplification and labeling, hybridization, and scanning. In some cases this may be manifested as systematic spatial variation on the surface of microarray in which expression measurements within an individual array may vary as a function of geographic position on the array surface. Results We hypothesized that an index of the degree of spatiality of gene expression measurements associated with their physical geographic locations on an array could indicate the summary of the physical reliability of the microarray. We introduced a novel way to formulate this index using a statistical analysis tool. Our approach regressed gene expression intensity measurements on a polynomial response surface of the microarray's Cartesian coordinates. We demonstrated this method using a fixed model and presented results from real and simulated datasets. Conclusion We demonstrated the potential of such a quantitative metric for assessing the reliability of individual arrays. Moreover, we showed that this procedure can be incorporated into laboratory practice as a means to set quality control specifications and as a tool to determine whether an array has sufficient quality to be retained in terms of spatial correlation of gene expression measurements. PMID:16430768

Molecular Breeding of Rice Restorer Lines and Hybrids for Brown Planthopper (BPH) Resistance Using the Bph14 and Bph15 Genes.

PubMed

Wang, Hongbo; Ye, Shengtuo; Mou, Tongmin

2016-12-01

The development of hybrid rice is a practical approach for increasing rice production. However, the brown planthopper (BPH), Nilaparvata lugens Stål, causes severe yield loss of rice (Oryza sativa L.) and can threaten food security. Therefore, breeding hybrid rice resistant to BPH is the most effective and economical strategy to maintain high and stable production. Fortunately, numerous BPH resistance genes have been identified, and abundant linkage markers are available for molecular marker-assisted selection (MAS) in breeding programs. Hence, we pyramided two BPH resistance genes, Bph14 and Bph15, into a susceptive CMS restorer line Huahui938 and its derived hybrids using MAS to improve the BPH resistance of hybrid rice. Three near-isogenic lines (NILs) with pyramided Bph14 and Bph15 were obtained by molecular marker-assisted backcross (MAB) and phenotypic selection. The genomic components of these NILs were detected using the whole-genome SNP (Single nucleotide polymorphism) array, RICE6K, suggesting that the recurrent parent genome (RPG) recovery of the NILs was 87.88, 87.70 and 86.62 %, respectively. BPH bioassays showed that the improved NILs and their derived hybrids carrying homozygous Bph14 and Bph15 were resistant to BPH. However, the hybrids with heterozygous Bph14 and Bph15 remained susceptible to BPH. The developed NILs showed no significant differences in major agronomic traits and rice qualities compared with the recurrent parent. Moreover, the improved hybrids derived from the NILs exhibited better agronomic performance and rice quality compared with the controls under natural field conditions. This study demonstrates that it is essential to stack Bph14 and Bph15 into both the maternal and paternal parents for developing BPH-resistant hybrid rice varieties. The SNP array with abundant DNA markers is an efficient tool for analyzing the RPG recovery of progenies and can be used to monitor the donor segments in NILs, thus being extremely important for rice molecular breeding.

Superconductivity of a Sn film controlled by an array of Co nanowires

NASA Astrophysics Data System (ADS)

Wei, Zhiyuan; Ye, Zuxin; Rathnayaka, Daya; Lyuksyutov, Igor; Wu, Wenhao; Naugle, Donald

2012-02-01

Superconducting properties of a hybrid structure composed of ferromagnetic Co nanowire arrays and a superconducting Sn film have been investigated. Ordered Co nanowires arrays with 60 nm, 150 nm and 200 nm diameter were electroplated into the pores of self organized anodic aluminum oxide (AAO) membranes. Hysteretic dependence of the Sn film superconducting properties on applied magnetic field and critical current enhancement at moderate fields has been observed. This behavior strongly depends on the ratio of the Sn film thickness to the Co nanowire diameter.

Superconductivity of a Sn film controlled by an array of Co nanowires

NASA Astrophysics Data System (ADS)

Wei, Z.; Ye, Z.; Rathnayaka, K. D. D.; Lyuksyutov, I. F.; Wu, W.; Naugle, D. G.

2012-09-01

Superconducting properties of a hybrid structure composed of ferromagnetic Co nanowire arrays and a superconducting Sn film have been investigated. Ordered Co nanowires arrays with 60 nm, 150 nm and 200 nm diameter were electroplated into the pores of self organized Anodic Aluminum Oxide (AAO) membranes. Hysteretic dependence of the Sn film superconducting properties on applied magnetic field and critical current enhancement at moderate fields has been observed. This behavior strongly depends on the ratio of the Sn film thickness to the Co nanowire diameter.

Lead/acid battery development for heat engine/electric hybrid vehicles. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giner, J.; Taylor, A.H.; Goebel, F.

A program was undertaken to develop a lead/acid battery system for use in a hybrid heat engine/electric vehicle. The basic requirements are that the battery be capable of supplying high-rate power pulses and of accepting high-rate charge pulses, both of short duration. The feasibility of developing a bipolar lead/acid battery system which conforms to these specifications was investigated by using a modular approach to system design. In the preferred design, a vertical array of lead strips placed on either side of each substrate are connected with adjacent strips on the opposite side only over the top of the substrate tomore » provide electrical conduction through the substrate. The following topics are discussed concerning this system: study of electrochemical problem areas relevant to design of a high-power-density battery; corrosion of substrate materials; development and mechanical testing of structures; life testing; design and preliminary cost analysis.« less

Frequency Diverse Array Receiver Architectures

DTIC Science & Technology

2015-06-29

completely associated with FDA, the Hybrid MIMO phased array (HMPAR) concept presented in [18] developed the basic beam patern synthesis theory for an...20], that analyzed beam paterns of chirp waveforms with slightly 6 different starting frequencies. In [21] and [11] they investigated using FDA for...forward-looking radar GMTI benefits. This research showed the ability of the range-dependent energy distribution characteristics of the FDA beam patern

Chemically Designed Metallic/Insulating Hybrid Nanostructures with Silver Nanocrystals for Highly Sensitive Wearable Pressure Sensors.

PubMed

Kim, Haneun; Lee, Seung-Wook; Joh, Hyungmok; Seong, Mingi; Lee, Woo Seok; Kang, Min Su; Pyo, Jun Beom; Oh, Soong Ju

2018-01-10

With the increase in interest in wearable tactile pressure sensors for e-skin, researches to make nanostructures to achieve high sensitivity have been actively conducted. However, limitations such as complex fabrication processes using expensive equipment still exist. Herein, simple lithography-free techniques to develop pyramid-like metal/insulator hybrid nanostructures utilizing nanocrystals (NCs) are demonstrated. Ligand-exchanged and unexchanged silver NC thin films are used as metallic and insulating components, respectively. The interfaces of each NC layer are chemically engineered to create discontinuous insulating layers, i.e., spacers for improved sensitivity, and eventually to realize fully solution-processed pressure sensors. Device performance analysis with structural, chemical, and electronic characterization and conductive atomic force microscopy study reveals that hybrid nanostructure based pressure sensor shows an enhanced sensitivity of higher than 500 kPa -1 , reliability, and low power consumption with a wide range of pressure sensing. Nano-/micro-hierarchical structures are also designed by combining hybrid nanostructures with conventional microstructures, exhibiting further enhanced sensing range and achieving a record sensitivity of 2.72 × 10 4 kPa -1 . Finally, all-solution-processed pressure sensor arrays with high pixel density, capable of detecting delicate signals with high spatial selectivity much better than the human tactile threshold, are introduced.

Hybrid antenna arrays with non-uniform Electromagnetic Band Gap lattices for wireless communication networks

NASA Astrophysics Data System (ADS)

Mourtzios, Ch.; Siakavara, K.

2015-08-01

A method to design hybrid antenna configurations with very low profile, suitable for smart and Multiple Input-Multiple Output antenna systems is proposed. The antennas are incorporated with novel Electromagnetic Band Gap (EBG) surfaces with non-similar cells. These non-uniform EBG surfaces have been properly designed to cause focusing, of the incident waves, thus enhancing the characteristics of operation of antenna elements positioned in close proximity to the surface and also to increase the isolation between them. Theoretical analysis of the reflection mechanism of this type of lattices as well as the prediction of the resulting performance of the antenna is presented. All these considerations are validated with implementation and simulation of the hybrid structures inside the Universal Mobile Telecommunications System frequency band. The results show that increment of the gain and isolation between the antenna elements can be obtained. Moreover, results for the correlation coefficient between the elements, for Gaussian distribution of the incoming waves have been received and the tolerance of the antennas to the variation of the polarization characteristics of the incoming waves has been investigated. A Genetic Algorithm has been constructed and applied to find the proper geometry of the hybrid antennas in order the correlation coefficient to be minimized and get almost independent from the polarization of incident waves.

Fγ: A new observable for photon-hadron discrimination in hybrid air shower events

NASA Astrophysics Data System (ADS)

Niechciol, M.; Risse, M.; Ruehl, P.; Settimo, M.; Younk, P. W.; Yushkov, A.

2018-01-01

To search for ultra-high-energy photons in primary cosmic rays, air shower observables are needed that allow a good separation between primary photons and primary hadrons. We present a new observable, Fγ, which can be extracted from ground-array data in hybrid events, where simultaneous measurements of the longitudinal and the lateral shower profile are performed. The observable is based on a template fit to the lateral distribution measured by the ground array with the template taking into account the complementary information from the measurement of the longitudinal profile, i.e. the primary energy and the geometry of the shower. Fγ shows a very good photon-hadron separation, which is even superior to the separation given by the well-known Xmax observable (the atmospheric depth of the shower maximum). At energies around 1 EeV (10 EeV), Fγ provides a background rejection better than 97.8 % (99.9 %) at a signal efficiency of 50 %. Advantages of the observable Fγ are its technical stability with respect to irregularities in the ground array (i.e. missing or temporarily non-operating stations) and that it can be applied over the full energy range accessible to the air shower detector, down to its threshold energy. Furthermore, Fγ complements nicely to Xmax such that both observables can well be combined to achieve an even better discrimination power, exploiting the rich information available in hybrid events.

Co(OH)2/RGO/NiO sandwich-structured nanotube arrays with special surface and synergistic effects as high-performance positive electrodes for asymmetric supercapacitors.

PubMed

Xu, Han; Zhang, Chi; Zhou, Wen; Li, Gao-Ren

2015-10-28

High power density, high energy density and excellent cycling stability are the main requirements for high-performance supercapacitors (SCs) that will be widely used for portable consumer electronics and hybrid electric vehicles. Here we investigate novel types of hybrid Co(OH)2/reduced graphene oxide (RGO)/NiO sandwich-structured nanotube arrays (SNTAs) as positive electrodes for asymmetric supercapacitors (ASCs). The synthesized Co(OH)2/RGO/NiO SNTAs exhibit a significantly improved specific capacity (∼1470 F g(-1) at 5 mV s(-1)) and excellent cycling stability with ∼98% Csp retention after 10 000 cycles because of the fast transport and short diffusion paths for electroactive species, the high utilization rate of electrode materials, and special synergistic effects among Co(OH)2, RGO, and NiO. The high-performance ASCs are assembled using Co(OH)2/RGO/NiO SNTAs as positive electrodes and active carbon (AC) as negative electrodes, and they exhibit a high energy density (115 Wh kg(-1)), a high power density (27.5 kW kg(-1)) and an excellent cycling stability (less 5% Csp loss after 10 000 cycles). This study shows an important breakthrough in the design and fabrication of multi-walled hybrid nanotube arrays as positive electrodes for ASCs.

Light Trapping with Silicon Light Funnel Arrays

PubMed Central

Nissan, Yuval; Gabay, Tamir; Shalev, Gil

2018-01-01

Silicon light funnels are three-dimensional subwavelength structures in the shape of inverted cones with respect to the incoming illumination. Light funnel (LF) arrays can serve as efficient absorbing layers on account of their light trapping capabilities, which are associated with the presence of high-density complex Mie modes. Specifically, light funnel arrays exhibit broadband absorption enhancement of the solar spectrum. In the current study, we numerically explore the optical coupling between surface light funnel arrays and the underlying substrates. We show that the absorption in the LF array-substrate complex is higher than the absorption in LF arrays of the same height (~10% increase). This, we suggest, implies that a LF array serves as an efficient surface element that imparts additional momentum components to the impinging illumination, and hence optically excites the substrate by near-field light concentration, excitation of traveling guided modes in the substrate, and mode hybridization. PMID:29562685

Six consecutive false positive cases from cell-free fetal DNA testing in a single referring centre

PubMed Central

Dugo, Nella; Padula, Francesco; Mobili, Luisa; Brizzi, Cristiana; D’Emidio, Laura; Cignini, Pietro; Mesoraca, Alvaro; Bizzoco, Domenico; Cima, Antonella; Giorlandino, Claudio

2014-01-01

Introduction recent studies have proposed the introduction of cell-free fetal DNA testing (NIPT-Non Invasive Prenatal Testing) in routine clinical practice emphasizing its high sensibility and specificity. In any case, false positive and false negative findings may result from placental mosaicism, because cell-free fetal DNA originates mainly from placenta. Case we report six cases of women who underwent chorionic villus sampling (CVS) or amniocentesis to confirm the results from NIPT: two Turner syndromes, two Triple X, one Patau syndrome, one Edward syndrome. Results using classic cytogenetic analysis and, also, Array - Comparative Genomic Hybridization (Array CGH) the karyotype of all 5 fetuses was found to be normal. Conclusion results from NIPT must always be confirmed by invasive prenatal diagnosis. It is mandatory to inform the patient that the CVS and amniocentesis still represent the only form of prenatal diagnostic test available. PMID:25332757

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.

PubMed

Zhao, Min; Wang, Qingguo; Wang, Quan; Jia, Peilin; Zhao, Zhongming

2013-01-01

Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome hybridization (arrayCGH) or genotyping arrays have been standard technologies to detect large regions subject to copy number changes in genomes until most recently high-resolution sequence data can be analyzed by next-generation sequencing (NGS). During the last several years, NGS-based analysis has been widely applied to identify CNVs in both healthy and diseased individuals. Correspondingly, the strong demand for NGS-based CNV analyses has fuelled development of numerous computational methods and tools for CNV detection. In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data. Additionally, we discuss their strengths and weaknesses and suggest directions for future development.

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

PubMed Central

2013-01-01

Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome hybridization (arrayCGH) or genotyping arrays have been standard technologies to detect large regions subject to copy number changes in genomes until most recently high-resolution sequence data can be analyzed by next-generation sequencing (NGS). During the last several years, NGS-based analysis has been widely applied to identify CNVs in both healthy and diseased individuals. Correspondingly, the strong demand for NGS-based CNV analyses has fuelled development of numerous computational methods and tools for CNV detection. In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data. Additionally, we discuss their strengths and weaknesses and suggest directions for future development. PMID:24564169

Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors

PubMed Central

Brunner, Clemens; Brunner-Herglotz, Bettina; Ziegler, Andrea; Frech, Christian; Amann, Gabriele; Ladenstein, Ruth; Ambros, Inge M.; Ambros, Peter F.

2016-01-01

Introduction Tumor touch imprints (TTIs) are routinely used for the molecular diagnosis of neuroblastomas by interphase fluorescence in-situ hybridization (I-FISH). However, in order to facilitate a comprehensive, up-to-date molecular diagnosis of neuroblastomas and to identify new markers to refine risk and therapy stratification methods, whole genome approaches are needed. We examined the applicability of an ultra-high density SNP array platform that identifies copy number changes of varying sizes down to a few exons for the detection of genomic changes in tumor DNA extracted from TTIs. Material and Methods DNAs were extracted from TTIs of 46 neuroblastoma and 4 other pediatric tumors. The DNAs were analyzed on the Cytoscan HD SNP array platform to evaluate numerical and structural genomic aberrations. The quality of the data obtained from TTIs was compared to that from randomly chosen fresh or fresh frozen solid tumors (n = 212) and I-FISH validation was performed. Results SNP array profiles were obtained from 48 (out of 50) TTI DNAs of which 47 showed genomic aberrations. The high marker density allowed for single gene analysis, e.g. loss of nine exons in the ATRX gene and the visualization of chromothripsis. Data quality was comparable to fresh or fresh frozen tumor SNP profiles. SNP array results were confirmed by I-FISH. Conclusion TTIs are an excellent source for SNP array processing with the advantage of simple handling, distribution and storage of tumor tissue on glass slides. The minimal amount of tumor tissue needed to analyze whole genomes makes TTIs an economic surrogate source in the molecular diagnostic work up of tumor samples. PMID:27560999

High-density fiber optic biosensor arrays

NASA Astrophysics Data System (ADS)

Epstein, Jason R.; Walt, David R.

2002-02-01

Novel approaches are required to coordinate the immense amounts of information derived from diverse genomes. This concept has influenced the expanded role of high-throughput DNA detection and analysis in the biological sciences. A high-density fiber optic DNA biosensor was developed consisting of oligonucleotide-functionalized, 3.1 mm diameter microspheres deposited into the etched wells on the distal face of a 500 micrometers imaging fiber bundle. Imaging fiber bundles containing thousands of optical fibers, each associated with a unique oligonucleotide probe sequence, were the foundation for an optically connected, individually addressable DNA detection platform. Different oligonucleotide-functionalized microspheres were combined in a stock solution, and randomly dispersed into the etched wells. Microsphere positions were registered from optical dyes incorporated onto the microspheres. The distribution process provided an inherent redundancy that increases the signal-to-noise ratio as the square root of the number of sensors examined. The representative amount of each probe-type in the array was dependent on their initial stock solution concentration, and as other sequences of interest arise, new microsphere elements can be added to arrays without altering the existing detection capabilities. The oligonucleotide probe sequences hybridize to fluorescently-labeled, complementary DNA target solutions. Fiber optic DNA microarray research has included DNA-protein interaction profiles, microbial strain differentiation, non-labeled target interrogation with molecular beacons, and single cell-based assays. This biosensor array is proficient in DNA detection linked to specific disease states, single nucleotide polymorphism (SNP's) discrimination, and gene expression analysis. This array platform permits multiple detection formats, provides smaller feature sizes, and enables sensor design flexibility. High-density fiber optic microarray biosensors provide a fast, reversible format with the detection limit of a few hundred molecules.

1-D Metal Nanobead Arrays within Encapsulated Nanowires via a Red-Ox-Induced Dewetting: Mechanism Study by Atom-Probe Tomography.

PubMed

Sun, Zhiyuan; Tzaguy, Avra; Hazut, Ori; Lauhon, Lincoln J; Yerushalmi, Roie; Seidman, David N

2017-12-13

Metal nanoparticle arrays are excellent candidates for a variety of applications due to the versatility of their morphology and structure at the nanoscale. Bottom-up self-assembly of metal nanoparticles provides an important complementary alternative to the traditional top-down lithography method and makes it possible to assemble structures with higher-order complexity, for example, nanospheres, nanocubes, and core-shell nanostructures. Here we present a mechanism study of the self-assembly process of 1-D noble metal nanoparticles arrays, composed of Au, Ag, and AuAg alloy nanoparticles. These are prepared within an encapsulated germanium nanowire, obtained by the oxidation of a metal-germanium nanowire hybrid structure. The resulting structure is a 1-D array of equidistant metal nanoparticles with the same diameter, the so-called nanobead (NB) array structure. Atom-probe tomography and transmission electron microscopy were utilized to investigate the details of the morphological and chemical evolution during the oxidation of the encapsulated metal-germanium nanowire hybrid-structures. The self-assembly of nanoparticles relies on the formation of a metal-germanium liquid alloy and the migration of the liquid alloy into the nanowire, followed by dewetting of the liquid during shape-confined oxidation where the liquid column breaks-up into nanoparticles due to the Plateau-Rayleigh instability. Our results demonstrate that the encapsulating oxide layer serves as a structural scaffold, retaining the overall shape during the eutectic liquid formation and demonstrates the relationship between the oxide mechanical properties and the final structural characteristics of the 1-D arrays. The mechanistic details revealed here provide a versatile tool-box for the bottom-up fabrication of 1-D arrays nanopatterning that can be modified for multiple applications according to the RedOx properties of the material system components.

Paper Capillary Enables Effective Sampling for Microfluidic Paper Analytical Devices.

PubMed

Shangguan, Jin-Wen; Liu, Yu; Wang, Sha; Hou, Yun-Xuan; Xu, Bi-Yi; Xu, Jing-Juan; Chen, Hong-Yuan

2018-06-06

Paper capillary is introduced to enable effective sampling on microfluidic paper analytical devices. By coupling mac-roscale capillary force of paper capillary and microscale capillary forces of native paper, fluid transport can be flexibly tailored with proper design. Subsequently, a hybrid-fluid-mode paper capillary device was proposed, which enables fast and reliable sampling in an arrayed form, with less surface adsorption and bias for different components. The resulting device thus well supports high throughput, quantitative, and repeatable assays all by hands operation. With all these merits, multiplex analysis of ions, proteins, and microbe have all been realized on this platform, which has paved the way to level-up analysis on μPADs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farahani, Poupak; Chiu, Sally; Bowlus, Christopher L.

Obesity is a complex disease. To date, over 100 chromosomal loci for body weight, body fat, regional white adipose tissue weight, and other obesity-related traits have been identified in humans and in animal models. For most loci, the underlying genes are not yet identified; some of these chromosomal loci will be alleles of known obesity genes, whereas many will represent alleles of unknown genes. Microarray analysis allows simultaneous multiple gene and pathway discovery. cDNA and oligonucleotide arrays are commonly used to identify differentially expressed genes by surveys of large numbers of known and unnamed genes. Two papers previously identified genesmore » differentially expressed in adipose tissue of mouse models of obesity and diabetes by analysis of hybridization to Affymetrix oligonucleotide chips.« less

Llamas: Large-area microphone arrays and sensing systems

NASA Astrophysics Data System (ADS)

Sanz-Robinson, Josue

Large-area electronics (LAE) provides a platform to build sensing systems, based on distributing large numbers of densely spaced sensors over a physically-expansive space. Due to their flexible, "wallpaper-like" form factor, these systems can be seamlessly deployed in everyday spaces. They go beyond just supplying sensor readings, but rather they aim to transform the wealth of data from these sensors into actionable inferences about our physical environment. This requires vertically integrated systems that span the entirety of the signal processing chain, including transducers and devices, circuits, and signal processing algorithms. To this end we develop hybrid LAE / CMOS systems, which exploit the complementary strengths of LAE, enabling spatially distributed sensors, and CMOS ICs, providing computational capacity for signal processing. To explore the development of hybrid sensing systems, based on vertical integration across the signal processing chain, we focus on two main drivers: (1) thin-film diodes, and (2) microphone arrays for blind source separation: 1) Thin-film diodes are a key building block for many applications, such as RFID tags or power transfer over non-contact inductive links, which require rectifiers for AC-to-DC conversion. We developed hybrid amorphous / nanocrystalline silicon diodes, which are fabricated at low temperatures (<200 °C) to be compatible with processing on plastic, and have high current densities (5 A/cm2 at 1 V) and high frequency operation (cutoff frequency of 110 MHz). 2) We designed a system for separating the voices of multiple simultaneous speakers, which can ultimately be fed to a voice-command recognition engine for controlling electronic systems. On a device level, we developed flexible PVDF microphones, which were used to create a large-area microphone array. On a circuit level we developed localized a-Si TFT amplifiers, and a custom CMOS IC, for system control, sensor readout and digitization. On a signal processing level we developed an algorithm for blind source separation in a real, reverberant room, based on beamforming and binary masking. It requires no knowledge about the location of the speakers or microphones. Instead, it uses cluster analysis techniques to determine the time delays for beamforming; thus, adapting to the unique acoustic environment of the room.

Customized Oligonucleotide Array-Based Comparative Genomic Hybridization as a Clinical Assay for Genomic Profiling of Chronic Lymphocytic Leukemia

PubMed Central

Sargent, Rachel; Jones, Dan; Abruzzo, Lynne V.; Yao, Hui; Bonderover, Jaime; Cisneros, Marissa; Wierda, William G.; Keating, Michael J.; Luthra, Rajyalakshmi

2009-01-01

Chromosome gains and losses used for risk stratification in chronic lymphocytic leukemia (CLL) are commonly assessed by multiprobe fluorescence in situ hybridization (FISH) studies. We designed and validated a customized array-comparative genomic hybridization (aCGH) platform as a clinical assay for CLL genomic profiling. A 60-mer, 44,000-probe oligonucleotide array with a 50-kb average spatial resolution was augmented with high-density probe tiling at loci that are frequently aberrant in CLL. Aberrations identified by aCGH were compared with those identified by a FISH panel, including locus-specific probes to ATM (11q22.3), the centromeric region of chromosome 12 (12p11.1–q11), D13S319 (13q14.3), LAMP1 (13q34), and TP53 (17p13.1). In 100 CLL samples, aCGH/FISH concordance was seen for 89% of FISH-called aberrations at the ATM (n = 18), D13S319 (n = 42), LAMP (n = 12), and TP53 (n = 22) loci and for chromosome 12 (n = 14). Eighty-four percentage of FISH/aCGH discordant calls were in samples either at or below the limit of aCGH sensitivity (10% to 25% FISH aberration-containing cells). Therefore, aCGH profiling is a feasible routine clinical test with comparable results to multiprobe FISH studies; however, it may be less sensitive than FISH in cases with low-level aberrations. Further, a customized array design can provide comprehensive genomic profiling with additional accuracy in both identifying and defining the extent of small aberrations at target loci. PMID:19074592

Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing

DOE PAGES

Chong, Xinyuan; Kim, Ki-joong; Zhang, Yujing; ...

2017-06-06

In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal–organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO 2) with high capacity. Additionally, experimental results show that this hybrid plasmonic–MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. Lastly, the demonstration of infrared absorption spectroscopy of CO 2 using the hybrid plasmonic–MOF device proves amore » promising strategy for future on-chip gas sensing with ultra-compact size.« less

Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chong, Xinyuan; Kim, Ki-joong; Zhang, Yujing

In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal–organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO 2) with high capacity. Additionally, experimental results show that this hybrid plasmonic–MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. Lastly, the demonstration of infrared absorption spectroscopy of CO 2 using the hybrid plasmonic–MOF device proves amore » promising strategy for future on-chip gas sensing with ultra-compact size.« less

Surface-enhanced localized surface plasmon resonance biosensing of avian influenza DNA hybridization using subwavelength metallic nanoarrays

NASA Astrophysics Data System (ADS)

Kim, Shin Ae; Byun, Kyung Min; Kim, Kyujung; Jang, Sung Min; Ma, Kyungjae; Oh, Youngjin; Kim, Donghyun; Kim, Sung Guk; Shuler, Michael L.; Kim, Sung June

2010-09-01

We demonstrated enhanced localized surface plasmon resonance (SPR) biosensing based on subwavelength gold nanoarrays built on a thin gold film. Arrays of nanogratings (1D) and nanoholes (2D) with a period of 200 nm were fabricated by electron-beam lithography and used for the detection of avian influenza DNA hybridization. Experimental results showed that both nanoarrays provided significant sensitivity improvement and, especially, 1D nanogratings exhibited higher SPR signal amplification compared with 2D nanohole arrays. The sensitivity enhancement is associated with changes in surface-limited reaction area and strong interactions between bound molecules and localized plasmon fields. Our approach is expected to improve both the sensitivity and sensing resolution and can be applicable to label-free detection of DNA without amplification by polymerase chain reaction.

High-resolution array comparative genomic hybridization analysis of human bronchial and salivary adenoid cystic carcinoma.

PubMed

Bernheim, Alain; Toujani, Saloua; Saulnier, Patrick; Robert, Thomas; Casiraghi, Odile; Validire, Pierre; Temam, Stéphane; Menard, Philippe; Dessen, Philippe; Fouret, Pierre

2008-05-01

Adenoid cystic carcinoma (ACC) is a rare but distinctive tumor. Oligonucleotide array comparative genomic hybridization has been applied for cataloging genomic copy number alterations (CNAs) in 17 frozen salivary or bronchial tumors. Only four whole chromosome CNAs were found, and most cases had 2-4 segmental CNAs. No high level amplification was observed. There were recurrent gains at 7p15.2, 17q21-25, and 22q11-13, and recurrent losses at 1p35, 6q22-25, 8q12-13, 9p21, 12q12-13, and 17p11-13. The minimal region of gain at 7p15.2 contained the HOXA cluster. The minimal common regions of deletions contained the CDKN2A/CDKN2B, TP53, and LIMA1 tumor suppressor genes. The recurrent deletion at 8q12.3-13.1 contained no straightforward tumor suppressor gene, but the MIRN124A2 microRNA gene, whose product regulates MMP2 and CDK6. Among unique CNAs, gains harbored CCND1, KIT/PDGFRA/KDR, MDM2, and JAK2. The CNAs involving CCND1, MDM2, KIT, CDKN2A/2B, and TP53 were validated by FISH and/or multiplex ligation-dependent probe amplification. Although most tumors overexpressed cyclin D1 compared with surrounding glands, the only case to overexpress MDM2 had the corresponding CNA. In conclusion, our report suggests that ACC is characterized by a relatively low level of structural complexity. Array CGH and immunohistochemical data implicate MDM2 as the oncogene targeted at 12q15. The gain at 4q12 warrants further exploration as it contains a cluster of receptor kinase genes (KIT/PDGFRA/KDR), whose products can be responsive to specific therapies.

Control Algorithms Charge Batteries Faster

NASA Technical Reports Server (NTRS)

2012-01-01

On March 29, 2011, NASA s Mercury Surface, Space Environment, Geochemistry and Ranging (MESSENGER) spacecraft beamed a milestone image to Earth: the first photo of Mercury taken from orbit around the solar system s innermost planet. (MESSENGER is also the first spacecraft to orbit Mercury.) Like most of NASA s deep space probes, MESSENGER is enabled by a complex power system that allows its science instruments and communications to function continuously as it travels millions of miles from Earth. "Typically, there isn't one particular power source that can support the entire mission," says Linda Taylor, electrical engineer in Glenn Research Center s Power Systems Analysis Branch. "If you have solar arrays and you are in orbit, at some point you re going to be in eclipse." Because of this, Taylor explains, spacecraft like MESSENGER feature hybrid power systems. MESSENGER is powered by a two-panel solar array coupled with a nickel hydrogen battery. The solar arrays provide energy to the probe and charge the battery; when the spacecraft s orbit carries it behind Mercury and out of the Sun s light, the spacecraft switches to battery power to continue operations. Typically, hybrid systems with multiple power inputs and a battery acting alternately as storage and a power source require multiple converters to handle the power flow between the devices, Taylor says. (Power converters change the qualities of electrical energy, such as from alternating current to direct current, or between different levels of voltage or frequency.) This contributes to a pair of major concerns for spacecraft design. "Weight and size are big drivers for any space application," Taylor says, noting that every pound added to a space vehicle incurs significant costs. For an innovative solution to managing power flows in a lightweight, cost-effective manner, NASA turned to a private industry partner.

Transcriptomic data analysis and differential gene expression of antioxidant pathways in king penguin juveniles (Aptenodytes patagonicus) before and after acclimatization to marine life.

PubMed

Rey, Benjamin; Dégletagne, Cyril; Duchamp, Claude

2016-12-01

In this article, we present differentially expressed gene profiles in the pectoralis muscle of wild juvenile king penguins that were either naturally acclimated to cold marine environment or experimentally immersed in cold water as compared with penguin juveniles that never experienced cold water immersion. Transcriptomic data were obtained by hybridizing penguins total cDNA on Affymetrix GeneChip Chicken Genome arrays and analyzed using maxRS algorithm , " Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays " (Dégletagne et al., 2010) [1] . We focused on genes involved in multiple antioxidant pathways. For better clarity, these differentially expressed genes were clustered into six functional groups according to their role in controlling redox homeostasis. The data are related to a comprehensive research study on the ontogeny of antioxidant functions in king penguins, "Hormetic response triggers multifaceted anti-oxidant strategies in immature king penguins (Aptenodytes patagonicus)" (Rey et al., 2016) [2] . The raw microarray dataset supporting the present analyses has been deposited at the Gene Expression Omnibus (GEO) repository under accessions GEO: GSE17725 and GEO: GSE82344.

Array-based comparative genomic hybridization in 190 Korean patients with developmental delay and/or intellectual disability: a single tertiary care university center study.

PubMed

Lee, Cha Gon; Park, Sang-Jin; Yun, Jun-No; Ko, Jung Min; Kim, Hyon-Ju; Yim, Shin-Young; Sohn, Young Bae

2013-11-01

This study analyzed and evaluated the demographic, clinical, and cytogenetic data [G-banded karyotyping and array-based comparative genomic hybridization (array CGH)] of patients with unexplained developmental delay or intellectual disability at a single Korean institution. We collected clinical and cytogenetic data based on retrospective charts at Ajou University Medical Center, Suwon, Korea from April 2008 to March 2012. A total of 190 patients were identified. Mean age was 5.1±1.87 years. Array CGH yielded abnormal results in 26 of 190 patients (13.7%). Copy number losses were about two-fold more frequent than gains. A total of 61.5% of all patients had copy number losses. The most common deletion disorders included 22q11.2 deletion syndrome, 15q11.2q12 deletion and 18q deletion syndrome. Copy number gains were identified in 34.6% of patients, and common diseases among these included Potocki-Lupski syndrome, 15q11-13 duplication syndrome and duplication 22q. Abnormal karyotype with normal array CGH results was exhibited in 2.6% of patients; theses included balanced translocation (n=2), inversion (n=2) and low-level mosaicism (n=1). Facial abnormalities (p<0.001) and failure to thrive were (p<0.001) also more frequent in the group of patients with abnormal CGH findings. Array CGH is a useful diagnostic tool in clinical settings in patients with developmental delay or intellectual disability combined with facial abnormalities or failure to thrive.

A segmentation/clustering model for the analysis of array CGH data.

PubMed

Picard, F; Robin, S; Lebarbier, E; Daudin, J-J

2007-09-01

Microarray-CGH (comparative genomic hybridization) experiments are used to detect and map chromosomal imbalances. A CGH profile can be viewed as a succession of segments that represent homogeneous regions in the genome whose representative sequences share the same relative copy number on average. Segmentation methods constitute a natural framework for the analysis, but they do not provide a biological status for the detected segments. We propose a new model for this segmentation/clustering problem, combining a segmentation model with a mixture model. We present a new hybrid algorithm called dynamic programming-expectation maximization (DP-EM) to estimate the parameters of the model by maximum likelihood. This algorithm combines DP and the EM algorithm. We also propose a model selection heuristic to select the number of clusters and the number of segments. An example of our procedure is presented, based on publicly available data sets. We compare our method to segmentation methods and to hidden Markov models, and we show that the new segmentation/clustering model is a promising alternative that can be applied in the more general context of signal processing.

Method of Identifying a Base in a Nucleic Acid

DOEpatents

Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

1999-01-01

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Identifying a base in a nucleic acid

DOEpatents

Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

2005-02-08

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Arc-Free High-Power dc Switch

NASA Technical Reports Server (NTRS)

Miller, W. N.; Gray, O. E.

1982-01-01

Hybrid switch allows high-power direct current to be turned on and off without arcing or erosion. Switch consists of bank of transistors in parallel with mechanical contacts. Transistor bank makes and breaks switched circuit; contacts carry current only during steady-state "on" condition. Designed for Space Shuttle orbiter, hybrid switch can be used also in high-power control circuits in aircraft, electric autos, industrial furnaces, and solar-cell arrays.

Thermally Stabilized Transmit/Receive Modules

NASA Technical Reports Server (NTRS)

Hoffman, James; DelCastillo, Linda; Miller, Jennifer; Birur, Gaj

2011-01-01

RF-hybrid technologies enable smaller packaging and mass reduction in radar instruments, especially for subsystems with dense electronics, such as electronically steered arrays. We are designing thermally stabilized RF-hybrid T/R modules using new materials for improved thermal performance of electronics. We are combining advanced substrate and housing materials with a thermal reservoir material, and develop new packaging techniques to significantly improve thermal-cycling reliability and performance stability over temperature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, G.L.; He, Z.; DeSantis, T.Z.

Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogeneticmore » microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning. Examples of the application of both arrays in different environmental samples will be described in the two subsequent sections.« less

Copy number analysis of NIPBL in a cohort of 510 patients reveals rare copy number variants and a mosaic deletion.

PubMed

Cheng, Yu-Wei; Tan, Christopher A; Minor, Agata; Arndt, Kelly; Wysinger, Latrice; Grange, Dorothy K; Kozel, Beth A; Robin, Nathaniel H; Waggoner, Darrel; Fitzpatrick, Carrie; Das, Soma; Del Gaudio, Daniela

2014-03-01

Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder characterized by growth retardation, intellectual disability, upper limb abnormalities, hirsutism, and characteristic facial features. In this study we explored the occurrence of intragenic NIPBL copy number variations (CNVs) in a cohort of 510 NIPBL sequence-negative patients with suspected CdLS. Copy number analysis was performed by custom exon-targeted oligonucleotide array-comparative genomic hybridization and/or MLPA. Whole-genome SNP array was used to further characterize rearrangements extending beyond the NIPBL gene. We identified NIPBL CNVs in 13 patients (2.5%) including one intragenic duplication and a deletion in mosaic state. Breakpoint sequences in two patients provided further evidence of a microhomology-mediated replicative mechanism as a potential predominant contributor to CNVs in NIPBL. Patients for whom clinical information was available share classical CdLS features including craniofacial and limb defects. Our experience in studying the frequency of NIBPL CNVs in the largest series of patients to date widens the mutational spectrum of NIPBL and emphasizes the clinical utility of performing NIPBL deletion/duplication analysis in patients with CdLS.

Precise annealing of focal plane arrays for optical detection

DOEpatents

Bender, Daniel A.

2015-09-22

Precise annealing of identified defective regions of a Focal Plane Array ("FPA") (e.g., exclusive of non-defective regions of the FPA) facilitates removal of defects from an FPA that has been hybridized and/or packaged with readout electronics. Radiation is optionally applied under operating conditions, such as under cryogenic temperatures, such that performance of an FPA can be evaluated before, during, and after annealing without requiring thermal cycling.

Precise annealing of focal plane arrays for optical detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bender, Daniel A.

2017-10-17

Precise annealing of identified defective regions of a Focal Plane Array ("FPA") (e.g., exclusive of non-defective regions of the FPA) facilitates removal of defects from an FPA that has been hybridized and/or packaged with readout electronics. Radiation is optionally applied under operating conditions, such as under cryogenic temperatures, such that performance of an FPA can be evaluated before, during, and after annealing without requiring thermal cycling.

Facile construction of vertically aligned EuS-ZnO hybrid core shell nanorod arrays for visible light driven photocatalytic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ranjith, K. S.; Kumar, D. Ranjith; Kumar, R. T. Rajendra, E-mail: rtrkumar@buc.edu.in

2015-06-24

We demonstrated the development of coupled semiconductor in the form of hybrid heterostructures for significant advancement in catalytic functional materials. In this article, we report the preparation of vertically aligned core shell ZnO-EuS nanorod photocatalyst arrays by a simple chemical solution process followed by sulfudation process. The XRD pattern confirmed formation of the hexagonal wurtzite structure of ZnO and cubic nature of the EuS. Cross sectional FESEM images show vertical rod array structure, and the size of the nanorods ranges from 80 to 120 nm. UV-Vis DRS spectra showed that the optical absorption of ZnO was significantly enhanced to the visiblemore » region by modification with EuS surfaces. TEM study confirmed that the surface of ZnO was drastically improved by the modification with EuS nanoparticle. The catalytic activity of EuS−ZnO core shell nanorod arrays were evaluated by the photodegradation of Methylene Blue (MB) dye under visible irradiation. The results revealed that the photocatalytic activity of EuS−ZnO was much higher than that of ZnO under natural sunlight. EuS−ZnO was found to be stable and reusable without appreciable loss of catalytic activity up to four consecutive cycles.« less

Modeling Charge Collection in Detector Arrays

NASA Technical Reports Server (NTRS)

Hardage, Donna (Technical Monitor); Pickel, J. C.

2003-01-01

A detector array charge collection model has been developed for use as an engineering tool to aid in the design of optical sensor missions for operation in the space radiation environment. This model is an enhancement of the prototype array charge collection model that was developed for the Next Generation Space Telescope (NGST) program. The primary enhancements were accounting for drift-assisted diffusion by Monte Carlo modeling techniques and implementing the modeling approaches in a windows-based code. The modeling is concerned with integrated charge collection within discrete pixels in the focal plane array (FPA), with high fidelity spatial resolution. It is applicable to all detector geometries including monolithc charge coupled devices (CCDs), Active Pixel Sensors (APS) and hybrid FPA geometries based on a detector array bump-bonded to a readout integrated circuit (ROIC).

The tapered slot antenna - A new integrated element for millimeter-wave applications

NASA Technical Reports Server (NTRS)

Yngvesson, K. Sigfrid; Kim, Young-Sik; Korzeniowski, T. L.; Kollberg, Erik L.; Johansson, Joakim F.

1989-01-01

Tapered slot antennas (TSAs) with a number of potential applications as single elements and focal-plane arrays are discussed. TSAs are fabricated with photolithographic techniques and integrated in either hybrid or MMIC circuits with receiver or transmitter components. They offer considerably narrower beams than other integrated antenna elements and have high aperture efficiency and packing density as array elements. Both the circuit and radiation properties of TSAs are reviewed. Topics covered include: antenna beamwidth, directivity, and gain of single-element TSAs; their beam shape and the effect of different taper shapes; and the input impedance and the effects of using thick dielectrics. These characteristics are also given for TSA arrays, as are the circuit properties of the array elements. Different array structures and their applications are also described.

Unraveling unusual X-chromosome patterns during fragile-X syndrome genetic testing.

PubMed

Esposito, Gabriella; Tremolaterra, Maria Roberta; Savarese, Maria; Spiniello, Michele; Patrizio, Maria Pia; Lombardo, Barbara; Pastore, Lucio; Salvatore, Francesco; Carsana, Antonella

2018-01-01

Fragile X syndrome (FXS) is the most common form of inherited intellectual disability (ID). Together with fragile X-associated tremor and ataxia (FXTAS) and fragile X-associated premature ovarian failure (POF)/primary ovarian insufficiency (POI), FXS depends on dysfunctional expression of the FMR1 gene on Xq27.3. In most cases, FXS is caused by a >200 CGG repeats in FMR1 5'-untranslated region (UTR) and by promoter hypermethylation that results in gene silencing. Males and females with unmethylated premutated alleles (repeats between 55 and 200) are at risk for FXTAS and POF/POI. FXS molecular testing relied on PCR and methylation-specific Southern blot analysis of the FMR1 5'UTR. Atypical Southern blot patterns were studied by X-chromosome microsatellite analysis, copy number dosage at DMD locus, amelogenin gender-marker analysis and array-comparative genomic hybridization (array-CGH). Six men affected by ID and three women affected by ID and POF/POI underwent FXS molecular testing. They had normal FMR1 CGG repeats, but atypical X chromosome patterns. Further investigations revealed that the six males had Klinefelter syndrome (XXY), one female was a Turner mosaic (X0/XX) and two women had novel rearrangements involving X chromosome. Diagnostic investigation of atypical patterns at FMR1 locus can address patients and/or their relatives to further verify the condition by performing karyotyping and/or array-CGH. Copyright © 2017. Published by Elsevier B.V.

Development of computer informational system of diagnostics integrated optical materials, elements, and devices

NASA Astrophysics Data System (ADS)

Volosovitch, Anatoly E.; Konopaltseva, Lyudmila I.

1995-11-01

Well-known methods of optical diagnostics, database for their storage, as well as expert system (ES) for their development are analyzed. A computer informational system is developed, which is based on a hybrid ES built on modern DBMS. As an example, the structural and constructive circuits of the hybrid integrated-optical devices based on laser diodes, diffusion waveguides, geodetic lenses, package-free linear photodiode arrays, etc. are presented. The features of methods and test results as well as the advanced directions of works related to the hybrid integrated-optical devices in the field of metrology are discussed.

High density harp or wire scanner for particle beam diagnostics

DOEpatents

Fritsche, C.T.; Krogh, M.L.

1996-05-21

Disclosed is a diagnostic detector head harp used to detect and characterize high energy particle beams using an array of closely spaced detector wires, typically carbon wires, spaced less than 0.1 cm (0.040 inch) connected to a hybrid microcircuit formed on a ceramic substrate. A method to fabricate harps to obtain carbon wire spacing and density not previously available utilizing hybrid microcircuit technology. The hybrid microcircuit disposed on the ceramic substrate connects electrically between the detector wires and diagnostic equipment which analyzes pulses generated in the detector wires by the high energy particle beams. 6 figs.

TRANSCRIPTIONAL PROFILING USING THE FLOWTHROUGH GENOSENSOR FINAL CRADA REPORT C/ORNL97-00472

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doktycz, M. J.; Yang, H.

1999-06-01

A Cooperative Research and Development Agreement (CRADA) between Lockheed Martin Energy Research Corporation (Contractor) and Gene Logic, Inc., (Participant) was carried out to evaluate the technical feasibility study of the application of the flowthrough genosensor for gene expression (transcriptional) profiling, over the current industry practice of using flat surface hybridization arrays to monitor the relative abundance of individual mRNA species in a cell. Various parameters, including substrate preparation, flow rates, hybridization conditions and sample concentrations, were evaluated on the flowthrough genosensor. The superiority of the flowthrough genosensor, in terms of hybridization rate and sensitivity were established.

Gold nanoparticle-embedded silk protein-ZnO nanorod hybrids for flexible bio-photonic devices

NASA Astrophysics Data System (ADS)

Gogurla, Narendar; Kundu, Subhas C.; Ray, Samit K.

2017-04-01

Silk protein has been used as a biopolymer substrate for flexible photonic devices. Here, we demonstrate ZnO nanorod array hybrid photodetectors on Au nanoparticle-embedded silk protein for flexible optoelectronics. Hybrid samples exhibit optical absorption at the band edge of ZnO as well as plasmonic energy due to Au nanoparticles, making them attractive for selective UV and visible wavelength detection. The device prepared on Au-silk protein shows a much lower dark current and a higher photo to dark-current ratio of ∼105 as compared to the control sample without Au nanoparticles. The hybrid device also exhibits a higher specific detectivity due to higher responsivity arising from the photo-generated hole trapping by Au nanoparticles. Sharp pulses in the transient photocurrent have been observed in devices prepared on glass and Au-silk protein substrates due to the light induced pyroelectric effect of ZnO, enabling the demonstration of self-powered photodetectors at zero bias. Flexible hybrid detectors have been demonstrated on Au-silk/polyethylene terephthalate substrates, exhibiting characteristics similar to those fabricated on rigid glass substrates. A study of the performance of photodetectors with different bending angles indicates very good mechanical stability of silk protein based flexible devices. This novel concept of ZnO nanorod array photodetectors on a natural silk protein platform provides an opportunity to realize integrated flexible and self-powered bio-photonic devices for medical applications in near future.

Single-step direct fabrication of pillar-on-pore hybrid nanostructures in anodizing aluminum for superior superhydrophobic efficiency.

PubMed

Jeong, Chanyoung; Choi, Chang-Hwan

2012-02-01

Conventional electrochemical anodizing processes of metals such as aluminum typically produce planar and homogeneous nanopore structures. If hydrophobically treated, such 2D planar and interconnected pore structures typically result in lower contact angle and larger contact angle hysteresis than 3D disconnected pillar structures and, hence, exhibit inferior superhydrophobic efficiency. In this study, we demonstrate for the first time that the anodizing parameters can be engineered to design novel pillar-on-pore (POP) hybrid nanostructures directly in a simple one-step fabrication process so that superior surface superhydrophobicity can also be realized effectively from the electrochemical anodization process. On the basis of the characteristic of forming a self-ordered porous morphology in a hexagonal array, the modulation of anodizing voltage and duration enabled the formulation of the hybrid-type nanostructures having controlled pillar morphology on top of a porous layer in both mild and hard anodization modes. The hybrid nanostructures of the anodized metal oxide layer initially enhanced the surface hydrophilicity significantly (i.e., superhydrophilic). However, after a hydrophobic monolayer coating, such hybrid nanostructures then showed superior superhydrophobic nonwetting properties not attainable by the plain nanoporous surfaces produced by conventional anodization conditions. The well-regulated anodization process suggests that electrochemical anodizing can expand its usefulness and efficacy to render various metallic substrates with great superhydrophilicity or -hydrophobicity by directly realizing pillar-like structures on top of a self-ordered nanoporous array through a simple one-step fabrication procedure.

Low latency counter event indication

DOEpatents

Gara, Alan G [Mount Kisco, NY; Salapura, Valentina [Chappaqua, NY

2008-09-16

A hybrid counter array device for counting events with interrupt indication includes a first counter portion comprising N counter devices, each for counting signals representing event occurrences and providing a first count value representing lower order bits. An overflow bit device associated with each respective counter device is additionally set in response to an overflow condition. The hybrid counter array includes a second counter portion comprising a memory array device having N addressable memory locations in correspondence with the N counter devices, each addressable memory location for storing a second count value representing higher order bits. An operatively coupled control device monitors each associated overflow bit device and initiates incrementing a second count value stored at a corresponding memory location in response to a respective overflow bit being set. The incremented second count value is compared to an interrupt threshold value stored in a threshold register, and, when the second counter value is equal to the interrupt threshold value, a corresponding "interrupt arm" bit is set to enable a fast interrupt indication. On a subsequent roll-over of the lower bits of that counter, the interrupt will be fired.

Low latency counter event indication

DOEpatents

Gara, Alan G.; Salapura, Valentina

2010-08-24

A hybrid counter array device for counting events with interrupt indication includes a first counter portion comprising N counter devices, each for counting signals representing event occurrences and providing a first count value representing lower order bits. An overflow bit device associated with each respective counter device is additionally set in response to an overflow condition. The hybrid counter array includes a second counter portion comprising a memory array device having N addressable memory locations in correspondence with the N counter devices, each addressable memory location for storing a second count value representing higher order bits. An operatively coupled control device monitors each associated overflow bit device and initiates incrementing a second count value stored at a corresponding memory location in response to a respective overflow bit being set. The incremented second count value is compared to an interrupt threshold value stored in a threshold register, and, when the second counter value is equal to the interrupt threshold value, a corresponding "interrupt arm" bit is set to enable a fast interrupt indication. On a subsequent roll-over of the lower bits of that counter, the interrupt will be fired.

SOSPAC- SOLAR SPACE POWER ANALYSIS CODE

NASA Technical Reports Server (NTRS)

Selcuk, M. K.

1994-01-01

The Solar Space Power Analysis Code, SOSPAC, was developed to examine the solar thermal and photovoltaic power generation options available for a satellite or spacecraft in low earth orbit. SOSPAC is a preliminary systems analysis tool and enables the engineer to compare the areas, weights, and costs of several candidate electric and thermal power systems. The configurations studied include photovoltaic arrays and parabolic dish systems to produce electricity only, and in various combinations to provide both thermal and electric power. SOSPAC has been used for comparison and parametric studies of proposed power systems for the NASA Space Station. The initial requirements are projected to be about 40 kW of electrical power, and a similar amount of thermal power with temperatures above 1000 degrees Centigrade. For objects in low earth orbit, the aerodynamic drag caused by suitably large photovoltaic arrays is very substantial. Smaller parabolic dishes can provide thermal energy at a collection efficiency of about 80%, but at increased cost. SOSPAC allows an analysis of cost and performance factors of five hybrid power generating systems. Input includes electrical and thermal power requirements, sun and shade durations for the satellite, and unit weight and cost for subsystems and components. Performance equations of the five configurations are derived, and the output tabulates total weights of the power plant assemblies, area of the arrays, efficiencies, and costs. SOSPAC is written in FORTRAN IV for batch execution and has been implemented on an IBM PC computer operating under DOS with a central memory requirement of approximately 60K of 8 bit bytes. This program was developed in 1985.

Two-loop controller for maximizing performance of a grid-connected photovoltaic - fuel cell hybrid power plant

NASA Astrophysics Data System (ADS)

Ro, Kyoungsoo

The study started with the requirement that a photovoltaic (PV) power source should be integrated with other supplementary power sources whether it operates in a stand-alone or grid-connected mode. First, fuel cells for a backup of varying PV power were compared in detail with batteries and were found to have more operational benefits. Next, maximizing performance of a grid-connected PV-fuel cell hybrid system by use of a two-loop controller was discussed. One loop is a neural network controller for maximum power point tracking, which extracts maximum available solar power from PV arrays under varying conditions of insolation, temperature, and system load. A real/reactive power controller (RRPC) is the other loop. The RRPC meets the system's requirement for real and reactive powers by controlling incoming fuel to fuel cell stacks as well as switching control signals to a power conditioning subsystem. The RRPC is able to achieve more versatile control of real/reactive powers than the conventional power sources since the hybrid power plant does not contain any rotating mass. Results of time-domain simulations prove not only effectiveness of the proposed computer models of the two-loop controller, but also their applicability for use in transient stability analysis of the hybrid power plant. Finally, environmental evaluation of the proposed hybrid plant was made in terms of plant's land requirement and lifetime COsb2 emissions, and then compared with that of the conventional fossil-fuel power generating forms.

Primary adenocarcinoma of the thymus: an immunohistochemical and molecular study with review of the literature.

PubMed

Maghbool, Maryam; Ramzi, Mani; Nagel, Inga; Bejarano, Pablo; Siebert, Reiner; Saeedzadeh, Abolfazl; Daneshbod, Yahya

2013-05-31

Primary adenocarcinoma of thymus is extremely rare. This is a case of primary adenocarcinoma with intestinal differentiation and focal mucin production in the thymus. Thymic cyst was associated with this tumor. Intestinal differentiation was confirmed by immunohistochemical stain with positivity for CDX-2, CK20, villin, MOC31 and focal positivity of CK7. Array comperative genomic hybridization (CGH) analysis showed a complex pattern of chromosomal imbalances including homozygous deletion at the HLA locus in chromosomal region 6p21.32. This rare tumor shows a similar genetic aberration with other studied thymic epithelial tumors.

What controls the hybridization thermodynamics of spherical nucleic acids?

PubMed

Randeria, Pratik S; Jones, Matthew R; Kohlstedt, Kevin L; Banga, Resham J; Olvera de la Cruz, Monica; Schatz, George C; Mirkin, Chad A

2015-03-18

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ∼30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows for the design of conjugates that hybridize free strands with significantly higher efficiencies, some of which approach 100%.

eSensor: an electrochemical detection-based DNA microarray technology enabling sample-to-answer molecular diagnostics

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Longiaru, Mathew

2009-05-01

DNA microarrays are becoming a widespread tool used in life science and drug screening due to its many benefits of miniaturization and integration. Microarrays permit a highly multiplexed DNA analysis. Recently, the development of new detection methods and simplified methodologies has rapidly expanded the use of microarray technologies from predominantly gene expression analysis into the arena of diagnostics. Osmetech's eSensor® is an electrochemical detection platform based on a low-to- medium density DNA hybridization array on a cost-effective printed circuit board substrate. eSensor® has been cleared by FDA for Warfarin sensitivity test and Cystic Fibrosis Carrier Detection. Other genetic-based diagnostic and infectious disease detection tests are under development. The eSensor® platform eliminates the need for an expensive laser-based optical system and fluorescent reagents. It allows one to perform hybridization and detection in a single and small instrument without any fluidic processing and handling. Furthermore, the eSensor® platform is readily adaptable to on-chip sample-to-answer genetic analyses using microfluidics technology. The eSensor® platform provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus have a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

High performance hybrid silicon micropillar solar cell based on light trapping characteristics of Cu nanoparticles

NASA Astrophysics Data System (ADS)

Zhang, Yulong; Fan, Zhiqiang; Zhang, Weijia; Ma, Qiang; Jiang, Zhaoyi; Ma, Denghao

2018-05-01

High performance silicon combined structure (micropillar with Cu nanoparticles) solar cell has been synthesized from N-type silicon substrates based on the micropillar array. The combined structure solar cell exhibited higher short circuit current rather than the silicon miropillar solar cell, which the parameters of micropillar array are the same. Due to the Cu nanoparticles were decorated on the surface of silicon micropillar array, the photovoltaic properties of cells have been improved. In addition, the optimal efficiency of 11.5% was measured for the combined structure solar cell, which is better than the silicon micropillar cell.

Single-cell copy number variation detection

PubMed Central

2011-01-01

Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition and recurrent genome artifact corrections. We demonstrate that the proposed channel clone normalization significantly improves the copy number variation detection in both simulated and real single-cell array CGH data. PMID:21854607

Identification of DNA copy number aberrations by array comparative genomic hybridization in patients with ruptured intracranial aneurysms.

PubMed

Choi, Jin Soo; Kim, Seong-Rim; Jeon, Yang-Whan; Lee, Kweon-Haeng; Rha, Hyoung Kyun

2009-02-01

We aimed to use array comparative genomic hybridization (CGH) to identify chromosomal loci that contribute to the pathogenesis of ruptured intracranial aneurysms (IAs) in a Korean population and to confirm the results using real-time polymerase chain reaction (PCR). Twenty-three patients with ruptured IAs were enrolled in this study. Array CGH revealed copy number aberrations in 19 chromosomal regions. Chromosomal gains were identified at a high frequency in regions 1p12, 4q24, 5p15.31, 5p15.33, 6p12.2, 6q22.33, 7p21.1, 9q22.1, 10q24.32, 10q26.3, 12q13.13, 17p12, 18q12.3, 18q23, 19p13.3, 20q13.33, 21q11.2, and 21q22.3, whereas chromosomal losses were identified at 15q11.2 and 22q11.21. Real-time PCR confirmed the results of the array CGH studies of the COL6A2, GRIN3B, MUC17, and PRODH genes. This is the first study to identify candidate regions by array CGH in patients with IAs. The identification of genes that may predispose an individual to the development of IAs may lead to a better understanding of the mechanism of IA formation. Multicenter studies comparing cohorts of patients of different ethnicities are needed to better understand the mechanism of IA formation.

Enabling Large Focal Plane Arrays Through Mosaic Hybridization

NASA Technical Reports Server (NTRS)

Miller, TImothy M.; Jhabvala, Christine A.; Leong, Edward; Costen, Nicholas P.; Sharp, Elmer; Adachi, Tomoko; Benford, Dominic

2012-01-01

We have demonstrated advances in mosaic hybridization that will enable very large format far-infrared detectors. Specifically we have produced electrical detector models via mosaic hybridization yielding superconducting circuit paths by hybridizing separately fabricated sub-units onto a single detector unit. The detector model was made on a 100mm diameter wafer while four model readout quadrant chips were made from a separate 100mm wafer. The individually fabricated parts were hybridized using a flip-chip bonder to assemble the detector-readout stack. Once all of the hybridized readouts were in place, a single, large and thick silicon substrate was placed on the stack and attached with permanent epoxy to provide strength and a Coefficient of Thermal Expansion match to the silicon components underneath. Wirebond pads on the readout chips connect circuits to warm readout electronics; and were used to validate the successful superconducting electrical interconnection of the model mosaic-hybrid detector. This demonstration is directly scalable to 150 mm diameter wafers, enabling pixel areas over ten times the area currently available.

Probe kit for identifying a base in a nucleic acid

DOEpatents

Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

2001-01-01

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Super-Lattice Light Emitting Diodes (SLEDS) on GaAs

DTIC Science & Technology

2016-03-31

Super-Lattice Light Emitting Diodes (SLEDS) on GaAs Kassem Nabha1, Russel Ricker2, Rodney McGee1, Nick Waite1, John Prineas2, Sydney Provence2...infrared light emitting diodes (LEDs). Typically, the LED arrays are mated with CMOS read-in integrated circuit (RIIC) chips using flip-chip bonding. In...circuit (RIIC) chips using flip-chip bonding. This established technology is called Hybrid-super-lattice light emitting diodes (Hybrid- SLEDS). In

Nucleic acid nanomaterials: Silver-wired DNA

NASA Astrophysics Data System (ADS)

Auffinger, Pascal; Ennifar, Eric

2017-10-01

DNA double helical structures are supramolecular assemblies that are typically held together by classical Watson-Crick pairing. Now, nucleotide chelation of silver ions supports an extended silver-DNA hybrid duplex featuring an uninterrupted silver array.

Digital detection of multiple minority mutants and expression levels of multiple colorectal cancer-related genes using digital-PCR coupled with bead-array.

PubMed

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed "multiplex ligation-dependent probe amplification-digital amplification coupled with hydrogel bead-array" (MLPA-DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA-DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA-DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC.

Modular nucleic acid assembled p/MHC microarrays for multiplexed sorting of antigen-specific T cells.

PubMed

Kwong, Gabriel A; Radu, Caius G; Hwang, Kiwook; Shu, Chengyi J; Ma, Chao; Koya, Richard C; Comin-Anduix, Begonya; Hadrup, Sine Reker; Bailey, Ryan C; Witte, Owen N; Schumacher, Ton N; Ribas, Antoni; Heath, James R

2009-07-22

The human immune system consists of a large number of T cells capable of recognizing and responding to antigens derived from various sources. The development of peptide-major histocompatibility (p/MHC) tetrameric complexes has enabled the direct detection of these antigen-specific T cells. With the goal of increasing throughput and multiplexing of T cell detection, protein microarrays spotted with defined p/MHC complexes have been reported, but studies have been limited due to the inherent instability and reproducibility of arrays produced via conventional spotted methods. Herein, we report on a platform for the detection of antigen-specific T cells on glass substrates that offers significant advantages over existing surface-bound schemes. In this approach, called "Nucleic Acid Cell Sorting (NACS)", single-stranded DNA oligomers conjugated site-specifically to p/MHC tetramers are employed to immobilize p/MHC tetramers via hybridization to a complementary-printed substrate. Fully assembled p/MHC arrays are used to detect and enumerate T cells captured from cellular suspensions, including primary human T cells collected from cancer patients. NACS arrays outperform conventional spotted arrays assessed in key criteria such as repeatability and homogeneity. The versatility of employing DNA sequences for cell sorting is exploited to enable the programmed, selective release of target populations of immobilized T cells with restriction endonucleases for downstream analysis. Because of the performance, facile and modular assembly of p/MHC tetramer arrays, NACS holds promise as a versatile platform for multiplexed T cell detection.

A case of female epispadias.

PubMed

Tantibhedhyangkul, Julierut; Copland, Susannah D; Haqq, Andrea M; Price, Thomas M

2008-11-01

To present a case of unrecognized female epispadias. Case report. University-based reproductive endocrinology and fertility clinic. A 16-year-old girl with epispadias, history of mild urinary incontinence, auditory neuropathy, and functional hyperandrogenism. None. Peripheral blood array-based comparative genomic hybridization. The patient was referred for evaluation of excessive weight gain, secondary amenorrhea, and abnormal external genitalia. Examination under anesthesia revealed bilateral labia minora hypertrophy, bifid clitoris, and a patulous urethra, consistent with female epispadias. Hormonal evaluation showed functional hyperandrogenism, and peripheral blood array-based comparative genomic hybridization showed no chromosomal deletions or duplications. Female epispadias is a rare abnormality, not commonly recognized by most practitioners. The diagnosis is supported by a history of urinary incontinence and physical findings of bifid clitoris and patulous urethra. The condition can have serious physical and psychological consequences leading to a gross disruption of social function.

Visible light focusing flat lenses based on hybrid dielectric-metal metasurface reflector-arrays

PubMed Central

Fan, Qingbin; Huo, Pengcheng; Wang, Daopeng; Liang, Yuzhang; Yan, Feng; Xu, Ting

2017-01-01

Conventional metasurface reflector-arrays based on metallic resonant nanoantenna to control the wavefront of light for focusing always suffer from strong ohmic loss at optical frequencies. Here, we overcome this challenge by constructing a non-resonant, hybrid dielectric-metal configuration consisting of TiO2 nanofins associated with an Ag reflector substrate that provides a broadband response and high polarization conversion efficiency in the visible range. A reflective flat lens based on this configuration shows an excellent focusing performance with the spot size close to the diffraction limit. Furthermore, by employing the superimposed phase distribution design to manipulate the wavefront of the reflected light, various functionalities, such as multifocal and achromatic focusing, are demonstrated for the flat lenses. Such a reflective flat lens will find various applications in visible light imaging and sensing systems. PMID:28332611

Paper-based solid-phase multiplexed nucleic acid hybridization assay with tunable dynamic range using immobilized quantum dots as donors in fluorescence resonance energy transfer.

PubMed

Noor, M Omair; Krull, Ulrich J

2013-08-06

A multiplexed solid-phase nucleic acid hybridization assay on a paper-based platform is presented using multicolor immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize two types of QD-probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) and red-emitting QDs (rQDs) served as donors with Cy3 and Alexa Fluor 647 (A647) acceptors. The gQD/Cy3 FRET pair served as an internal standard, while the rQD/A647 FRET pair served as a detection channel, combining the control and analytical test zones in one physical location. Hybridization of dye-labeled oligonucleotide targets provided the proximity for FRET sensitized emission from the acceptor dyes, which served as an analytical signal. Hybridization assays in the multicolor format provided a limit of detection of 90 fmol and an upper limit of dynamic range of 3.5 pmol. The use of an array of detection zones was designed to provide improved analytical figures of merit compared to that which could be achieved on one type of array design in terms of relative concentration of multicolor QDs. The hybridization assays showed excellent resistance to nonspecific adsorption of oligonucleotides. Selectivity of the two-plex hybridization assay was demonstrated by single nucleotide polymorphism (SNP) detection at a contrast ratio of 50:1. Additionally, it is shown that the use of preformed QD-probe oligonucleotide conjugates and consideration of the relative number density of the two types of QD-probe conjugates in the two-color assay format is advantageous to maximize assay sensitivity and the upper limit of dynamic range.

Quasi-Ballistic Carbon Nanotube Array Transistors with Current Density Exceeding Si and GaAs

DTIC Science & Technology

2016-09-02

performance of surfactant- encapsulated and conjugated polymer –wrapped CNTs in aligned arrays prepared by dielectrophoresis (20) and shear-casting (21); how... conjugated polymer poly[(9,9-dioctylfluorenyl- 2,7-diyl)-alt-co-(6,60-(2,20-bipyridine))] (PFO-BPy) in toluene to se- lectively wrap the semiconducting...Malenfant, J. Humes, J. Kroeger, A hybrid enrichment process combining conjugated polymer extraction and silica gel adsorption for high purity

Maximizing omnidirectional light harvesting in metal oxide hyperbranched array architectures

NASA Astrophysics Data System (ADS)

Wu, Wu-Qiang; Feng, Hao-Lin; Rao, Hua-Shang; Xu, Yang-Fan; Kuang, Dai-Bin; Su, Cheng-Yong

2014-05-01

The scrupulous design of nanoarchitectures and smart hybridization of specific active materials are closely related to the overall photovoltaic performance of an anode electrode. Here we present a solution-based strategy for the fabrication of well-aligned metal oxide-based nanowire-nanosheet-nanorod hyperbranched arrays on transparent conducting oxide substrates. For these hyperbranched arrays, we observe a twofold increment in dye adsorption and enhanced light trapping and scattering capability compared with the pristine titanium dioxide nanowires, and thus a power conversion efficiency of 9.09% is achieved. Our growth approach presents a strategy to broaden the photoresponse and maximize the light-harvesting efficiency of arrays architectures, and may lead to applications for energy conversion and storage, catalysis, water splitting and gas sensing.

Maximizing omnidirectional light harvesting in metal oxide hyperbranched array architectures.

PubMed

Wu, Wu-Qiang; Feng, Hao-Lin; Rao, Hua-Shang; Xu, Yang-Fan; Kuang, Dai-Bin; Su, Cheng-Yong

2014-05-29

The scrupulous design of nanoarchitectures and smart hybridization of specific active materials are closely related to the overall photovoltaic performance of an anode electrode. Here we present a solution-based strategy for the fabrication of well-aligned metal oxide-based nanowire-nanosheet-nanorod hyperbranched arrays on transparent conducting oxide substrates. For these hyperbranched arrays, we observe a twofold increment in dye adsorption and enhanced light trapping and scattering capability compared with the pristine titanium dioxide nanowires, and thus a power conversion efficiency of 9.09% is achieved. Our growth approach presents a strategy to broaden the photoresponse and maximize the light-harvesting efficiency of arrays architectures, and may lead to applications for energy conversion and storage, catalysis, water splitting and gas sensing.

Highlights from the Telescope Array Experiment

NASA Astrophysics Data System (ADS)

Sagawa, H.

2014-10-01

The Telescope Array (TA) is the largest experiment in the Northern Hemisphere currently studying the origin and nature of ultra-high-energy cosmic rays above ˜1018 eV by measuring their energy spectrum, mass composition, and arrival directions. It is located in the western desert of central Utah, USA. The TA detector consists of a surface array of 507 scintillation counters, deployed on a square grid of 1.2-km spacing that covers approximately 700 km2, and 38 fluorescence telescopes located at three sites looking over the surface array. The TA commenced hybrid observation with both sets of detectors in 2008. Here, we present recent results from these 5 years of data and outline our ongoing and near future plans.

Numerical simulation of the modulation transfer function (MTF) in infrared focal plane arrays: simulation methodology and MTF optimization

NASA Astrophysics Data System (ADS)

Schuster, J.

2018-02-01

Military requirements demand both single and dual-color infrared (IR) imaging systems with both high resolution and sharp contrast. To quantify the performance of these imaging systems, a key measure of performance, the modulation transfer function (MTF), describes how well an optical system reproduces an objects contrast in the image plane at different spatial frequencies. At the center of an IR imaging system is the focal plane array (FPA). IR FPAs are hybrid structures consisting of a semiconductor detector pixel array, typically fabricated from HgCdTe, InGaAs or III-V superlattice materials, hybridized with heat/pressure to a silicon read-out integrated circuit (ROIC) with indium bumps on each pixel providing the mechanical and electrical connection. Due to the growing sophistication of the pixel arrays in these FPAs, sophisticated modeling techniques are required to predict, understand, and benchmark the pixel array MTF that contributes to the total imaging system MTF. To model the pixel array MTF, computationally exhaustive 2D and 3D numerical simulation approaches are required to correctly account for complex architectures and effects such as lateral diffusion from the pixel corners. It is paramount to accurately model the lateral di_usion (pixel crosstalk) as it can become the dominant mechanism limiting the detector MTF if not properly mitigated. Once the detector MTF has been simulated, it is directly decomposed into its constituent contributions to reveal exactly what is limiting the total detector MTF, providing a path for optimization. An overview of the MTF will be given and the simulation approach will be discussed in detail, along with how different simulation parameters effect the MTF calculation. Finally, MTF optimization strategies (crosstalk mitigation) will be discussed.

Hybrid fusion of linear, non-linear and spectral models for the dynamic modeling of sEMG and skeletal muscle force: an application to upper extremity amputation.

PubMed

Potluri, Chandrasekhar; Anugolu, Madhavi; Schoen, Marco P; Subbaram Naidu, D; Urfer, Alex; Chiu, Steve

2013-11-01

Estimating skeletal muscle (finger) forces using surface Electromyography (sEMG) signals poses many challenges. In general, the sEMG measurements are based on single sensor data. In this paper, two novel hybrid fusion techniques for estimating the skeletal muscle force from the sEMG array sensors are proposed. The sEMG signals are pre-processed using five different filters: Butterworth, Chebychev Type II, Exponential, Half-Gaussian and Wavelet transforms. Dynamic models are extracted from the acquired data using Nonlinear Wiener Hammerstein (NLWH) models and Spectral Analysis Frequency Dependent Resolution (SPAFDR) models based system identification techniques. A detailed comparison is provided for the proposed filters and models using 18 healthy subjects. Wavelet transforms give higher mean correlation of 72.6 ± 1.7 (mean ± SD) and 70.4 ± 1.5 (mean ± SD) for NLWH and SPAFDR models, respectively, when compared to the other filters used in this work. Experimental verification of the fusion based hybrid models with wavelet transform shows a 96% mean correlation and 3.9% mean relative error with a standard deviation of ± 1.3 and ± 0.9 respectively between the overall hybrid fusion algorithm estimated and the actual force for 18 test subjects' k-fold cross validation data. © 2013 Elsevier Ltd. All rights reserved.

Dose–response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol

PubMed Central

Hook, Sharon E.; Skillman, Ann D.; Small, Jack A.; Schultz, Irvin R.

2008-01-01

Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss, were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as “expression signatures”. Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that diffierent doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose. PMID:16725192

Atomic Layer Deposition on Carbon Nanotubes and their Assemblies

NASA Astrophysics Data System (ADS)

Stano, Kelly Lynn

Global issues related to energy and the environment have motivated development of advanced material solutions outside of traditional metals ceramics, and polymers. Taking inspiration from composites, where the combination of two or more materials often yields superior properties, the field of organic-inorganic hybrids has recently emerged. Carbon nanotube (CNT)-inorganic hybrids have drawn widespread and increasing interest in recent years due to their multifunctionality and potential impact across several technologically important application areas. Before the impacts of CNT-inorganic hybrids can be realized however, processing techniques must be developed for their scalable production. Optimization in chemical vapor deposition (CVD) methods for synthesis of CNTs and vertically aligned CNT arrays has created production routes both high throughput and economically feasible. Additionally, control of CVD parameters has allowed for growth of CNT arrays that are able to be drawn into aligned sheets and further processed to form a variety of aligned 1, 2, and 3-dimensional bulk assemblies including ribbons, yarns, and foams. To date, there have only been a few studies on utilizing these bulk assemblies for the production of CNT-inorganic hybrids. Wet chemical methods traditionally used for fabricating CNT-inorganic hybrids are largely incompatible with CNT assemblies, since wetting and drying the delicate structures with solvents can destroy their structure. It is therefore necessary to investigate alternative processing strategies in order to advance the field of CNT-inorganic hybrids. In this dissertation, atomic layer deposition (ALD) is evaluated as a synthetic route for the production of large-scale CNT-metal oxide hybrids as well as pure metal oxide architectures utilizing CNT arrays, ribbons, and ultralow density foams as deposition templates. Nucleation and growth behavior of alumina was evaluated as a function of CNT surface chemistry. While highly graphitic and defect-free CNTs were shown to produce alumina beads on their surfaces, plasma-treated CNTs with a high concentration of oxygen- containing functional groups on their surface promoted conformal film formation. Furthermore, it was determined that ultrahigh aspect ratio CNT assemblies could be uniformly coated throughout the cross-section by orienting the CNT axes parallel to the direction of precursor flow, as well as by removing any barriers to the pump/purge process such as growth substrates or non-porous sample holders. Heat treatment of CNT-alumina hybrids in air not only led to the crystallization of alumina, but also oxidative removal of CNTs from the core-shell structure. In the case of CNT arrays, this resulted in a weak array of alumina nanotubes. When the same process was applied to alumina-coated CNT foams (CNTFs) however, a robust and resilient aerogel-like material remained post-calcination. Further inspection of this novel material revealed that the foam was made up of a three-dimensional network of interconnect alumina nanotubes resulting from the direct templating of alumina on the CNTF structure. With an average density of 1.2 mg cm-3, it is an order of magnitude lower than the lowest density alumina aerogel reported to date, and is among the lowest density for any inorganic aerogel reported to date as well. The structure, and therefore, properties of these novel foams could be easily tuned by varying the thickness of the alumina coating. Evaluation of the compressive behavior of all foams revealed that their mechanical properties exceed those of various foams with similar densities. This was found to be a result of efficient load transfer through the structure due to good connectivity among nanotube ligaments. This connectivity also provided unprecedented elastic recoverability following compression, particularly for thin-walled samples with CNTFs still intact. Structural stability to liquid infiltration and drying increased with the number of ALD cycles, as well as thermal insulation ability.

Insertional translocation leading to a 4q13 duplication including the EPHA5 gene in two siblings with attention-deficit hyperactivity disorder.

PubMed

Matoso, Eunice; Melo, Joana B; Ferreira, Susana I; Jardim, Ana; Castelo, Teresa M; Weise, Anja; Carreira, Isabel M

2013-08-01

An insertional translocation (IT) can result in pure segmental aneusomy for the inserted genomic segment allowing to define a more accurate clinical phenotype. Here, we report on two siblings sharing an unbalanced IT inherited from the mother with a history of learning difficulty. An 8-year-old girl with developmental delay, speech disability, and attention-deficit hyperactivity disorder (ADHD), showed by GTG banding analysis a subtle interstitial alteration in 21q21. Oligonucleotide array comparative genomic hybridization (array-CGH) analysis showed a 4q13.1-q13.3 duplication spanning 8.6 Mb. Fluorescence in situ hybridization (FISH) with bacterial artificial chromosome (BAC) clones confirmed the rearrangement, a der(21)ins(21;4)(q21;q13.1q13.3). The duplication described involves 50 RefSeq genes including the EPHA5 gene that encodes for the EphA5 receptor involved in embryonic development of the brain and also in synaptic remodeling and plasticity thought to underlie learning and memory. The same rearrangement was observed in a younger brother with behavioral problems and also exhibiting ADHD. ADHD is among the most heritable of neuropsychiatric disorders. There are few reports of patients with duplications involving the proximal region of 4q and a mild phenotype. To the best of our knowledge this is the first report of a duplication restricted to band 4q13. This abnormality could be easily missed in children who have nonspecific cognitive impairment. The presence of this behavioral disorder in the two siblings reinforces the hypothesis that the region involved could include genes involved in ADHD. Copyright © 2013 Wiley Periodicals, Inc.

Proof of concept: preimplantation genetic screening without embryo biopsy through analysis of cell-free DNA in spent embryo culture media.

PubMed

Shamonki, Mousa I; Jin, Helen; Haimowitz, Zachary; Liu, Lian

2016-11-01

To assess whether preimplantation genetic screening (PGS) is possible by testing for free embryonic DNA in spent IVF media from embryos undergoing trophectoderm biopsy. Prospective cohort analysis. Academic fertility center. Seven patients undergoing IVF and 57 embryos undergoing trophectoderm biopsy for PGS. On day 3 of development, each embryo was placed in a separate media droplet. All biopsied embryos received a PGS result by array comparative genomic hybridization. Preimplantation genetic screening was performed on amplified DNA extracted from media and results were compared with PGS results for the corresponding biopsy. [1] Presence of DNA in spent IVF culture media. [2] Correlation between genetic screening result from spent media and corresponding biopsy. Fifty-five samples had detectable DNA ranging from 2-642 ng/μL after a 2-hour amplification. Six samples with the highest DNA levels underwent PGS, rendering one result with a derivative log ratio SD (DLRSD) of <0.85 (a quality control metric of oligonucleotide array comparative genomic hybridization). The fluid sample and trophectoderm results were identical demonstrating (45XY, -13). Three samples were reamplified 1 hour later and tested showing improving DLRSD. One of the three samples with a DLRSD of 0.85 demonstrated (46XY), consistent with the biopsy. Overnight DNA amplification showed DNA in all samples. We demonstrate two novel findings: the presence of free embryonic DNA in spent media and a result that is consistent with trophectoderm biopsy. Improvements in DNA collection, amplification, and testing may allow for PGS without biopsy in the future. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Characterization of canine osteosarcoma by array comparative genomic hybridization and RT-qPCR: signatures of genomic imbalance in canine osteosarcoma parallel the human counterpart.

PubMed

Angstadt, Andrea Y; Motsinger-Reif, Alison; Thomas, Rachael; Kisseberth, William C; Guillermo Couto, C; Duval, Dawn L; Nielsen, Dahlia M; Modiano, Jaime F; Breen, Matthew

2011-11-01

Osteosarcoma (OS) is the most commonly diagnosed malignant bone tumor in humans and dogs, characterized in both species by extremely complex karyotypes exhibiting high frequencies of genomic imbalance. Evaluation of genomic signatures in human OS using array comparative genomic hybridization (aCGH) has assisted in uncovering genetic mechanisms that result in disease phenotype. Previous low-resolution (10-20 Mb) aCGH analysis of canine OS identified a wide range of recurrent DNA copy number aberrations, indicating extensive genomic instability. In this study, we profiled 123 canine OS tumors by 1 Mb-resolution aCGH to generate a dataset for direct comparison with current data for human OS, concluding that several high frequency aberrations in canine and human OS are orthologous. To ensure complete coverage of gene annotation, we identified the human refseq genes that map to these orthologous aberrant dog regions and found several candidate genes warranting evaluation for OS involvement. Specifically, subsequenct FISH and qRT-PCR analysis of RUNX2, TUSC3, and PTEN indicated that expression levels correlated with genomic copy number status, showcasing RUNX2 as an OS associated gene and TUSC3 as a possible tumor suppressor candidate. Together these data demonstrate the ability of genomic comparative oncology to identify genetic abberations which may be important for OS progression. Large scale screening of genomic imbalance in canine OS further validates the use of the dog as a suitable model for human cancers, supporting the idea that dysregulation discovered in canine cancers will provide an avenue for complementary study in human counterparts. Copyright © 2011 Wiley-Liss, Inc.

Array-based detection of genetic alterations associated with disease

DOEpatents

Pinkel, Daniel; Albertson, Donna G.; Gray, Joe W.

2017-09-05

The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.

Array-based detection of genetic alterations associated with disease

DOEpatents

Pinkel, Daniel; Albertson, Donna G.; Gray, Joe W.

2007-09-11

The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.

High density harp or wire scanner for particle beam diagnostics

DOEpatents

Fritsche, Craig T.; Krogh, Michael L.

1996-05-21

A diagnostic detector head harp (23) used to detect and characterize high energy particle beams using an array of closely spaced detector wires (21), typically carbon wires, spaced less than 0.1 cm (0.040 inch) connected to a hybrid microcircuit (25) formed on a ceramic substrate (26). A method to fabricate harps (23) to obtain carbon wire spacing and density not previously available utilizing hybrid microcircuit technology. The hybrid microcircuit (25) disposed on the ceramic substrate (26) connects electrically between the detector wires (21) and diagnostic equipment (37) which analyzes pulses generated in the detector wires (21) by the high energy particle beams.

Nuclear Matrix Proteins in Disparity of Prostate Cancer

DTIC Science & Technology

2011-07-01

using G3PDH 3’ primer and PCR primer 1 followed by two rounds of hybridization. In the first hybridization, the RsaI-digested driver cDNA was mixed...determined using β-actin to confirm the reduced relative abundance of the housekeeping gene after SSH. The SSH nested PCR products were cloned using pCR®2.1...variability of DNA concentration. Additionally, negative and positive controls ( housekeeping genes) from the Ambion™ ArrayControls™ Set were included

Integrated ion sensor device applications based on printed hybrid material systems (Conference Presentation)

NASA Astrophysics Data System (ADS)

List-Kratochvil, Emil J. W.

2016-09-01

Comfortable, wearable sensors and computers will enhance every person's awareness of his or her health condition, environment, chemical pollutants, potential hazards, and information of interest. In agriculture and in the food industry there is a need for a constant control of the condition and needs of plants, animals, and farm products. Yet many of these applications depend upon the development of novel, cheap devices and sensors that are easy to implement and to integrate. Organic semiconductors as well as several inorganic materials and hybrid material systems have proven to combine a number of intriguing optical and electronic properties with simple processing methods. As it will be reviewed in this contribution, these materials are believed to find their application in printed electronic devices allowing for the development of smart disposable devices in food-, health-, and environmental monitoring, diagnostics and control, possibly integrated into arrays of sensor elements for multi-parameter detection. In this contribution we review past and recent achievements in the field. Followed by a brief introduction, we will focus on two topics being on the agenda recently: a) the use of electrolyte-gated organic field-effect transistor (EGOFET) and ion-selective membrane based sensors for in-situ sensing of ions and biological substances and b) the development of hybrid material based resistive switches and their integration into fully functional, printed hybrid crossbar sensor array structures.

Electrochemical biosensor for Mycobacterium tuberculosis DNA detection based on gold nanotubes array electrode platform.

PubMed

Torati, Sri Ramulu; Reddy, Venu; Yoon, Seok Soo; Kim, CheolGi

2016-04-15

The template assisted electrochemical deposition technique was used for the synthesis of gold nanotubes array (AuNTsA). The morphological structure of the synthesized AuNTsA was observed by scanning electron microscopy and found that the individual nanotubes are around 1.5 μm in length with a diameter of 200 nm. Nanotubes are vertically aligned to the Au thick film, which is formed during the synthesis process of nanotubes. The electrochemical performance of the AuNTsA was compared with the bare Au electrode and found that AuNTsA has better electron transfer surface than bare Au electrode which is due to the high surface area. Hence, the AuNTsA was used as an electrode for the fabrication of DNA hybridization biosensor for detection of Mycobacterium Tuberculosis DNA. The DNA hybridization biosensor constructed by AuNTsA electrode was characterized by cyclic voltammetry technique with Fe(CN)6(3-/4-) as an electrochemical redox indicator. The selectivity of the fabricated biosensor was illustrated by hybridization with complementary DNA and non-complementary DNA with probe DNA immobilized AuNTsA electrode using methylene blue as a hybridization indicator. The developed electrochemical DNA biosensor shows good linear range of complementary DNA concentration from 0.01 ng/μL to 100 ng/μL with high detection limit. Copyright © 2015 Elsevier B.V. All rights reserved.

An alternative method to amplify RNA without loss of signal conservation for expression analysis with a proteinase DNA microarray in the ArrayTube format.

PubMed

Schüler, Susann; Wenz, Ingrid; Wiederanders, B; Slickers, P; Ehricht, R

2006-06-12

Recent developments in DNA microarray technology led to a variety of open and closed devices and systems including high and low density microarrays for high-throughput screening applications as well as microarrays of lower density for specific diagnostic purposes. Beside predefined microarrays for specific applications manufacturers offer the production of custom-designed microarrays adapted to customers' wishes. Array based assays demand complex procedures including several steps for sample preparation (RNA extraction, amplification and sample labelling), hybridization and detection, thus leading to a high variability between several approaches and resulting in the necessity of extensive standardization and normalization procedures. In the present work a custom designed human proteinase DNA microarray of lower density in ArrayTube format was established. This highly economic open platform only requires standard laboratory equipment and allows the study of the molecular regulation of cell behaviour by proteinases. We established a procedure for sample preparation and hybridization and verified the array based gene expression profile by quantitative real-time PCR (QRT-PCR). Moreover, we compared the results with the well established Affymetrix microarray. By application of standard labelling procedures with e.g. Klenow fragment exo-, single primer amplification (SPA) or In Vitro Transcription (IVT) we noticed a loss of signal conservation for some genes. To overcome this problem we developed a protocol in accordance with the SPA protocol, in which we included target specific primers designed individually for each spotted oligomer. Here we present a complete array based assay in which only the specific transcripts of interest are amplified in parallel and in a linear manner. The array represents a proof of principle which can be adapted to other species as well. As the designed protocol for amplifying mRNA starts from as little as 100 ng total RNA, it presents an alternative method for detecting even low expressed genes by microarray experiments in a highly reproducible and sensitive manner. Preservation of signal integrity is demonstrated out by QRT-PCR measurements. The little amounts of total RNA necessary for the analyses make this method applicable for investigations with limited material as in clinical samples from, for example, organ or tumour biopsies. Those are arguments in favour of the high potential of our assay compared to established procedures for amplification within the field of diagnostic expression profiling. Nevertheless, the screening character of microarray data must be mentioned, and independent methods should verify the results.

Evaluation of microfabricated deformable mirror systems

NASA Astrophysics Data System (ADS)

Cowan, William D.; Lee, Max K.; Bright, Victor M.; Welsh, Byron M.

1998-09-01

This paper presents recent result for aberration correction and beam steering experiments using polysilicon surface micromachined piston micromirror arrays. Microfabricated deformable mirrors offer a substantial cost reduction for adaptive optic systems. In addition to the reduced mirror cost, microfabricated mirrors typically require low control voltages, thus eliminating high voltage amplifiers. The greatly reduced cost per channel of adaptive optic systems employing microfabricated deformable mirrors promise high order aberration correction at low cost. Arrays of piston micromirrors with 128 active elements were tested. Mirror elements are on a 203 micrometers 12 by 12 square grid. The overall array size is 2.4 mm square. The arrays were fabricated in the commercially available DARPA supported MUMPs surface micromachining foundry process. The cost per mirror array in this prototyping process is less than 200 dollars. Experimental results are presented for a hybrid correcting element comprised of a lenslet array and piston micromirror array, and for a piston micromirror array only. Also presented is a novel digital deflection micromirror which requires no digital to analog converters, further reducing the cost of adaptive optics system.

A Novel Method for Rapid Hybridization of DNA to a Solid Support

PubMed Central

Pettersson, Erik; Ahmadian, Afshin; Ståhl, Patrik L.

2013-01-01

Here we present a novel approach entitled Magnetic Forced Hybridization (MFH) that provides the means for efficient and direct hybridization of target nucleic acids to complementary probes immobilized on a glass surface in less than 15 seconds at ambient temperature. In addition, detection is carried out instantly since the beads become visible on the surface. The concept of MFH was tested for quality control of array manufacturing, and was combined with a multiplex competitive hybridization (MUCH) approach for typing of Human Papilloma Virus (HPV). Magnetic Forced Hybridization of bead-DNA constructs to a surface achieves a significant reduction in diagnostic testing time. In addition, readout of results by visual inspection of the unassisted eye eliminates the need for additional expensive instrumentation. The method uses the same set of beads throughout the whole process of manipulating and washing DNA constructs prior to detection, as in the actual detection step itself. PMID:23950946

Evaluation of the efficacy of constitutional array-based comparative genomic hybridization in the diagnosis of aneuploidy using genomic and amplified DNA.

PubMed

Tan, Niap H; Palmer, Rodger; Wang, Rubin

2010-02-01

Array-based comparative genomic hybridization (array CGH) is a new molecular technique that has the potential to revolutionize cytogenetics. However, use of high resolution array CGH in the clinical setting is plagued by the problem of widespread copy number variations (CNV) in the human genome. Constitutional microarray, containing only clones that interrogate regions of known constitutional syndromes, may circumvent the dilemma of detecting CNV of unknown clinical significance. The present study investigated the efficacy of constitutional microarray in the diagnosis of trisomy. Test samples included genomic DNA from trisomic cell lines, amplification products of 50 ng of genomic DNA and whole genome amplification products of single cells. DNA amplification was achieved by means of multiple displacement amplification (MDA) over 16 h. The trisomic and sex chromosomes copy number imbalances in the genomic DNA were correctly identified by the constitutional microarrays. However, there was a failure to detect the trisomy in the amplification products of 50 ng of genomic DNA and whole genome amplification products of single cells. Using carefully selected clones, Spectral Genomics constitutional microarray was able to detect the chromosomal copy number imbalances in genomic DNA without the confounding effects of CNV. The diagnostic failure in amplified DNA samples could be attributed to the amplification process. The MDA duration of 16 h generated excessive amount of biases and shortening the duration might minimize the problem.

A scintillator geometry suitable for very small PET gantries

NASA Astrophysics Data System (ADS)

Gonzalez, A. J.; Gonzalez-Montoro, A.; Aguilar, A.; Cañizares, G.; Martí, R.; Iranzo, S.; Lamprou, E.; Sanchez, S.; Sanchez, F.; Benlloch, J. M.

2017-12-01

In this work we are describing a novel approach to the scintillator crystal configuration as used in nuclear medicine imaging. Our design is related to the coupling in one PET module of the two separate crystal configurations used so far there: monolithic and crystal arrays. The particular design we have studied is based on a two-layer scintillator approach (hybrid) composed of a monolithic LYSO crystal (5-6 mm thickness) and a LYSO crystal array with 4-5 mm height (0.8 and 1 mm pixels). We show here the detector block performance, in terms of spatial, energy and DOI information, to be used as a module in the design of PET scanners. The design we propose allows one to achieve accurate three-dimensional spatial resolution (including DOI information) while assuring high detection efficiency at reasonable cost. Moreover, the proposed design improves the spatial response uniformity across the whole detector module, and especially at the edge region. The crystal arrays are mounted in the front and were well resolved. The monolithic crystal inserted between crystal array and the photosensor, provided measured FWHM resolution as good as 1.5-1.7 mm including the 1 mm source size. The monolithic block achieved a DOI resolution (FWHM) nearing 3 mm. We compared these results with an approach in which we use a single monolithic block with total volume equals to the hybrid approach. In general, comparable performances were obtained.

Impact of data layouts on the efficiency of GPU-accelerated IDW interpolation.

PubMed

Mei, Gang; Tian, Hong

2016-01-01

This paper focuses on evaluating the impact of different data layouts on the computational efficiency of GPU-accelerated Inverse Distance Weighting (IDW) interpolation algorithm. First we redesign and improve our previous GPU implementation that was performed by exploiting the feature of CUDA dynamic parallelism (CDP). Then we implement three versions of GPU implementations, i.e., the naive version, the tiled version, and the improved CDP version, based upon five data layouts, including the Structure of Arrays (SoA), the Array of Structures (AoS), the Array of aligned Structures (AoaS), the Structure of Arrays of aligned Structures (SoAoS), and the Hybrid layout. We also carry out several groups of experimental tests to evaluate the impact. Experimental results show that: the layouts AoS and AoaS achieve better performance than the layout SoA for both the naive version and tiled version, while the layout SoA is the best choice for the improved CDP version. We also observe that: for the two combined data layouts (the SoAoS and the Hybrid), there are no notable performance gains when compared to other three basic layouts. We recommend that: in practical applications, the layout AoaS is the best choice since the tiled version is the fastest one among three versions. The source code of all implementations are publicly available.

Directional hearing aid using hybrid adaptive beamformer (HAB) and binaural ITE array

NASA Astrophysics Data System (ADS)

Shaw, Scott T.; Larow, Andy J.; Gibian, Gary L.; Sherlock, Laguinn P.; Schulein, Robert

2002-05-01

A directional hearing aid algorithm called the Hybrid Adaptive Beamformer (HAB), developed for NIH/NIA, can be applied to many different microphone array configurations. In this project the HAB algorithm was applied to a new array employing in-the-ear microphones at each ear (HAB-ITE), to see if previous HAB performance could be achieved with a more cosmetically acceptable package. With diotic output, the average benefit in threshold SNR was 10.9 dB for three HoH and 11.7 dB for five normal-hearing subjects. These results are slightly better than previous results of equivalent tests with a 3-in. array. With an innovative binaural fitting, a small benefit beyond that provided by diotic adaptive beamforming was observed: 12.5 dB for HoH and 13.3 dB for normal-hearing subjects, a 1.6 dB improvement over the diotic presentation. Subjectively, the binaural fitting preserved binaural hearing abilities, giving the user a sense of space, and providing left-right localization. Thus the goal of creating an adaptive beamformer that simultaneously provides excellent noise reduction and binaural hearing was achieved. Further work remains before the HAB-ITE can be incorporated into a real product, optimizing binaural adaptive beamforming, and integrating the concept with other technologies to produce a viable product prototype. [Work supported by NIH/NIDCD.

Identification of clinically relevant viridans streptococci by an oligonucleotide array.

PubMed

Chen, Chao Chien; Teng, Lee Jene; Kaiung, Seng; Chang, Tsung Chain

2005-04-01

Viridans streptococci (VS) are common etiologic agents of subacute infective endocarditis and are capable of causing a variety of pyogenic infections. Many species of VS are difficult to differentiate by phenotypic traits. An oligonucleotide array based on 16S-23S rRNA gene intergenic spacer (ITS) sequences was developed to identify 11 clinically relevant VS. These 11 species were Streptococcus anginosus, S. constellatus, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. salivarius, S. sanguinis, and S. uberis. The method consisted of PCR amplification of the ITS regions by using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species-specific oligonucleotides immobilized on a nylon membrane. After 120 strains of the 11 species of VG and 91 strains of other bacteria were tested, the sensitivity and specificity of the oligonucleotide array were found to be 100% (120 of 120 strains) and 95.6% (87 of 91 strains), respectively. S. pneumoniae cross-hybridized to the probes used for the identification of S. mitis, and simple biochemical tests such as optochin susceptibility or bile solubility should be used to differentiate S. pneumoniae from S. mitis. In conclusion, identification of species of VS by use of the present oligonucleotide array is accurate and could be used as an alternative reliable method for species identification of strains of VS.

Estimating the efficiency of fish cross-species cDNA microarray hybridization.

PubMed

Cohen, Raphael; Chalifa-Caspi, Vered; Williams, Timothy D; Auslander, Meirav; George, Stephen G; Chipman, James K; Tom, Moshe

2007-01-01

Using an available cross-species cDNA microarray is advantageous for examining multigene expression patterns in non-model organisms, saving the need for construction of species-specific arrays. The aim of the present study was to estimate relative efficiency of cross-species hybridizations across bony fishes, using bioinformatics tools. The methodology may serve also as a model for similar evaluations in other taxa. The theoretical evaluation was done by substituting comparative whole-transcriptome sequence similarity information into the thermodynamic hybridization equation. Complementary DNA sequence assemblages of nine fish species belonging to common families or suborders and distributed across the bony fish taxonomic branch were selected for transcriptome-wise comparisons. Actual cross-species hybridizations among fish of different taxonomic distances were used to validate and eventually to calibrate the theoretically computed relative efficiencies.

Design and simulation of a superposition compound eye system based on hybrid diffractive-refractive lenses.

PubMed

Zhang, Shuqing; Zhou, Luyang; Xue, Changxi; Wang, Lei

2017-09-10

Compound eyes offer a promising field of miniaturized imaging systems. In one application of a compound eye, superposition of compound eye systems forms a composite image by superposing the images produced by different channels. The geometric configuration of superposition compound eye systems is achieved by three micro-lens arrays with different pitches and focal lengths. High resolution is indispensable for the practicability of superposition compound eye systems. In this paper, hybrid diffractive-refractive lenses are introduced into the design of a compound eye system for this purpose. With the help of ZEMAX, two superposition compound eye systems with and without hybrid diffractive-refractive lenses were separately designed. Then, we demonstrate the effectiveness of using a hybrid diffractive-refractive lens to improve the image quality.

Design, processing and testing of LSI arrays hybrid microelectronics task

NASA Technical Reports Server (NTRS)

Himmel, R. P.; Stuhlbarg, S. M.; Salmassy, S.

1978-01-01

Those factors affecting the cost of electronic subsystems utilizing LSI microcircuits were determined and the most efficient methods for low cost packaging of LSI devices as a function of density and reliability were developed.

Automated detection and quantitation of bacterial RNA by using electrical microarrays.

PubMed

Elsholz, B; Wörl, R; Blohm, L; Albers, J; Feucht, H; Grunwald, T; Jürgen, B; Schweder, T; Hintsche, Rainer

2006-07-15

Low-density electrical 16S rRNA specific oligonucleotide microarrays and an automated analysis system have been developed for the identification and quantitation of pathogens. The pathogens are Escherichia coli, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus epidermidis, which are typically involved in urinary tract infections. Interdigitated gold array electrodes (IDA-electrodes), which have structures in the nanometer range, have been used for very sensitive analysis. Thiol-modified oligonucleotides are immobilized on the gold IDA as capture probes. They mediate the specific recognition of the target 16S rRNA by hybridization. Additionally three unlabeled oligonucleotides are hybridized in close proximity to the capturing site. They are supporting molecules, because they improve the RNA hybridization at the capturing site. A biotin labeled detector oligonucleotide is also allowed to hybridize to the captured RNA sequence. The biotin labels enable the binding of avidin alkaline phophatase conjugates. The phosphatase liberates the electrochemical mediator p-aminophenol from its electrically inactive phosphate derivative. The electrical signals were generated by amperometric redox cycling and detected by a unique multipotentiostat. The read out signals of the microarray are position specific current and change over time in proportion to the analyte concentration. If two additional biotins are introduced into the affinity binding complex via the supporting oligonucleotides, the sensitivity of the assays increase more than 60%. The limit of detection of Escherichia coli total RNA has been determined to be 0.5 ng/microL. The control of fluidics for variable assay formats as well as the multichannel electrical read out and data handling have all been fully automated. The fast and easy procedure does not require any amplification of the targeted nucleic acids by PCR.

Development of 256 x 256 Element Impurity Band Conduction Infrared Detector Arrays for Astronomy

NASA Technical Reports Server (NTRS)

Domingo, George

1997-01-01

This report describes the work performed on a one and a half year advance technology program to develop Impurity Band Conduction (IBC) detectors with very low dark current, high quantum efficiency, and with good repeatable processes. The program fabricated several epitaxial growths of Si:As detecting layers from 15 to 35 microns thick and analyzed the performance versus the thickness and the Arsenic concentration of these epitaxial layers. Some of the epitaxial runs did not yield because of excessive residual impurities. The thicker epitaxial layers and the ones with higher Arsenic concentration resulted in good detectors with low dark currents and good quantum efficiency. The program hybridized six detector die from the best detector wafers to a low noise, 256 x 256 readout array and delivered the hybrids to NASA Ames for a more detailed study of the performance of the detectors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ming, Xianshun; Liu, Xinyu; Sun, Liqun

We develop the theory of all-dielectric absorbers based on temporal coupled mode theory (TCMT), with parameters extracted from eigenfrequency simulations. An infinite square array of cylindrical resonators embedded in air is investigated, and we find that it supports two eigenmodes of opposite symmetry that are each responsible for half of the total absorption. The even and odd eigenmodes are found to be the hybrid electric (EH111) and hybrid magnetic (HE111) waveguide modes of a dielectric wire of circular cross section, respectively. The geometry of the cylindrical array is shown to be useful for individual tuning of the radiative loss ratesmore » of the eigenmodes, thus permitting frequency degeneracy. Further, by specifying the resonators’ loss tangent, the material loss rate can be made to equal the radiative loss rate, thus achieving a state of degenerate critical coupling and perfect absorption. Our results are supported by S-parameter simulations, and agree well with waveguide theory.« less

Broadband and high-efficiency vortex beam generator based on a hybrid helix array.

PubMed

Fang, Chaoqun; Wu, Chao; Gong, Zhijie; Zhao, Song; Sun, Anqi; Wei, Zeyong; Li, Hongqiang

2018-04-01

The vortex beam which carries the orbital angular momentum has versatile applications, such as high-resolution imaging, optical communications, and particle manipulation. Generating vortex beams with the Pancharatnam-Berry (PB) phase has drawn considerable attention for its unique spin-to-orbital conversion features. Despite the PB phase being frequency independent, an optical element with broadband high-efficiency circular polarization conversion feature is still needed for the broadband high-efficiency vortex beam generation. In this work, a broadband and high-efficiency vortex beam generator based on the PB phase is built with a hybrid helix array. Such devices can generate vortex beams with arbitrary topological charge. Moreover, vortex beams with opposite topological charge can be generated with an opposite handedness incident beam that propagates backward. The measured efficiency of our device is above 65% for a wide frequency range, with the relative bandwidth of 46.5%.

Polarization independent subtractive color printing based on ultrathin hexagonal nanodisk-nanohole hybrid structure arrays.

PubMed

Zhao, Jiancun; Yu, Xiaochang; Yang, Xiaoming; Xiang, Quan; Duan, Huigao; Yu, Yiting

2017-09-18

Structural color printing based on plasmonic metasurfaces has been recognized as a promising alternative to the conventional dye colorants, though the color brightness and polarization tolerance are still a great challenge for practical applications. In this work, we report a novel plasmonic metasurface for subtractive color printing employing the ultrathin hexagonal nanodisk-nanohole hybrid structure arrays. Through both the experimental and numerical investigations, the subtractive color thus generated taking advantages of extraordinary low transmission (ELT) exhibits high brightness, polarization independence and wide color tunability by varying key geometrical parameters. In addition, other regular patterns including square, pentagonal and circular shapes are also surveyed, and reveal a high color brightness, wide gamut and polarization independence as well. These results indicate that the demonstrated plasmonic metasurface has various potential applications in high-definition displays, high-density optical data storage, imaging and filtering technologies.

Graphene-enhanced plasmonic nanohole arrays for environmental sensing in aqueous samples

PubMed Central

Genslein, Christa; Hausler, Peter; Kirchner, Eva-Maria; Bierl, Rudolf; Baeumner, Antje J

2016-01-01

The label-free nature of surface plasmon resonance techniques (SPR) enables a fast, specific, and sensitive analysis of molecular interactions. However, detection of highly diluted concentrations and small molecules is still challenging. It is shown here that in contrast to continuous gold films, gold nanohole arrays can significantly improve the performance of SPR devices in angle-dependent measurement mode, as a signal amplification arises from localized surface plasmons at the nanostructures. This leads consequently to an increased sensing capability of molecules bound to the nanohole array surface. Furthermore, a reduced graphene oxide (rGO) sensor surface was layered over the nanohole array. Reduced graphene oxide is a 2D nanomaterial consisting of sp2-hybridized carbon atoms and is an attractive receptor surface for SPR as it omits any bulk phase and therefore allows fast response times. In fact, it was found that nanohole arrays demonstrated a higher shift in the resonance angle of 250–380% compared to a continuous gold film. At the same time the nanohole array structure as characterized by its diameter-to-periodicity ratio had minimal influence on the binding capacity of the sensor surface. As a simple and environmentally highly relevant model, binding of the plasticizer diethyl phthalate (DEP) via π-stacking was monitored on the rGO gold nanohole array realizing a limit of detection of as low as 20 nM. The concentration-dependent signal change was studied with the best performing rGO-modified nanohole arrays. Compared to continuous gold films a diameter-to-periodicity ratio (D/P) of 0.43 lead to a 12-fold signal enhancement. Finally, the effect of environmental waters on the sensor was evaluated using samples from sea, lake and river waters spiked with analytically relevant amounts of DEP during which significant changes in the SPR signal are observed. It is expected that this concept can be successfully transferred to enhance the sensitivity in SPR sensors. PMID:28144507

Feasibility Study of Seawater Electrolysis for Photovoltaic/Fuel Cell Hybrid Power System for the Coastal Areas in Thailand

NASA Astrophysics Data System (ADS)

Srisiriwat, A.; Pirom, W.

2017-10-01

Solar photovoltaic cell and fuel cell are the practicable options to realize as a possible hybrid power system because the power of the sun cannot be utilized at night or cloudy days but hydrogen has been found as an ideal energy carrier for being transportable, storable, and converting energy though fuel cell. Hydrogen storage is chosen for its ability to obtain a clean energy option. Electrolysis, which is the simplest process to produce hydrogen, can be powered by the dc voltage from the photovoltaic cell instead of using the battery as power supply. This paper concentrates on a feasibility study of seawater electrolysis using photovoltaic power integrated fuel cell system for the coastal cities in Thailand. The proposed system composed of photovoltaic arrays, seawater electrolyzer and fuel cell is presented when the 10-kW of fuel cell electrical power is considered. The feasibility study of hydrogen production and energy analysis of this proposed system is also evaluated.

Genetic Dosage Compensation in a Family with Velo-cardio-facial/DiGeorge/22q11.2 Deletion Syndrome

PubMed Central

Alkalay, Avishai A.; Guo, Tingwei; Montagna, Cristina; Digilio, M. Cristina; Marino, Bruno; Dallapiccola, Bruno; Morrow, Bernice

2014-01-01

Cytogenetic studies of a male child carrying the 22q11.2 deletion common in patients with velo-cardio-facial/DiGeorge syndrome revealed an unexpected rearrangement of the 22q11.2 region in his normal appearing mother. The mother carries a 3 Mb deletion on one copy and a reciprocal, similar sized duplication on the other copy of chromosome 22q11.2 as revealed by fluorescence in situ hybridization and array comparative genome hybridization analysis. The most parsimonious mechanism for the rearrangement is a mitotic non-allelic homologous recombination event in a cell in the early embryo soon after fertilization. The normal phenotype of the mother can be explained by the theory of genetic dosage compensation. This is the second documented case of such an event for this or any genomic disorder. This finding helps to reinforce this phenomenon in a human model, and has significant implications for genetic counseling of future children. PMID:21337693

Alagille syndrome with deletion 20p12.2-p12.3 and hypoplastic left heart.

PubMed

Robert, Marie Leema P; Lopez, Tony; Crolla, John; Huang, Shuwen; Owen, Carol; Burvill-Holmes, Lisa; Stumper, Oliver; Turnpenny, Peter D

2007-10-01

We report a male patient born at 37-weeks gestation, weighing 1.885 kg (<0.4th centile). Shortly after birth, he was diagnosed with hypoplastic left heart syndrome for which he underwent a Norwood procedure. Subsequently, he developed problems with failure to thrive and developmental delay. At the age of 4 years his delay in growth and development led to further investigations, which revealed a small de-novo interstitial deletion of chromosome 20p12.2. JAGGED1 haploinsufficiency was confirmed by fluorescence in situ hybridization. Array-comparative genomic hybridization analysis confirmed and quantified an approximate 5.4 Mb interstitial deletion involving the chromosomal region 20p12.2-p12.3. This precise interstitial deletion has not been previously reported. Further clinical evaluation revealed posterior embryotoxon and butterfly vertebrae. He has normal liver function tests, facial features consistent with Alagille syndrome, and mild learning difficulties. To our knowledge this is the first report of Alagille syndrome associated with hypoplastic left heart syndrome.

Optimization of friction and wear behaviour of Al7075-Al2O3-B4C metal matrix composites using Taguchi method

NASA Astrophysics Data System (ADS)

Dhanalakshmi, S.; Mohanasundararaju, N.; Venkatakrishnan, P. G.; Karthik, V.

2018-02-01

The present study deals with investigations relating to dry sliding wear behaviour of the Al 7075 alloy, reinforced with Al2O3 and B4C. The hybrid composites are produced through Liquid Metallurgy route - Stir casting method. The amount of Al2O3 particles is varied as 3, 6, 9, 12 and 15 wt% and the amount of B4C is kept constant as 3wt%. Experiments were conducted based on the plan of experiments generated through Taguchi’s technique. A L27 Orthogonal array was selected for analysis of the data. The investigation is to find the effect of applied load, sliding speed and sliding distance on wear rate and Coefficient of Friction (COF) of the hybrid Al7075- Al2O3-B4C composite and to determine the optimal parameters for obtaining minimum wear rate. The samples were examined using scanning electronic microscopy after wear testing and analyzed.

Monte Carlo simulation of simultaneous radiation detection in the hybrid tomography system ClearPET-XPAD3/CT

NASA Astrophysics Data System (ADS)

Dávila, H. Olaya; Sevilla, A. C.; Castro, H. F.; Martínez, S. A.

2016-07-01

Using the Geant4 based simulation framework SciFW1, a detailed simulation was performed for a detector array in the hybrid tomography prototype for small animals called ClearPET / XPAD, which was built in the Centre de Physique des Particules de Marseille. The detector system consists of an array of phoswich scintillation detectors: LSO (Lutetium Oxy-ortosilicate doped with cerium Lu2SiO5:Ce) and LuYAP (Lutetium Ortoaluminate of Yttrium doped with cerium Lu0.7Y0.3AlO3:Ce) for Positron Emission Tomography (PET) and hybrid pixel detector XPAD for Computed Tomography (CT). Simultaneous acquisition of deposited energy and the corresponding time - position for each recorded event were analyzed, independently, for both detectors. interference between detection modules for PET and CT. Information about amount of radiation reaching each phoswich crystal and XPAD detector using a phantom in order to study the effectiveness by radiation attenuation and influence the positioning of the radioactive source 22Na was obtained. The simulation proposed will improve distribution of detectors rings and interference values will be taken into account in the new versions of detectors.

Thermal tuning of infrared resonant absorbers based on hybrid gold-VO{sub 2} nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kocer, Hasan; Department of Electrical Engineering, Turkish Military Academy, 06654 Ankara; Butun, Serkan

2015-04-20

Resonant absorbers based on plasmonic materials, metamaterials, and thin films enable spectrally selective absorption filters, where absorption is maximized at the resonance wavelength. By controlling the geometrical parameters of nano/microstructures and materials' refractive indices, resonant absorbers are designed to operate at wide range of wavelengths for applications including absorption filters, thermal emitters, thermophotovoltaic devices, and sensors. However, once resonant absorbers are fabricated, it is rather challenging to control and tune the spectral absorption response. Here, we propose and demonstrate thermally tunable infrared resonant absorbers using hybrid gold-vanadium dioxide (VO{sub 2}) nanostructure arrays. Absorption intensity is tuned from 90% to 20%more » and 96% to 32% using hybrid gold-VO{sub 2} nanowire and nanodisc arrays, respectively, by heating up the absorbers above the phase transition temperature of VO{sub 2} (68 °C). Phase change materials such as VO{sub 2} deliver useful means of altering optical properties as a function of temperature. Absorbers with tunable spectral response can find applications in sensor and detector applications, in which external stimulus such as heat, electrical signal, or light results in a change in the absorption spectrum and intensity.« less

Elaboration of ammonia gas sensors based on electrodeposited polypyrrole--cobalt phthalocyanine hybrid films.

PubMed

Patois, Tilia; Sanchez, Jean-Baptiste; Berger, Franck; Fievet, Patrick; Segut, Olivier; Moutarlier, Virginie; Bouvet, Marcel; Lakard, Boris

2013-12-15

The electrochemical incorporation of a sulfonated cobalt phthalocyanine (sCoPc) in conducting polypyrrole (PPy) was done, in the presence or absence of LiClO4, in order to use the resulting hybrid material for the sensing of ammonia. After electrochemical deposition, the morphological features and structural properties of polypyrrole/phthalocyanine hybrid films were investigated and compared to those of polypyrrole films. A gas sensor consisting in platinum microelectrodes arrays was fabricated using silicon microtechnologies, and the polypyrrole and polypyrrole/phthalocyanine films were electrochemically deposited on the platinum microelectrodes arrays of this gas sensor. When exposed to ammonia, polymer-based gas sensors exhibited a decrease in conductance due to the electron exchange between ammonia and sensitive polymer-based layer. The characteristics of the gas sensors (response time, response amplitude, reversibility) were studied for ammonia concentrations varying from 1 ppm to 100 ppm. Polypyrrole/phthalocyanine films exhibited a high sensitivity and low detection limit to ammonia as well as a fast and reproducible response at room temperature. The response to ammonia exposition of polypyrrole films was found to be strongly enhanced thanks to the incorporation of the phthalocyanine in the polypyrrole matrix. © 2013 Elsevier B.V. All rights reserved.

A multiple-scattering polaritonic-operator method for hybrid arrays of metal nanoparticles and quantum emitters

NASA Astrophysics Data System (ADS)

Chatzidakis, Georgios D.; Yannopapas, Vassilios

2018-05-01

We present a new technique for the study of hybrid collections of quantum emitters (atoms, molecules, quantum dots) with nanoparticles. The technique is based on a multiple-scattering polaritonic-operator formalism in conjunction with an electromagnetic coupled dipole method. Apart from collections of quantum emitters and nanoparticles, the method can equally treat the interaction of a collection of quantum emitters with a single nano-object of arbitrary shape in which case the nano-object is treated as a finite three-dimensional lattice of point scatterers. We have applied our method to the case of linear array (chain) of dimers of quantum emitters and metallic nanoparticles wherein the corresponding (geometrical and physical) parameters of the dimers are chosen so as the interaction between the emitter and the nanoparticle lies in the strong-coupling regime in order to enable the formation of plexciton states in the dimer. In particular, for a linear chain of dimers, we show that the corresponding light spectra reveal a multitude of plexciton modes resulting from the hybridization of the plexciton resonances of each individual dimer in a manner similar to the tight-binding description of electrons in solids.

A photoelectrochemical immunosensor for tris(2,3-dibromopropyl) isocyanurate detection with a multiple hybrid CdTe/Au-TiO2 nanotube arrays.

PubMed

Feng, Hui; Zhou, Liping; Li, Jiezhen; Tran T, ThanhThuy; Wang, Niya; Yuan, Lijuan; Yan, Zhihong; Cai, Qingyun

2013-10-07

In this paper, tris(2,3-dibromopropyl) isocyanurate (TBC) is for the first time as far as we know determined by ultrasensitive photoelectrochemical (PEC) immunoassay using an antibody-modified ternary hybrid CdTe/Au-TiO2 nanotube arrays (NTAs) photoelectrode, developed by the pulse electrodeposition technique. The as-prepared hybrid shows enhanced photon absorption and photocurrent response, which subsequently increased the photoelectrical conversion efficiency in the visible region. TBC-antibody (Ab) was developed in rabbits as a result of immunization with the BSA-TBC conjugate and covalently cross-linked onto the CdTe/Au-TiO2 NTAs. Since the photocurrent is highly dependent on the TiO2 surface properties, the specific interaction between TBC and the antibody results in a sensitive change in the photocurrent, which displayed a linear range of 5.0 × 10(-11) to 5.0 × 10(-5) M and a low detection limit of 5.0 × 10(-11) M for TBC determination. This proposed strategy highlights the application of TiO2 nanotube in visible-light-activated photoelectrochemical biosensing, which could largely reduce the destructive effect of UV light on biomolecules.

GEAR: genomic enrichment analysis of regional DNA copy number changes.

PubMed

Kim, Tae-Min; Jung, Yu-Chae; Rhyu, Mun-Gan; Jung, Myeong Ho; Chung, Yeun-Jun

2008-02-01

We developed an algorithm named GEAR (genomic enrichment analysis of regional DNA copy number changes) for functional interpretation of genome-wide DNA copy number changes identified by array-based comparative genomic hybridization. GEAR selects two types of chromosomal alterations with potential biological relevance, i.e. recurrent and phenotype-specific alterations. Then it performs functional enrichment analysis using a priori selected functional gene sets to identify primary and clinical genomic signatures. The genomic signatures identified by GEAR represent functionally coordinated genomic changes, which can provide clues on the underlying molecular mechanisms related to the phenotypes of interest. GEAR can help the identification of key molecular functions that are activated or repressed in the tumor genomes leading to the improved understanding on the tumor biology. GEAR software is available with online manual in the website, http://www.systemsbiology.co.kr/GEAR/.

Method for producing a hybridization of detector array and integrated circuit for readout

NASA Technical Reports Server (NTRS)

Fossum, Eric R. (Inventor); Grunthaner, Frank J. (Inventor)

1993-01-01

A process is explained for fabricating a detector array in a layer of semiconductor material on one substrate and an integrated readout circuit in a layer of semiconductor material on a separate substrate in order to select semiconductor material for optimum performance of each structure, such as GaAs for the detector array and Si for the integrated readout circuit. The detector array layer is lifted off its substrate, laminated on the metallized surface on the integrated surface, etched with reticulating channels to the surface of the integrated circuit, and provided with interconnections between the detector array pixels and the integrated readout circuit through the channels. The adhesive material for the lamination is selected to be chemically stable to provide electrical and thermal insulation and to provide stress release between the two structures fabricated in semiconductor materials that may have different coefficients of thermal expansion.

CdS nanorods/organic hybrid LED array and the piezo-phototronic effect of the device for pressure mapping.

PubMed

Bao, Rongrong; Wang, Chunfeng; Dong, Lin; Shen, Changyu; Zhao, Kun; Pan, Caofeng

2016-04-21

As widely applied in light-emitting diodes and optical devices, CdS has attracted the attention of many researchers due to its nonlinear properties and piezo-electronic effect. Here, we demonstrate a LED array composed of PSS and CdS nanorods and research the piezo-photonic effect of the array device. The emission intensity of the device depends on the electron-hole recombination at the interface of the p-n junction which can be adjusted using the piezo-phototronic effect and can be used to map the pressure applied on the surface of the device with spatial resolution as high as 1.5 μm. A flexible LED device array has been prepared using a CdS nanorod array on a Au/Cr/kapton substrate. This device may be used in the field of strain mapping using its high pressure spatial-resolution and flexibility.

Flexible Supercapacitors Based on Polyaniline Arrays Coated Graphene Aerogel Electrodes

NASA Astrophysics Data System (ADS)

Yang, Yu; Xi, Yunlong; Li, Junzhi; Wei, Guodong; Klyui, N. I.; Han, Wei

2017-06-01

Flexible supercapacitors(SCs) made by reduced graphene oxide (rGO)-based aerogel usually suffer from the low energy density, short cycle life and bad flexibility. In this study, a new, synthetic strategy was developed for enhancing the electrochemical performances of rGO aerogel-based supercapacitor via electrodeposition polyaniline arrays on the prepared ultralight rGO aerogel. The novel hybrid composites with coated polyaniline (PANI) arrays growing on the rGO surface can take full advantage of the rich open-pore and excellent conductivity of the crosslinking framework structure of 3D rGO aerogel and high capacitance contribution from the PANI. The obtained hybrid composites exhibit excellent electrochemical performance with a specific capacitance of 432 F g-1 at the current density of 1 A g-1, robust cycling stability to maintain 85% after 10,000 charge/discharge cycles and high energy density of 25 W h kg-1. Furthermore, the flexible all-solid-state supercapacitor have superior flexibility and outstanding stability under different bending states from the straight state to the 90° status. The high-performance flexible all-solid-state SCs together with the lighting tests demonstrate it possible for applications in portable electronics.

Flexible Supercapacitors Based on Polyaniline Arrays Coated Graphene Aerogel Electrodes.

PubMed

Yang, Yu; Xi, Yunlong; Li, Junzhi; Wei, Guodong; Klyui, N I; Han, Wei

2017-12-01

Flexible supercapacitors(SCs) made by reduced graphene oxide (rGO)-based aerogel usually suffer from the low energy density, short cycle life and bad flexibility. In this study, a new, synthetic strategy was developed for enhancing the electrochemical performances of rGO aerogel-based supercapacitor via electrodeposition polyaniline arrays on the prepared ultralight rGO aerogel. The novel hybrid composites with coated polyaniline (PANI) arrays growing on the rGO surface can take full advantage of the rich open-pore and excellent conductivity of the crosslinking framework structure of 3D rGO aerogel and high capacitance contribution from the PANI. The obtained hybrid composites exhibit excellent electrochemical performance with a specific capacitance of 432 F g -1 at the current density of 1 A g -1 , robust cycling stability to maintain 85% after 10,000 charge/discharge cycles and high energy density of 25 W h kg -1 . Furthermore, the flexible all-solid-state supercapacitor have superior flexibility and outstanding stability under different bending states from the straight state to the 90° status. The high-performance flexible all-solid-state SCs together with the lighting tests demonstrate it possible for applications in portable electronics.

Design and Fabrication of a Hybrid Superhydrophobic-Hydrophilic Surface That Exhibits Stable Dropwise Condensation.

PubMed

Mondal, Bikash; Mac Giolla Eain, Marc; Xu, QianFeng; Egan, Vanessa M; Punch, Jeff; Lyons, Alan M

2015-10-28

Condensation of water vapor is an essential process in power generation, water collection, and thermal management. Dropwise condensation, where condensed droplets are removed from the surface before coalescing into a film, has been shown to increase the heat transfer efficiency and water collection ability of many surfaces. Numerous efforts have been made to create surfaces which can promote dropwise condensation, including superhydrophobic surfaces on which water droplets are highly mobile. However, the challenge with using such surfaces in condensing environments is that hydrophobic coatings can degrade and/or water droplets on superhydrophobic surfaces transition from the mobile Cassie to the wetted Wenzel state over time and condensation shifts to a less-effective filmwise mechanism. To meet the need for a heat-transfer surface that can maintain stable dropwise condensation, we designed and fabricated a hybrid superhydrophobic-hydrophilic surface. An array of hydrophilic needles, thermally connected to a heat sink, was forced through a robust superhydrophobic polymer film. Condensation occurs preferentially on the needle surface due to differences in wettability and temperature. As the droplet grows, the liquid drop on the needle remains in the Cassie state and does not wet the underlying superhydrophobic surface. The water collection rate on this surface was studied using different surface tilt angles, needle array pitch values, and needle heights. Water condensation rates on the hybrid surface were shown to be 4 times greater than for a planar copper surface and twice as large for silanized silicon or superhydrophobic surfaces without hydrophilic features. A convection-conduction heat transfer model was developed; predicted water condensation rates were in good agreement with experimental observations. This type of hybrid superhydrophobic-hydrophilic surface with a larger array of needles is low-cost, robust, and scalable and so could be used for heat transfer and water collection applications.

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

Enabling Large Focal Plane Arrays Through Mosaic Hybridization

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Jhabvala, Christine A.; Leong, Edward; Costen, Nick P.; Sharp, Elmer; Adachi, Tomoko; Benford, Dominic J.

2012-01-01

We have demonstrated advances in mosaic hybridization that will enable very large format far-infrared detectors. Specifically we have produced electrical detector models via mosaic hybridization yielding superconducting circuit patbs by hybridizing separately fabricated sub-units onto a single detector unit. The detector model was made on a 100mm diameter wafer while four model readout quadrant chips were made from a separate 100mm wafer. The individually fabric.ted parts were hybridized using a Suss FCI50 flip chip bonder to assemble the detector-readout stack. Once all of the hybridized readouts were in place, a single, large and thick silicon substrate was placed on the stack and attached with permanent epoxy to provide strength and a Coefficient of Thermal Expansion match to the silicon components underneath. Wirebond pads on the readout chips connect circuits to warm readout electronics; and were used to validate the successful superconducting electrical interconnection of the model mosaic-hybrid detector. This demonstration is directly scalable to 150 mm diameter wafers, enabling pixel areas over ten times the area currently available.